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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1562 by gezelter, Thu May 12 17:00:14 2011 UTC vs.
Revision 1761 by gezelter, Fri Jun 22 20:01:37 2012 UTC

#	Line 36 | Line 36
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
44		#include "nonbonded/NonBondedInteraction.hpp"
45		#include "brains/SnapshotManager.hpp"
46	+	#include "brains/PairList.hpp"
47
48		using namespace std;
49		namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	+
53	+	// In a parallel computation, row and colum scans must visit all
54	+	// surrounding cells (not just the 14 upper triangular blocks that
55	+	// are used when the processor can see all pairs)
56	+	#ifdef IS_MPI
57	+	cellOffsets_.clear();
58	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
66	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	+	#endif
86	+	}
87	+
88	+
89		/**
90		* distributeInitialData is essentially a copy of the older fortran
91		* SimulationSetup
92		*/
53	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96	<	#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);
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	<	// gather the information for atomtype IDs (atids):
312	<	vector<int> identsLocal = info_->getIdentArray();
313	<	identsRow.reserve(nAtomsInRow);
314	<	identsCol.reserve(nAtomsInCol);
311	>	RealType tol = 1e-6;
312	>	largestRcut_ = 0.0;
313	>	RealType rc;
314	>	int atid;
315	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
316
317	<	AtomCommIntRow->gather(identsLocal, identsRow);
318	<	AtomCommIntColumn->gather(identsLocal, identsCol);
317	>	map<int, RealType> atypeCutoff;
318	>
319	>	for (set<AtomType*>::iterator at = atypes.begin();
320	>	at != atypes.end(); ++at){
321	>	atid = (*at)->getIdent();
322	>	if (userChoseCutoff_)
323	>	atypeCutoff[atid] = userCutoff_;
324	>	else
325	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
326	>	}
327
328	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
329	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
330	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
331	<
332	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
333	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
334	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
328	>	vector<RealType> gTypeCutoffs;
329	>	// first we do a single loop over the cutoff groups to find the
330	>	// largest cutoff for any atypes present in this group.
331	>	#ifdef IS_MPI
332	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
333	>	groupRowToGtype.resize(nGroupsInRow_);
334	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
335	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
336	>	for (vector<int>::iterator ia = atomListRow.begin();
337	>	ia != atomListRow.end(); ++ia) {
338	>	int atom1 = (*ia);
339	>	atid = identsRow[atom1];
340	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
341	>	groupCutoffRow[cg1] = atypeCutoff[atid];
342	>	}
343	>	}
344
345	<	// still need:
346	<	// topoDist
347	<	// exclude
345	>	bool gTypeFound = false;
346	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
347	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
348	>	groupRowToGtype[cg1] = gt;
349	>	gTypeFound = true;
350	>	}
351	>	}
352	>	if (!gTypeFound) {
353	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
354	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
355	>	}
356	>
357	>	}
358	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
359	>	groupColToGtype.resize(nGroupsInCol_);
360	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
361	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
362	>	for (vector<int>::iterator jb = atomListCol.begin();
363	>	jb != atomListCol.end(); ++jb) {
364	>	int atom2 = (*jb);
365	>	atid = identsCol[atom2];
366	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
367	>	groupCutoffCol[cg2] = atypeCutoff[atid];
368	>	}
369	>	}
370	>	bool gTypeFound = false;
371	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
372	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
373	>	groupColToGtype[cg2] = gt;
374	>	gTypeFound = true;
375	>	}
376	>	}
377	>	if (!gTypeFound) {
378	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
379	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
380	>	}
381	>	}
382	>	#else
383	>
384	>	vector<RealType> groupCutoff(nGroups_, 0.0);
385	>	groupToGtype.resize(nGroups_);
386	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
387	>	groupCutoff[cg1] = 0.0;
388	>	vector<int> atomList = getAtomsInGroupRow(cg1);
389	>	for (vector<int>::iterator ia = atomList.begin();
390	>	ia != atomList.end(); ++ia) {
391	>	int atom1 = (*ia);
392	>	atid = idents[atom1];
393	>	if (atypeCutoff[atid] > groupCutoff[cg1])
394	>	groupCutoff[cg1] = atypeCutoff[atid];
395	>	}
396	>
397	>	bool gTypeFound = false;
398	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
399	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
400	>	groupToGtype[cg1] = gt;
401	>	gTypeFound = true;
402	>	}
403	>	}
404	>	if (!gTypeFound) {
405	>	gTypeCutoffs.push_back( groupCutoff[cg1] );
406	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
407	>	}
408	>	}
409		#endif
410	+
411	+	// Now we find the maximum group cutoff value present in the simulation
412	+
413	+	RealType groupMax = *max_element(gTypeCutoffs.begin(),
414	+	gTypeCutoffs.end());
415	+
416	+	#ifdef IS_MPI
417	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
418	+	MPI::MAX);
419	+	#endif
420	+
421	+	RealType tradRcut = groupMax;
422	+
423	+	for (int i = 0; i < gTypeCutoffs.size();  i++) {
424	+	for (int j = 0; j < gTypeCutoffs.size();  j++) {
425	+	RealType thisRcut;
426	+	switch(cutoffPolicy_) {
427	+	case TRADITIONAL:
428	+	thisRcut = tradRcut;
429	+	break;
430	+	case MIX:
431	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
432	+	break;
433	+	case MAX:
434	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
435	+	break;
436	+	default:
437	+	sprintf(painCave.errMsg,
438	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
439	+	"hit an unknown cutoff policy!\n");
440	+	painCave.severity = OPENMD_ERROR;
441	+	painCave.isFatal = 1;
442	+	simError();
443	+	break;
444	+	}
445	+
446	+	pair<int,int> key = make_pair(i,j);
447	+	gTypeCutoffMap[key].first = thisRcut;
448	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
449	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
450	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
451	+	// sanity check
452	+
453	+	if (userChoseCutoff_) {
454	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
455	+	sprintf(painCave.errMsg,
456	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
457	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
458	+	painCave.severity = OPENMD_ERROR;
459	+	painCave.isFatal = 1;
460	+	simError();
461	+	}
462	+	}
463	+	}
464	+	}
465		}
466	+
467	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
468	+	int i, j;
469	+	#ifdef IS_MPI
470	+	i = groupRowToGtype[cg1];
471	+	j = groupColToGtype[cg2];
472	+	#else
473	+	i = groupToGtype[cg1];
474	+	j = groupToGtype[cg2];
475	+	#endif
476	+	return gTypeCutoffMap[make_pair(i,j)];
477	+	}
478	+
479	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
480	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
481	+	if (toposForAtom[atom1][j] == atom2)
482	+	return topoDist[atom1][j];
483	+	}
484	+	return 0;
485	+	}
486	+
487	+	void ForceMatrixDecomposition::zeroWorkArrays() {
488	+	pairwisePot = 0.0;
489	+	embeddingPot = 0.0;
490	+	excludedPot = 0.0;
491	+	excludedSelfPot = 0.0;
492	+
493	+	#ifdef IS_MPI
494	+	if (storageLayout_ & DataStorage::dslForce) {
495	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
496	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
497	+	}
498	+
499	+	if (storageLayout_ & DataStorage::dslTorque) {
500	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
501	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
502	+	}
503	+
504	+	fill(pot_row.begin(), pot_row.end(),
505	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
506	+
507	+	fill(pot_col.begin(), pot_col.end(),
508	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
509	+
510	+	fill(expot_row.begin(), expot_row.end(),
511	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
512	+
513	+	fill(expot_col.begin(), expot_col.end(),
514	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
515	+
516	+	if (storageLayout_ & DataStorage::dslParticlePot) {
517	+	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
518	+	0.0);
519	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
520	+	0.0);
521	+	}
522	+
523	+	if (storageLayout_ & DataStorage::dslDensity) {
524	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
525	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
526	+	}
527	+
528	+	if (storageLayout_ & DataStorage::dslFunctional) {
529	+	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
530	+	0.0);
531	+	fill(atomColData.functional.begin(), atomColData.functional.end(),
532	+	0.0);
533	+	}
534	+
535	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
536	+	fill(atomRowData.functionalDerivative.begin(),
537	+	atomRowData.functionalDerivative.end(), 0.0);
538	+	fill(atomColData.functionalDerivative.begin(),
539	+	atomColData.functionalDerivative.end(), 0.0);
540	+	}
541	+
542	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
543	+	fill(atomRowData.skippedCharge.begin(),
544	+	atomRowData.skippedCharge.end(), 0.0);
545	+	fill(atomColData.skippedCharge.begin(),
546	+	atomColData.skippedCharge.end(), 0.0);
547	+	}
548	+
549	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
550	+	fill(atomRowData.flucQFrc.begin(),
551	+	atomRowData.flucQFrc.end(), 0.0);
552	+	fill(atomColData.flucQFrc.begin(),
553	+	atomColData.flucQFrc.end(), 0.0);
554	+	}
555	+
556	+	if (storageLayout_ & DataStorage::dslElectricField) {
557	+	fill(atomRowData.electricField.begin(),
558	+	atomRowData.electricField.end(), V3Zero);
559	+	fill(atomColData.electricField.begin(),
560	+	atomColData.electricField.end(), V3Zero);
561	+	}
562	+
563	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
564	+	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
565	+	0.0);
566	+	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
567	+	0.0);
568	+	}
569	+
570	+	#endif
571	+	// even in parallel, we need to zero out the local arrays:
572	+
573	+	if (storageLayout_ & DataStorage::dslParticlePot) {
574	+	fill(snap_->atomData.particlePot.begin(),
575	+	snap_->atomData.particlePot.end(), 0.0);
576	+	}
577
578	+	if (storageLayout_ & DataStorage::dslDensity) {
579	+	fill(snap_->atomData.density.begin(),
580	+	snap_->atomData.density.end(), 0.0);
581	+	}
582
583	+	if (storageLayout_ & DataStorage::dslFunctional) {
584	+	fill(snap_->atomData.functional.begin(),
585	+	snap_->atomData.functional.end(), 0.0);
586	+	}
587
588	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
589	+	fill(snap_->atomData.functionalDerivative.begin(),
590	+	snap_->atomData.functionalDerivative.end(), 0.0);
591	+	}
592	+
593	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
594	+	fill(snap_->atomData.skippedCharge.begin(),
595	+	snap_->atomData.skippedCharge.end(), 0.0);
596	+	}
597	+
598	+	if (storageLayout_ & DataStorage::dslElectricField) {
599	+	fill(snap_->atomData.electricField.begin(),
600	+	snap_->atomData.electricField.end(), V3Zero);
601	+	}
602	+	}
603	+
604	+
605		void ForceMatrixDecomposition::distributeData()  {
606		snap_ = sman_->getCurrentSnapshot();
607		storageLayout_ = sman_->getStorageLayout();
608		#ifdef IS_MPI
609
610		// gather up the atomic positions
611	<	AtomCommVectorRow->gather(snap_->atomData.position,
611	>	AtomPlanVectorRow->gather(snap_->atomData.position,
612		atomRowData.position);
613	<	AtomCommVectorColumn->gather(snap_->atomData.position,
613	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
614		atomColData.position);
615
616		// gather up the cutoff group positions
617	<	cgCommVectorRow->gather(snap_->cgData.position,
617	>
618	>	cgPlanVectorRow->gather(snap_->cgData.position,
619		cgRowData.position);
620	<	cgCommVectorColumn->gather(snap_->cgData.position,
620	>
621	>	cgPlanVectorColumn->gather(snap_->cgData.position,
622		cgColData.position);
623	+
624	+
625	+
626	+	if (needVelocities_) {
627	+	// gather up the atomic velocities
628	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
629	+	atomColData.velocity);
630	+
631	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
632	+	cgColData.velocity);
633	+	}
634	+
635
636		// if needed, gather the atomic rotation matrices
637		if (storageLayout_ & DataStorage::dslAmat) {
638	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
638	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
639		atomRowData.aMat);
640	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
640	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
641		atomColData.aMat);
642		}
643
644		// if needed, gather the atomic eletrostatic frames
645		if (storageLayout_ & DataStorage::dslElectroFrame) {
646	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
646	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
647		atomRowData.electroFrame);
648	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
648	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
649		atomColData.electroFrame);
650		}
651	+
652	+	// if needed, gather the atomic fluctuating charge values
653	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
654	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
655	+	atomRowData.flucQPos);
656	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
657	+	atomColData.flucQPos);
658	+	}
659	+
660		#endif
661		}
662
663	+	/* collects information obtained during the pre-pair loop onto local
664	+	* data structures.
665	+	*/
666		void ForceMatrixDecomposition::collectIntermediateData() {
667		snap_ = sman_->getCurrentSnapshot();
668		storageLayout_ = sman_->getStorageLayout();
#	Line 162 | Line 670 | namespace OpenMD {
670
671		if (storageLayout_ & DataStorage::dslDensity) {
672
673	<	AtomCommRealRow->scatter(atomRowData.density,
673	>	AtomPlanRealRow->scatter(atomRowData.density,
674		snap_->atomData.density);
675
676		int n = snap_->atomData.density.size();
677	<	std::vector<RealType> rho_tmp(n, 0.0);
678	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
677	>	vector<RealType> rho_tmp(n, 0.0);
678	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
679		for (int i = 0; i < n; i++)
680		snap_->atomData.density[i] += rho_tmp[i];
681		}
682	+
683	+	if (storageLayout_ & DataStorage::dslElectricField) {
684	+
685	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
686	+	snap_->atomData.electricField);
687	+
688	+	int n = snap_->atomData.electricField.size();
689	+	vector<Vector3d> field_tmp(n, V3Zero);
690	+	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
691	+	for (int i = 0; i < n; i++)
692	+	snap_->atomData.electricField[i] += field_tmp[i];
693	+	}
694		#endif
695		}
696	<
696	>
697	>	/*
698	>	* redistributes information obtained during the pre-pair loop out to
699	>	* row and column-indexed data structures
700	>	*/
701		void ForceMatrixDecomposition::distributeIntermediateData() {
702		snap_ = sman_->getCurrentSnapshot();
703		storageLayout_ = sman_->getStorageLayout();
704		#ifdef IS_MPI
705		if (storageLayout_ & DataStorage::dslFunctional) {
706	<	AtomCommRealRow->gather(snap_->atomData.functional,
706	>	AtomPlanRealRow->gather(snap_->atomData.functional,
707		atomRowData.functional);
708	<	AtomCommRealColumn->gather(snap_->atomData.functional,
708	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
709		atomColData.functional);
710		}
711
712		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
713	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
713	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
714		atomRowData.functionalDerivative);
715	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
715	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
716		atomColData.functionalDerivative);
717		}
718		#endif
#	Line 202 | Line 726 | namespace OpenMD {
726		int n = snap_->atomData.force.size();
727		vector<Vector3d> frc_tmp(n, V3Zero);
728
729	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
729	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
730		for (int i = 0; i < n; i++) {
731		snap_->atomData.force[i] += frc_tmp[i];
732		frc_tmp[i] = 0.0;
733		}
734
735	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
736	<	for (int i = 0; i < n; i++)
735	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
736	>	for (int i = 0; i < n; i++) {
737		snap_->atomData.force[i] += frc_tmp[i];
738	<
739	<
738	>	}
739	>
740		if (storageLayout_ & DataStorage::dslTorque) {
741
742	<	int nt = snap_->atomData.force.size();
742	>	int nt = snap_->atomData.torque.size();
743		vector<Vector3d> trq_tmp(nt, V3Zero);
744
745	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
746	<	for (int i = 0; i < n; i++) {
745	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
746	>	for (int i = 0; i < nt; i++) {
747		snap_->atomData.torque[i] += trq_tmp[i];
748		trq_tmp[i] = 0.0;
749		}
750
751	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
752	<	for (int i = 0; i < n; i++)
751	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
752	>	for (int i = 0; i < nt; i++)
753		snap_->atomData.torque[i] += trq_tmp[i];
754		}
231	–
232	–	int nLocal = snap_->getNumberOfAtoms();
755
756	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
757	<	vector<RealType> (nLocal, 0.0));
756	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
757	>
758	>	int ns = snap_->atomData.skippedCharge.size();
759	>	vector<RealType> skch_tmp(ns, 0.0);
760	>
761	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
762	>	for (int i = 0; i < ns; i++) {
763	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
764	>	skch_tmp[i] = 0.0;
765	>	}
766	>
767	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
768	>	for (int i = 0; i < ns; i++)
769	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
770	>
771	>	}
772
773	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
774	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
775	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
776	<	pot_local[i] += pot_temp[i][ii];
773	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
774	>
775	>	int nq = snap_->atomData.flucQFrc.size();
776	>	vector<RealType> fqfrc_tmp(nq, 0.0);
777	>
778	>	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
779	>	for (int i = 0; i < nq; i++) {
780	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
781	>	fqfrc_tmp[i] = 0.0;
782		}
783	+
784	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
785	+	for (int i = 0; i < nq; i++)
786	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
787	+
788		}
789	+
790	+	nLocal_ = snap_->getNumberOfAtoms();
791	+
792	+	vector<potVec> pot_temp(nLocal_,
793	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
794	+	vector<potVec> expot_temp(nLocal_,
795	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
796	+
797	+	// scatter/gather pot_row into the members of my column
798	+
799	+	AtomPlanPotRow->scatter(pot_row, pot_temp);
800	+	AtomPlanPotRow->scatter(expot_row, expot_temp);
801	+
802	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
803	+	pairwisePot += pot_temp[ii];
804	+
805	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
806	+	excludedPot += expot_temp[ii];
807	+
808	+	if (storageLayout_ & DataStorage::dslParticlePot) {
809	+	// This is the pairwise contribution to the particle pot.  The
810	+	// embedding contribution is added in each of the low level
811	+	// non-bonded routines.  In single processor, this is done in
812	+	// unpackInteractionData, not in collectData.
813	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
814	+	for (int i = 0; i < nLocal_; i++) {
815	+	// factor of two is because the total potential terms are divided
816	+	// by 2 in parallel due to row/ column scatter
817	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
818	+	}
819	+	}
820	+	}
821	+
822	+	fill(pot_temp.begin(), pot_temp.end(),
823	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
824	+	fill(expot_temp.begin(), expot_temp.end(),
825	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
826	+
827	+	AtomPlanPotColumn->scatter(pot_col, pot_temp);
828	+	AtomPlanPotColumn->scatter(expot_col, expot_temp);
829	+
830	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
831	+	pairwisePot += pot_temp[ii];
832	+
833	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
834	+	excludedPot += expot_temp[ii];
835	+
836	+	if (storageLayout_ & DataStorage::dslParticlePot) {
837	+	// This is the pairwise contribution to the particle pot.  The
838	+	// embedding contribution is added in each of the low level
839	+	// non-bonded routines.  In single processor, this is done in
840	+	// unpackInteractionData, not in collectData.
841	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
842	+	for (int i = 0; i < nLocal_; i++) {
843	+	// factor of two is because the total potential terms are divided
844	+	// by 2 in parallel due to row/ column scatter
845	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
846	+	}
847	+	}
848	+	}
849	+
850	+	if (storageLayout_ & DataStorage::dslParticlePot) {
851	+	int npp = snap_->atomData.particlePot.size();
852	+	vector<RealType> ppot_temp(npp, 0.0);
853	+
854	+	// This is the direct or embedding contribution to the particle
855	+	// pot.
856	+
857	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
858	+	for (int i = 0; i < npp; i++) {
859	+	snap_->atomData.particlePot[i] += ppot_temp[i];
860	+	}
861	+
862	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
863	+
864	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
865	+	for (int i = 0; i < npp; i++) {
866	+	snap_->atomData.particlePot[i] += ppot_temp[i];
867	+	}
868	+	}
869	+
870	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
871	+	RealType ploc1 = pairwisePot[ii];
872	+	RealType ploc2 = 0.0;
873	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
874	+	pairwisePot[ii] = ploc2;
875	+	}
876	+
877	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
878	+	RealType ploc1 = excludedPot[ii];
879	+	RealType ploc2 = 0.0;
880	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
881	+	excludedPot[ii] = ploc2;
882	+	}
883	+
884	+	// Here be dragons.
885	+	MPI::Intracomm col = colComm.getComm();
886	+
887	+	col.Allreduce(MPI::IN_PLACE,
888	+	&snap_->frameData.conductiveHeatFlux[0], 3,
889	+	MPI::REALTYPE, MPI::SUM);
890	+
891	+
892		#endif
893	+
894		}
895
896	+	/**
897	+	* Collects information obtained during the post-pair (and embedding
898	+	* functional) loops onto local data structures.
899	+	*/
900	+	void ForceMatrixDecomposition::collectSelfData() {
901	+	snap_ = sman_->getCurrentSnapshot();
902	+	storageLayout_ = sman_->getStorageLayout();
903	+
904	+	#ifdef IS_MPI
905	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
906	+	RealType ploc1 = embeddingPot[ii];
907	+	RealType ploc2 = 0.0;
908	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
909	+	embeddingPot[ii] = ploc2;
910	+	}
911	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
912	+	RealType ploc1 = excludedSelfPot[ii];
913	+	RealType ploc2 = 0.0;
914	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
915	+	excludedSelfPot[ii] = ploc2;
916	+	}
917	+	#endif
918	+
919	+	}
920	+
921	+
922	+
923	+	int ForceMatrixDecomposition::getNAtomsInRow() {
924	+	#ifdef IS_MPI
925	+	return nAtomsInRow_;
926	+	#else
927	+	return nLocal_;
928	+	#endif
929	+	}
930	+
931	+	/**
932	+	* returns the list of atoms belonging to this group.
933	+	*/
934	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
935	+	#ifdef IS_MPI
936	+	return groupListRow_[cg1];
937	+	#else
938	+	return groupList_[cg1];
939	+	#endif
940	+	}
941	+
942	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
943	+	#ifdef IS_MPI
944	+	return groupListCol_[cg2];
945	+	#else
946	+	return groupList_[cg2];
947	+	#endif
948	+	}
949
950		Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
951		Vector3d d;
#	Line 257 | Line 960 | namespace OpenMD {
960		return d;
961		}
962
963	+	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
964	+	#ifdef IS_MPI
965	+	return cgColData.velocity[cg2];
966	+	#else
967	+	return snap_->cgData.velocity[cg2];
968	+	#endif
969	+	}
970
971	+	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
972	+	#ifdef IS_MPI
973	+	return atomColData.velocity[atom2];
974	+	#else
975	+	return snap_->atomData.velocity[atom2];
976	+	#endif
977	+	}
978	+
979	+
980		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
981
982		Vector3d d;
#	Line 284 | Line 1003 | namespace OpenMD {
1003		snap_->wrapVector(d);
1004		return d;
1005		}
1006	+
1007	+	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1008	+	#ifdef IS_MPI
1009	+	return massFactorsRow[atom1];
1010	+	#else
1011	+	return massFactors[atom1];
1012	+	#endif
1013	+	}
1014	+
1015	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1016	+	#ifdef IS_MPI
1017	+	return massFactorsCol[atom2];
1018	+	#else
1019	+	return massFactors[atom2];
1020	+	#endif
1021	+
1022	+	}
1023
1024		Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
1025		Vector3d d;
#	Line 298 | Line 1034 | namespace OpenMD {
1034		return d;
1035		}
1036
1037	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1038	+	return excludesForAtom[atom1];
1039	+	}
1040	+
1041	+	/**
1042	+	* We need to exclude some overcounted interactions that result from
1043	+	* the parallel decomposition.
1044	+	*/
1045	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1046	+	int unique_id_1, unique_id_2, group1, group2;
1047	+
1048	+	#ifdef IS_MPI
1049	+	// in MPI, we have to look up the unique IDs for each atom
1050	+	unique_id_1 = AtomRowToGlobal[atom1];
1051	+	unique_id_2 = AtomColToGlobal[atom2];
1052	+	group1 = cgRowToGlobal[cg1];
1053	+	group2 = cgColToGlobal[cg2];
1054	+	#else
1055	+	unique_id_1 = AtomLocalToGlobal[atom1];
1056	+	unique_id_2 = AtomLocalToGlobal[atom2];
1057	+	group1 = cgLocalToGlobal[cg1];
1058	+	group2 = cgLocalToGlobal[cg2];
1059	+	#endif
1060	+
1061	+	if (unique_id_1 == unique_id_2) return true;
1062	+
1063	+	#ifdef IS_MPI
1064	+	// this prevents us from doing the pair on multiple processors
1065	+	if (unique_id_1 < unique_id_2) {
1066	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1067	+	} else {
1068	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1069	+	}
1070	+	#endif
1071	+
1072	+	#ifndef IS_MPI
1073	+	if (group1 == group2) {
1074	+	if (unique_id_1 < unique_id_2) return true;
1075	+	}
1076	+	#endif
1077	+
1078	+	return false;
1079	+	}
1080	+
1081	+	/**
1082	+	* We need to handle the interactions for atoms who are involved in
1083	+	* the same rigid body as well as some short range interactions
1084	+	* (bonds, bends, torsions) differently from other interactions.
1085	+	* We'll still visit the pairwise routines, but with a flag that
1086	+	* tells those routines to exclude the pair from direct long range
1087	+	* interactions.  Some indirect interactions (notably reaction
1088	+	* field) must still be handled for these pairs.
1089	+	*/
1090	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1091	+
1092	+	// excludesForAtom was constructed to use row/column indices in the MPI
1093	+	// version, and to use local IDs in the non-MPI version:
1094	+
1095	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1096	+	i != excludesForAtom[atom1].end(); ++i) {
1097	+	if ( (*i) == atom2 ) return true;
1098	+	}
1099	+
1100	+	return false;
1101	+	}
1102	+
1103	+
1104		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1105		#ifdef IS_MPI
1106		atomRowData.force[atom1] += fg;
#	Line 312 | Line 1115 | namespace OpenMD {
1115		#else
1116		snap_->atomData.force[atom2] += fg;
1117		#endif
315	–
1118		}
1119
1120		// filling interaction blocks with pointers
1121	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1121	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1122	>	int atom1, int atom2) {
1123
1124	<	InteractionData idat;
1124	>	idat.excluded = excludeAtomPair(atom1, atom2);
1125	>
1126		#ifdef IS_MPI
1127	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1128	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1129	+	//                         ff_->getAtomType(identsCol[atom2]) );
1130	+
1131		if (storageLayout_ & DataStorage::dslAmat) {
1132		idat.A1 = &(atomRowData.aMat[atom1]);
1133		idat.A2 = &(atomColData.aMat[atom2]);
1134		}
1135	<
1135	>
1136		if (storageLayout_ & DataStorage::dslElectroFrame) {
1137		idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1138		idat.eFrame2 = &(atomColData.electroFrame[atom2]);
#	Line 340 | Line 1148 | namespace OpenMD {
1148		idat.rho2 = &(atomColData.density[atom2]);
1149		}
1150
1151	+	if (storageLayout_ & DataStorage::dslFunctional) {
1152	+	idat.frho1 = &(atomRowData.functional[atom1]);
1153	+	idat.frho2 = &(atomColData.functional[atom2]);
1154	+	}
1155	+
1156		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1157		idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1158		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1159		}
1160	+
1161	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1162	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1163	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1164	+	}
1165	+
1166	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1167	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1168	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1169	+	}
1170	+
1171	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1172	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1173	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1174	+	}
1175	+
1176		#else
1177	+
1178	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1179	+
1180		if (storageLayout_ & DataStorage::dslAmat) {
1181		idat.A1 = &(snap_->atomData.aMat[atom1]);
1182		idat.A2 = &(snap_->atomData.aMat[atom2]);
#	Line 360 | Line 1192 | namespace OpenMD {
1192		idat.t2 = &(snap_->atomData.torque[atom2]);
1193		}
1194
1195	<	if (storageLayout_ & DataStorage::dslDensity) {
1195	>	if (storageLayout_ & DataStorage::dslDensity) {
1196		idat.rho1 = &(snap_->atomData.density[atom1]);
1197		idat.rho2 = &(snap_->atomData.density[atom2]);
1198		}
1199
1200	+	if (storageLayout_ & DataStorage::dslFunctional) {
1201	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1202	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1203	+	}
1204	+
1205		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1206		idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1207		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1208		}
1209	+
1210	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1211	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1212	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1213	+	}
1214	+
1215	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1216	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1217	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1218	+	}
1219	+
1220	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1221	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1222	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1223	+	}
1224	+
1225		#endif
373	–
1226		}
375	–	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
376	–	InteractionData idat;
377	–	skippedCharge1
378	–	skippedCharge2
379	–	rij
380	–	d
381	–	electroMult
382	–	sw
383	–	f
384	–	#ifdef IS_MPI
1227
1228	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1229	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1230	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1228	>
1229	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1230	>	#ifdef IS_MPI
1231	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1232	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1233	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1234	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1235	>
1236	>	atomRowData.force[atom1] += *(idat.f1);
1237	>	atomColData.force[atom2] -= *(idat.f1);
1238	>
1239	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1240	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1241	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1242		}
1243	<	if (storageLayout_ & DataStorage::dslTorque) {
1244	<	idat.t1 = &(atomRowData.torque[atom1]);
1245	<	idat.t2 = &(atomColData.torque[atom2]);
1243	>
1244	>	if (storageLayout_ & DataStorage::dslElectricField) {
1245	>	atomRowData.electricField[atom1] += *(idat.eField1);
1246	>	atomColData.electricField[atom2] += *(idat.eField2);
1247		}
1248
1249	+	#else
1250	+	pairwisePot += *(idat.pot);
1251	+	excludedPot += *(idat.excludedPot);
1252	+
1253	+	snap_->atomData.force[atom1] += *(idat.f1);
1254	+	snap_->atomData.force[atom2] -= *(idat.f1);
1255	+
1256	+	if (idat.doParticlePot) {
1257	+	// This is the pairwise contribution to the particle pot.  The
1258	+	// embedding contribution is added in each of the low level
1259	+	// non-bonded routines.  In parallel, this calculation is done
1260	+	// in collectData, not in unpackInteractionData.
1261	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1262	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1263	+	}
1264
1265	<	}
1266	<	SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
1267	<	}
1265	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1266	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1267	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1268	>	}
1269
1270	+	if (storageLayout_ & DataStorage::dslElectricField) {
1271	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1272	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1273	+	}
1274
1275	+	#endif
1276	+
1277	+	}
1278	+
1279		/*
1280		* buildNeighborList
1281		*
1282		* first element of pair is row-indexed CutoffGroup
1283		* second element of pair is column-indexed CutoffGroup
1284		*/
1285	<	vector<pair<int, int> >  buildNeighborList() {
1286	<	Vector3d dr, invWid, rs, shift;
1287	<	Vector3i cc, m1v, m2s;
1288	<	RealType rrNebr;
1289	<	int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;
1285	>	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1286	>
1287	>	vector<pair<int, int> > neighborList;
1288	>	groupCutoffs cuts;
1289	>	bool doAllPairs = false;
1290
1291	+	#ifdef IS_MPI
1292	+	cellListRow_.clear();
1293	+	cellListCol_.clear();
1294	+	#else
1295	+	cellList_.clear();
1296	+	#endif
1297
1298	<	vector<pair<int, int> > neighborList;
1299	<	Vector3i nCells;
1300	<	Vector3d invWid, r;
417	<
418	<	rList_ = (rCut_ + skinThickness_);
419	<	rl2 = rList_ * rList_;
420	<
421	<	snap_ = sman_->getCurrentSnapshot();
1298	>	RealType rList_ = (largestRcut_ + skinThickness_);
1299	>	RealType rl2 = rList_ * rList_;
1300	>	Snapshot* snap_ = sman_->getCurrentSnapshot();
1301		Mat3x3d Hmat = snap_->getHmat();
1302		Vector3d Hx = Hmat.getColumn(0);
1303		Vector3d Hy = Hmat.getColumn(1);
1304		Vector3d Hz = Hmat.getColumn(2);
1305
1306	<	nCells.x() = (int) ( Hx.length() )/ rList_;
1307	<	nCells.y() = (int) ( Hy.length() )/ rList_;
1308	<	nCells.z() = (int) ( Hz.length() )/ rList_;
1306	>	nCells_.x() = (int) ( Hx.length() )/ rList_;
1307	>	nCells_.y() = (int) ( Hy.length() )/ rList_;
1308	>	nCells_.z() = (int) ( Hz.length() )/ rList_;
1309
1310	<	for (i = 0; i < nGroupsInRow; i++) {
432	<	rs = cgRowData.position[i];
433	<	snap_->scaleVector(rs);
434	<	}
1310	>	// handle small boxes where the cell offsets can end up repeating cells
1311
1312	+	if (nCells_.x() < 3) doAllPairs = true;
1313	+	if (nCells_.y() < 3) doAllPairs = true;
1314	+	if (nCells_.z() < 3) doAllPairs = true;
1315
1316	<	VDiv (invWid, cells, region);
1317	<	for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
1318	<	for (n = 0; n < nMol; n ++) {
1319	<	VSAdd (rs, mol[n].r, 0.5, region);
1320	<	VMul (cc, rs, invWid);
442	<	c = VLinear (cc, cells) + nMol;
443	<	cellList[n] = cellList[c];
444	<	cellList[c] = n;
445	<	}
446	<	nebrTabLen = 0;
447	<	for (m1z = 0; m1z < cells.z(); m1z++) {
448	<	for (m1y = 0; m1y < cells.y(); m1y++) {
449	<	for (m1x = 0; m1x < cells.x(); m1x++) {
450	<	Vector3i m1v(m1x, m1y, m1z);
451	<	m1 = VLinear(m1v, cells) + nMol;
452	<	for (offset = 0; offset < nOffset_; offset++) {
453	<	m2v = m1v + cellOffsets_[offset];
454	<	shift = V3Zero();
1316	>	Mat3x3d invHmat = snap_->getInvHmat();
1317	>	Vector3d rs, scaled, dr;
1318	>	Vector3i whichCell;
1319	>	int cellIndex;
1320	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1321
1322	<	if (m2v.x() >= cells.x) {
1323	<	m2v.x() = 0;
1324	<	shift.x() = region.x();
1325	<	} else if (m2v.x() < 0) {
1326	<	m2v.x() = cells.x() - 1;
1327	<	shift.x() = - region.x();
462	<	}
1322	>	#ifdef IS_MPI
1323	>	cellListRow_.resize(nCtot);
1324	>	cellListCol_.resize(nCtot);
1325	>	#else
1326	>	cellList_.resize(nCtot);
1327	>	#endif
1328
1329	<	if (m2v.y() >= cells.y()) {
1330	<	m2v.y() = 0;
466	<	shift.y() = region.y();
467	<	} else if (m2v.y() < 0) {
468	<	m2v.y() = cells.y() - 1;
469	<	shift.y() = - region.y();
470	<	}
1329	>	if (!doAllPairs) {
1330	>	#ifdef IS_MPI
1331
1332	<	m2 = VLinear (m2v, cells) + nMol;
1333	<	for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
1334	<	for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
1335	<	if (m1 != m2 || j2 < j1) {
1336	<	dr = mol[j1].r - mol[j2].r;
1337	<	VSub (dr, mol[j1].r, mol[j2].r);
1338	<	VVSub (dr, shift);
1339	<	if (VLenSq (dr) < rrNebr) {
1340	<	neighborList.push_back(make_pair(j1, j2));
1332	>	for (int i = 0; i < nGroupsInRow_; i++) {
1333	>	rs = cgRowData.position[i];
1334	>
1335	>	// scaled positions relative to the box vectors
1336	>	scaled = invHmat * rs;
1337	>
1338	>	// wrap the vector back into the unit box by subtracting integer box
1339	>	// numbers
1340	>	for (int j = 0; j < 3; j++) {
1341	>	scaled[j] -= roundMe(scaled[j]);
1342	>	scaled[j] += 0.5;
1343	>	}
1344	>
1345	>	// find xyz-indices of cell that cutoffGroup is in.
1346	>	whichCell.x() = nCells_.x() * scaled.x();
1347	>	whichCell.y() = nCells_.y() * scaled.y();
1348	>	whichCell.z() = nCells_.z() * scaled.z();
1349	>
1350	>	// find single index of this cell:
1351	>	cellIndex = Vlinear(whichCell, nCells_);
1352	>
1353	>	// add this cutoff group to the list of groups in this cell;
1354	>	cellListRow_[cellIndex].push_back(i);
1355	>	}
1356	>	for (int i = 0; i < nGroupsInCol_; i++) {
1357	>	rs = cgColData.position[i];
1358	>
1359	>	// scaled positions relative to the box vectors
1360	>	scaled = invHmat * rs;
1361	>
1362	>	// wrap the vector back into the unit box by subtracting integer box
1363	>	// numbers
1364	>	for (int j = 0; j < 3; j++) {
1365	>	scaled[j] -= roundMe(scaled[j]);
1366	>	scaled[j] += 0.5;
1367	>	}
1368	>
1369	>	// find xyz-indices of cell that cutoffGroup is in.
1370	>	whichCell.x() = nCells_.x() * scaled.x();
1371	>	whichCell.y() = nCells_.y() * scaled.y();
1372	>	whichCell.z() = nCells_.z() * scaled.z();
1373	>
1374	>	// find single index of this cell:
1375	>	cellIndex = Vlinear(whichCell, nCells_);
1376	>
1377	>	// add this cutoff group to the list of groups in this cell;
1378	>	cellListCol_[cellIndex].push_back(i);
1379	>	}
1380	>
1381	>	#else
1382	>	for (int i = 0; i < nGroups_; i++) {
1383	>	rs = snap_->cgData.position[i];
1384	>
1385	>	// scaled positions relative to the box vectors
1386	>	scaled = invHmat * rs;
1387	>
1388	>	// wrap the vector back into the unit box by subtracting integer box
1389	>	// numbers
1390	>	for (int j = 0; j < 3; j++) {
1391	>	scaled[j] -= roundMe(scaled[j]);
1392	>	scaled[j] += 0.5;
1393	>	}
1394	>
1395	>	// find xyz-indices of cell that cutoffGroup is in.
1396	>	whichCell.x() = nCells_.x() * scaled.x();
1397	>	whichCell.y() = nCells_.y() * scaled.y();
1398	>	whichCell.z() = nCells_.z() * scaled.z();
1399	>
1400	>	// find single index of this cell:
1401	>	cellIndex = Vlinear(whichCell, nCells_);
1402	>
1403	>	// add this cutoff group to the list of groups in this cell;
1404	>	cellList_[cellIndex].push_back(i);
1405	>	}
1406	>
1407	>	#endif
1408	>
1409	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1410	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1411	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1412	>	Vector3i m1v(m1x, m1y, m1z);
1413	>	int m1 = Vlinear(m1v, nCells_);
1414	>
1415	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1416	>	os != cellOffsets_.end(); ++os) {
1417	>
1418	>	Vector3i m2v = m1v + (*os);
1419	>
1420	>
1421	>	if (m2v.x() >= nCells_.x()) {
1422	>	m2v.x() = 0;
1423	>	} else if (m2v.x() < 0) {
1424	>	m2v.x() = nCells_.x() - 1;
1425	>	}
1426	>
1427	>	if (m2v.y() >= nCells_.y()) {
1428	>	m2v.y() = 0;
1429	>	} else if (m2v.y() < 0) {
1430	>	m2v.y() = nCells_.y() - 1;
1431	>	}
1432	>
1433	>	if (m2v.z() >= nCells_.z()) {
1434	>	m2v.z() = 0;
1435	>	} else if (m2v.z() < 0) {
1436	>	m2v.z() = nCells_.z() - 1;
1437	>	}
1438	>
1439	>	int m2 = Vlinear (m2v, nCells_);
1440	>
1441	>	#ifdef IS_MPI
1442	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1443	>	j1 != cellListRow_[m1].end(); ++j1) {
1444	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1445	>	j2 != cellListCol_[m2].end(); ++j2) {
1446	>
1447	>	// In parallel, we need to visit *all* pairs of row
1448	>	// & column indicies and will divide labor in the
1449	>	// force evaluation later.
1450	>	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1451	>	snap_->wrapVector(dr);
1452	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1453	>	if (dr.lengthSquare() < cuts.third) {
1454	>	neighborList.push_back(make_pair((*j1), (*j2)));
1455	>	}
1456	>	}
1457	>	}
1458	>	#else
1459	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1460	>	j1 != cellList_[m1].end(); ++j1) {
1461	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1462	>	j2 != cellList_[m2].end(); ++j2) {
1463	>
1464	>	// Always do this if we're in different cells or if
1465	>	// we're in the same cell and the global index of
1466	>	// the j2 cutoff group is greater than or equal to
1467	>	// the j1 cutoff group.  Note that Rappaport's code
1468	>	// has a "less than" conditional here, but that
1469	>	// deals with atom-by-atom computation.  OpenMD
1470	>	// allows atoms within a single cutoff group to
1471	>	// interact with each other.
1472	>
1473	>
1474	>
1475	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1476	>
1477	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1478	>	snap_->wrapVector(dr);
1479	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1480	>	if (dr.lengthSquare() < cuts.third) {
1481	>	neighborList.push_back(make_pair((*j1), (*j2)));
1482	>	}
1483		}
1484		}
1485		}
1486	+	#endif
1487		}
1488		}
1489		}
1490		}
1491	+	} else {
1492	+	// branch to do all cutoff group pairs
1493	+	#ifdef IS_MPI
1494	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1495	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1496	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1497	+	snap_->wrapVector(dr);
1498	+	cuts = getGroupCutoffs( j1, j2 );
1499	+	if (dr.lengthSquare() < cuts.third) {
1500	+	neighborList.push_back(make_pair(j1, j2));
1501	+	}
1502	+	}
1503	+	}
1504	+	#else
1505	+	// include all groups here.
1506	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1507	+	// include self group interactions j2 == j1
1508	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1509	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1510	+	snap_->wrapVector(dr);
1511	+	cuts = getGroupCutoffs( j1, j2 );
1512	+	if (dr.lengthSquare() < cuts.third) {
1513	+	neighborList.push_back(make_pair(j1, j2));
1514	+	}
1515	+	}
1516	+	}
1517	+	#endif
1518		}
1519	+
1520	+	// save the local cutoff group positions for the check that is
1521	+	// done on each loop:
1522	+	saved_CG_positions_.clear();
1523	+	for (int i = 0; i < nGroups_; i++)
1524	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1525	+
1526	+	return neighborList;
1527		}
490	–
491	–
1528		} //end namespace OpenMD

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