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

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
44		#include "nonbonded/NonBondedInteraction.hpp"
45		#include "brains/SnapshotManager.hpp"
46	+	#include "brains/PairList.hpp"
47
48		using namespace std;
49		namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	+
53	+	// In a parallel computation, row and colum scans must visit all
54	+	// surrounding cells (not just the 14 upper triangular blocks that
55	+	// are used when the processor can see all pairs)
56	+	#ifdef IS_MPI
57	+	cellOffsets_.clear();
58	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
66	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	+	#endif
86	+	}
87	+
88	+
89		/**
90		* distributeInitialData is essentially a copy of the older fortran
91		* SimulationSetup
92		*/
53	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96	+	ff_ = info_->getForceField();
97		nLocal_ = snap_->getNumberOfAtoms();
98	<	nGroups_ = snap_->getNumberOfCutoffGroups();
99	<
98	>
99	>	nGroups_ = info_->getNLocalCutoffGroups();
100		// gather the information for atomtype IDs (atids):
101	<	vector<int> identsLocal = info_->getIdentArray();
101	>	idents = info_->getIdentArray();
102		AtomLocalToGlobal = info_->getGlobalAtomIndices();
103		cgLocalToGlobal = info_->getGlobalGroupIndices();
104		vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
65	–	vector<RealType> massFactorsLocal = info_->getMassFactors();
66	–	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
105
106	+	massFactors = info_->getMassFactors();
107	+
108	+	PairList* excludes = info_->getExcludedInteractions();
109	+	PairList* oneTwo = info_->getOneTwoInteractions();
110	+	PairList* oneThree = info_->getOneThreeInteractions();
111	+	PairList* oneFour = info_->getOneFourInteractions();
112	+
113	+	if (needVelocities_)
114	+	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
115	+	DataStorage::dslVelocity);
116	+	else
117	+	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118	+
119		#ifdef IS_MPI
120
121	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
122	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
72	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
73	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
121	>	MPI::Intracomm row = rowComm.getComm();
122	>	MPI::Intracomm col = colComm.getComm();
123
124	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
125	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
126	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
127	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
124	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
125	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
126	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
127	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
128	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
129
130	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
131	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
132	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
133	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
130	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
131	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
132	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
133	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
134	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
135
136	<	nAtomsInRow_ = AtomCommIntRow->getSize();
137	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
138	<	nGroupsInRow_ = cgCommIntRow->getSize();
139	<	nGroupsInCol_ = cgCommIntColumn->getSize();
136	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
137	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
138	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
139	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
140
141	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
142	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
143	+	nGroupsInRow_ = cgPlanIntRow->getSize();
144	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
145	+
146		// Modify the data storage objects with the correct layouts and sizes:
147		atomRowData.resize(nAtomsInRow_);
148		atomRowData.setStorageLayout(storageLayout_);
#	Line 95 | Line 151 | namespace OpenMD {
151		cgRowData.resize(nGroupsInRow_);
152		cgRowData.setStorageLayout(DataStorage::dslPosition);
153		cgColData.resize(nGroupsInCol_);
154	<	cgColData.setStorageLayout(DataStorage::dslPosition);
154	>	if (needVelocities_)
155	>	// we only need column velocities if we need them.
156	>	cgColData.setStorageLayout(DataStorage::dslPosition |
157	>	DataStorage::dslVelocity);
158	>	else
159	>	cgColData.setStorageLayout(DataStorage::dslPosition);
160	>
161	>	identsRow.resize(nAtomsInRow_);
162	>	identsCol.resize(nAtomsInCol_);
163
164	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
165	<	vector<RealType> (nAtomsInRow_, 0.0));
102	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
103	<	vector<RealType> (nAtomsInCol_, 0.0));
164	>	AtomPlanIntRow->gather(idents, identsRow);
165	>	AtomPlanIntColumn->gather(idents, identsCol);
166
167	<	identsRow.reserve(nAtomsInRow_);
168	<	identsCol.reserve(nAtomsInCol_);
169	<
108	<	AtomCommIntRow->gather(identsLocal, identsRow);
109	<	AtomCommIntColumn->gather(identsLocal, identsCol);
110	<
111	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
112	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
113	<
114	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
115	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
167	>	// allocate memory for the parallel objects
168	>	atypesRow.resize(nAtomsInRow_);
169	>	atypesCol.resize(nAtomsInCol_);
170
171	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
172	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
171	>	for (int i = 0; i < nAtomsInRow_; i++)
172	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
173	>	for (int i = 0; i < nAtomsInCol_; i++)
174	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
175
176	+	pot_row.resize(nAtomsInRow_);
177	+	pot_col.resize(nAtomsInCol_);
178	+
179	+	expot_row.resize(nAtomsInRow_);
180	+	expot_col.resize(nAtomsInCol_);
181	+
182	+	AtomRowToGlobal.resize(nAtomsInRow_);
183	+	AtomColToGlobal.resize(nAtomsInCol_);
184	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
185	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
186	+
187	+	cgRowToGlobal.resize(nGroupsInRow_);
188	+	cgColToGlobal.resize(nGroupsInCol_);
189	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
190	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
191	+
192	+	massFactorsRow.resize(nAtomsInRow_);
193	+	massFactorsCol.resize(nAtomsInCol_);
194	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
195	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
196	+
197		groupListRow_.clear();
198	<	groupListRow_.reserve(nGroupsInRow_);
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++) {
#	Line 129 | Line 206 | namespace OpenMD {
206		}
207
208		groupListCol_.clear();
209	<	groupListCol_.reserve(nGroupsInCol_);
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_.reserve(nGroups_);
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)
298	>	if (globalGroupMembership[aid] == gid) {
299		groupList_[i].push_back(j);
300	+	}
301		}
302		}
303
304	+
305	+	createGtypeCutoffMap();
306	+
307	+	}
308
309	<	// still need:
310	<	// topoDist
311	<	// exclude
309	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
310	>
311	>	RealType tol = 1e-6;
312	>	largestRcut_ = 0.0;
313	>	int atid;
314	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315	>
316	>	map<int, RealType> atypeCutoff;
317	>
318	>	for (set<AtomType*>::iterator at = atypes.begin();
319	>	at != atypes.end(); ++at){
320	>	atid = (*at)->getIdent();
321	>	if (userChoseCutoff_)
322	>	atypeCutoff[atid] = userCutoff_;
323	>	else
324	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
325	>	}
326	>
327	>	vector<RealType> gTypeCutoffs;
328	>	// first we do a single loop over the cutoff groups to find the
329	>	// largest cutoff for any atypes present in this group.
330	>	#ifdef IS_MPI
331	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
332	>	groupRowToGtype.resize(nGroupsInRow_);
333	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
334	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
335	>	for (vector<int>::iterator ia = atomListRow.begin();
336	>	ia != atomListRow.end(); ++ia) {
337	>	int atom1 = (*ia);
338	>	atid = identsRow[atom1];
339	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
340	>	groupCutoffRow[cg1] = atypeCutoff[atid];
341	>	}
342	>	}
343
344	+	bool gTypeFound = false;
345	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
346	+	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
347	+	groupRowToGtype[cg1] = gt;
348	+	gTypeFound = true;
349	+	}
350	+	}
351	+	if (!gTypeFound) {
352	+	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
353	+	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
354	+	}
355	+
356	+	}
357	+	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
358	+	groupColToGtype.resize(nGroupsInCol_);
359	+	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
360	+	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
361	+	for (vector<int>::iterator jb = atomListCol.begin();
362	+	jb != atomListCol.end(); ++jb) {
363	+	int atom2 = (*jb);
364	+	atid = identsCol[atom2];
365	+	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
366	+	groupCutoffCol[cg2] = atypeCutoff[atid];
367	+	}
368	+	}
369	+	bool gTypeFound = false;
370	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
371	+	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
372	+	groupColToGtype[cg2] = gt;
373	+	gTypeFound = true;
374	+	}
375	+	}
376	+	if (!gTypeFound) {
377	+	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
378	+	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
379	+	}
380	+	}
381	+	#else
382	+
383	+	vector<RealType> groupCutoff(nGroups_, 0.0);
384	+	groupToGtype.resize(nGroups_);
385	+	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
386	+	groupCutoff[cg1] = 0.0;
387	+	vector<int> atomList = getAtomsInGroupRow(cg1);
388	+	for (vector<int>::iterator ia = atomList.begin();
389	+	ia != atomList.end(); ++ia) {
390	+	int atom1 = (*ia);
391	+	atid = idents[atom1];
392	+	if (atypeCutoff[atid] > groupCutoff[cg1])
393	+	groupCutoff[cg1] = atypeCutoff[atid];
394	+	}
395	+
396	+	bool gTypeFound = false;
397	+	for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
398	+	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
399	+	groupToGtype[cg1] = gt;
400	+	gTypeFound = true;
401	+	}
402	+	}
403	+	if (!gTypeFound) {
404	+	gTypeCutoffs.push_back( groupCutoff[cg1] );
405	+	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
406	+	}
407	+	}
408	+	#endif
409	+
410	+	// Now we find the maximum group cutoff value present in the simulation
411	+
412	+	RealType groupMax = *max_element(gTypeCutoffs.begin(),
413	+	gTypeCutoffs.end());
414	+
415	+	#ifdef IS_MPI
416	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
417	+	MPI::MAX);
418	+	#endif
419	+
420	+	RealType tradRcut = groupMax;
421	+
422	+	for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
423	+	for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {
424	+	RealType thisRcut;
425	+	switch(cutoffPolicy_) {
426	+	case TRADITIONAL:
427	+	thisRcut = tradRcut;
428	+	break;
429	+	case MIX:
430	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
431	+	break;
432	+	case MAX:
433	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
434	+	break;
435	+	default:
436	+	sprintf(painCave.errMsg,
437	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
438	+	"hit an unknown cutoff policy!\n");
439	+	painCave.severity = OPENMD_ERROR;
440	+	painCave.isFatal = 1;
441	+	simError();
442	+	break;
443	+	}
444	+
445	+	pair<int,int> key = make_pair(i,j);
446	+	gTypeCutoffMap[key].first = thisRcut;
447	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
448	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
449	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
450	+	// sanity check
451	+
452	+	if (userChoseCutoff_) {
453	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
454	+	sprintf(painCave.errMsg,
455	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
456	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
457	+	painCave.severity = OPENMD_ERROR;
458	+	painCave.isFatal = 1;
459	+	simError();
460	+	}
461	+	}
462	+	}
463	+	}
464		}
465	+
466	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467	+	int i, j;
468	+	#ifdef IS_MPI
469	+	i = groupRowToGtype[cg1];
470	+	j = groupColToGtype[cg2];
471	+	#else
472	+	i = groupToGtype[cg1];
473	+	j = groupToGtype[cg2];
474	+	#endif
475	+	return gTypeCutoffMap[make_pair(i,j)];
476	+	}
477	+
478	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
479	+	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
480	+	if (toposForAtom[atom1][j] == atom2)
481	+	return topoDist[atom1][j];
482	+	}
483	+	return 0;
484	+	}
485	+
486	+	void ForceMatrixDecomposition::zeroWorkArrays() {
487	+	pairwisePot = 0.0;
488	+	embeddingPot = 0.0;
489	+	excludedPot = 0.0;
490	+	excludedSelfPot = 0.0;
491	+
492	+	#ifdef IS_MPI
493	+	if (storageLayout_ & DataStorage::dslForce) {
494	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
495	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
496	+	}
497	+
498	+	if (storageLayout_ & DataStorage::dslTorque) {
499	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
500	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
501	+	}
502
503	+	fill(pot_row.begin(), pot_row.end(),
504	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
505
506	+	fill(pot_col.begin(), pot_col.end(),
507	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
508
509	+	fill(expot_row.begin(), expot_row.end(),
510	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
511	+
512	+	fill(expot_col.begin(), expot_col.end(),
513	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
514	+
515	+	if (storageLayout_ & DataStorage::dslParticlePot) {
516	+	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
517	+	0.0);
518	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
519	+	0.0);
520	+	}
521	+
522	+	if (storageLayout_ & DataStorage::dslDensity) {
523	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
524	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
525	+	}
526	+
527	+	if (storageLayout_ & DataStorage::dslFunctional) {
528	+	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
529	+	0.0);
530	+	fill(atomColData.functional.begin(), atomColData.functional.end(),
531	+	0.0);
532	+	}
533	+
534	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
535	+	fill(atomRowData.functionalDerivative.begin(),
536	+	atomRowData.functionalDerivative.end(), 0.0);
537	+	fill(atomColData.functionalDerivative.begin(),
538	+	atomColData.functionalDerivative.end(), 0.0);
539	+	}
540	+
541	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
542	+	fill(atomRowData.skippedCharge.begin(),
543	+	atomRowData.skippedCharge.end(), 0.0);
544	+	fill(atomColData.skippedCharge.begin(),
545	+	atomColData.skippedCharge.end(), 0.0);
546	+	}
547	+
548	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
549	+	fill(atomRowData.flucQFrc.begin(),
550	+	atomRowData.flucQFrc.end(), 0.0);
551	+	fill(atomColData.flucQFrc.begin(),
552	+	atomColData.flucQFrc.end(), 0.0);
553	+	}
554	+
555	+	if (storageLayout_ & DataStorage::dslElectricField) {
556	+	fill(atomRowData.electricField.begin(),
557	+	atomRowData.electricField.end(), V3Zero);
558	+	fill(atomColData.electricField.begin(),
559	+	atomColData.electricField.end(), V3Zero);
560	+	}
561	+
562	+	#endif
563	+	// even in parallel, we need to zero out the local arrays:
564	+
565	+	if (storageLayout_ & DataStorage::dslParticlePot) {
566	+	fill(snap_->atomData.particlePot.begin(),
567	+	snap_->atomData.particlePot.end(), 0.0);
568	+	}
569	+
570	+	if (storageLayout_ & DataStorage::dslDensity) {
571	+	fill(snap_->atomData.density.begin(),
572	+	snap_->atomData.density.end(), 0.0);
573	+	}
574	+
575	+	if (storageLayout_ & DataStorage::dslFunctional) {
576	+	fill(snap_->atomData.functional.begin(),
577	+	snap_->atomData.functional.end(), 0.0);
578	+	}
579	+
580	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
581	+	fill(snap_->atomData.functionalDerivative.begin(),
582	+	snap_->atomData.functionalDerivative.end(), 0.0);
583	+	}
584	+
585	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
586	+	fill(snap_->atomData.skippedCharge.begin(),
587	+	snap_->atomData.skippedCharge.end(), 0.0);
588	+	}
589	+
590	+	if (storageLayout_ & DataStorage::dslElectricField) {
591	+	fill(snap_->atomData.electricField.begin(),
592	+	snap_->atomData.electricField.end(), V3Zero);
593	+	}
594	+	}
595	+
596	+
597		void ForceMatrixDecomposition::distributeData()  {
598		snap_ = sman_->getCurrentSnapshot();
599		storageLayout_ = sman_->getStorageLayout();
600		#ifdef IS_MPI
601
602		// gather up the atomic positions
603	<	AtomCommVectorRow->gather(snap_->atomData.position,
603	>	AtomPlanVectorRow->gather(snap_->atomData.position,
604		atomRowData.position);
605	<	AtomCommVectorColumn->gather(snap_->atomData.position,
605	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
606		atomColData.position);
607
608		// gather up the cutoff group positions
609	<	cgCommVectorRow->gather(snap_->cgData.position,
609	>
610	>	cgPlanVectorRow->gather(snap_->cgData.position,
611		cgRowData.position);
612	<	cgCommVectorColumn->gather(snap_->cgData.position,
612	>
613	>	cgPlanVectorColumn->gather(snap_->cgData.position,
614		cgColData.position);
615	+
616	+
617	+
618	+	if (needVelocities_) {
619	+	// gather up the atomic velocities
620	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
621	+	atomColData.velocity);
622	+
623	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
624	+	cgColData.velocity);
625	+	}
626	+
627
628		// if needed, gather the atomic rotation matrices
629		if (storageLayout_ & DataStorage::dslAmat) {
630	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
630	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
631		atomRowData.aMat);
632	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
632	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
633		atomColData.aMat);
634		}
635	<
636	<	// if needed, gather the atomic eletrostatic frames
637	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
638	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
639	<	atomRowData.electroFrame);
640	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
641	<	atomColData.electroFrame);
635	>
636	>	// if needed, gather the atomic eletrostatic information
637	>	if (storageLayout_ & DataStorage::dslDipole) {
638	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
639	>	atomRowData.dipole);
640	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
641	>	atomColData.dipole);
642	>	}
643	>
644	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
645	>	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
646	>	atomRowData.quadrupole);
647	>	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
648	>	atomColData.quadrupole);
649		}
650	+
651	+	// if needed, gather the atomic fluctuating charge values
652	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
653	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
654	+	atomRowData.flucQPos);
655	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
656	+	atomColData.flucQPos);
657	+	}
658	+
659		#endif
660		}
661
662	+	/* collects information obtained during the pre-pair loop onto local
663	+	* data structures.
664	+	*/
665		void ForceMatrixDecomposition::collectIntermediateData() {
666		snap_ = sman_->getCurrentSnapshot();
667		storageLayout_ = sman_->getStorageLayout();
#	Line 203 | Line 669 | namespace OpenMD {
669
670		if (storageLayout_ & DataStorage::dslDensity) {
671
672	<	AtomCommRealRow->scatter(atomRowData.density,
672	>	AtomPlanRealRow->scatter(atomRowData.density,
673		snap_->atomData.density);
674
675		int n = snap_->atomData.density.size();
676	<	std::vector<RealType> rho_tmp(n, 0.0);
677	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
676	>	vector<RealType> rho_tmp(n, 0.0);
677	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
678		for (int i = 0; i < n; i++)
679		snap_->atomData.density[i] += rho_tmp[i];
680		}
681	+
682	+	// this isn't necessary if we don't have polarizable atoms, but
683	+	// we'll leave it here for now.
684	+	if (storageLayout_ & DataStorage::dslElectricField) {
685	+
686	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
687	+	snap_->atomData.electricField);
688	+
689	+	int n = snap_->atomData.electricField.size();
690	+	vector<Vector3d> field_tmp(n, V3Zero);
691	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
692	+	field_tmp);
693	+	for (int i = 0; i < n; i++)
694	+	snap_->atomData.electricField[i] += field_tmp[i];
695	+	}
696		#endif
697		}
698	<
698	>
699	>	/*
700	>	* redistributes information obtained during the pre-pair loop out to
701	>	* row and column-indexed data structures
702	>	*/
703		void ForceMatrixDecomposition::distributeIntermediateData() {
704		snap_ = sman_->getCurrentSnapshot();
705		storageLayout_ = sman_->getStorageLayout();
706		#ifdef IS_MPI
707		if (storageLayout_ & DataStorage::dslFunctional) {
708	<	AtomCommRealRow->gather(snap_->atomData.functional,
708	>	AtomPlanRealRow->gather(snap_->atomData.functional,
709		atomRowData.functional);
710	<	AtomCommRealColumn->gather(snap_->atomData.functional,
710	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
711		atomColData.functional);
712		}
713
714		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
715	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
715	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
716		atomRowData.functionalDerivative);
717	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
717	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
718		atomColData.functionalDerivative);
719		}
720		#endif
#	Line 243 | Line 728 | namespace OpenMD {
728		int n = snap_->atomData.force.size();
729		vector<Vector3d> frc_tmp(n, V3Zero);
730
731	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
731	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
732		for (int i = 0; i < n; i++) {
733		snap_->atomData.force[i] += frc_tmp[i];
734		frc_tmp[i] = 0.0;
735		}
736
737	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
738	<	for (int i = 0; i < n; i++)
737	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
738	>	for (int i = 0; i < n; i++) {
739		snap_->atomData.force[i] += frc_tmp[i];
740	<
741	<
740	>	}
741	>
742		if (storageLayout_ & DataStorage::dslTorque) {
743
744	<	int nt = snap_->atomData.force.size();
744	>	int nt = snap_->atomData.torque.size();
745		vector<Vector3d> trq_tmp(nt, V3Zero);
746
747	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
748	<	for (int i = 0; i < n; i++) {
747	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
748	>	for (int i = 0; i < nt; i++) {
749		snap_->atomData.torque[i] += trq_tmp[i];
750		trq_tmp[i] = 0.0;
751		}
752
753	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
754	<	for (int i = 0; i < n; i++)
753	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
754	>	for (int i = 0; i < nt; i++)
755		snap_->atomData.torque[i] += trq_tmp[i];
756		}
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<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
812	<	vector<RealType> (nLocal_, 0.0));
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 i = 0; i < N_INTERACTION_FAMILIES; i++) {
850	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
851	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
852	<	pot_local[i] += pot_temp[i][ii];
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		*/
#	Line 312 | Line 975 | namespace OpenMD {
975		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
976		#endif
977
978	<	snap_->wrapVector(d);
978	>	if (usePeriodicBoundaryConditions_) {
979	>	snap_->wrapVector(d);
980	>	}
981		return d;
982		}
983
984	+	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
985	+	#ifdef IS_MPI
986	+	return cgColData.velocity[cg2];
987	+	#else
988	+	return snap_->cgData.velocity[cg2];
989	+	#endif
990	+	}
991
992	+	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
993	+	#ifdef IS_MPI
994	+	return atomColData.velocity[atom2];
995	+	#else
996	+	return snap_->atomData.velocity[atom2];
997	+	#endif
998	+	}
999	+
1000	+
1001		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
1002
1003		Vector3d d;
#	Line 326 | Line 1007 | namespace OpenMD {
1007		#else
1008		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1009		#endif
1010	<
1011	<	snap_->wrapVector(d);
1010	>	if (usePeriodicBoundaryConditions_) {
1011	>	snap_->wrapVector(d);
1012	>	}
1013		return d;
1014		}
1015
#	Line 339 | Line 1021 | namespace OpenMD {
1021		#else
1022		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1023		#endif
1024	<
1025	<	snap_->wrapVector(d);
1024	>	if (usePeriodicBoundaryConditions_) {
1025	>	snap_->wrapVector(d);
1026	>	}
1027		return d;
1028		}
1029
#	Line 348 | Line 1031 | namespace OpenMD {
1031		#ifdef IS_MPI
1032		return massFactorsRow[atom1];
1033		#else
1034	<	return massFactorsLocal[atom1];
1034	>	return massFactors[atom1];
1035		#endif
1036		}
1037
#	Line 356 | Line 1039 | namespace OpenMD {
1039		#ifdef IS_MPI
1040		return massFactorsCol[atom2];
1041		#else
1042	<	return massFactorsLocal[atom2];
1042	>	return massFactors[atom2];
1043		#endif
1044
1045		}
#	Line 369 | Line 1052 | namespace OpenMD {
1052		#else
1053		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1054		#endif
1055	<
1056	<	snap_->wrapVector(d);
1055	>	if (usePeriodicBoundaryConditions_) {
1056	>	snap_->wrapVector(d);
1057	>	}
1058		return d;
1059		}
1060
1061	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1062	+	return excludesForAtom[atom1];
1063	+	}
1064	+
1065	+	/**
1066	+	* We need to exclude some overcounted interactions that result from
1067	+	* the parallel decomposition.
1068	+	*/
1069	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1070	+	int unique_id_1, unique_id_2;
1071	+
1072	+	#ifdef IS_MPI
1073	+	// in MPI, we have to look up the unique IDs for each atom
1074	+	unique_id_1 = AtomRowToGlobal[atom1];
1075	+	unique_id_2 = AtomColToGlobal[atom2];
1076	+	// group1 = cgRowToGlobal[cg1];
1077	+	// group2 = cgColToGlobal[cg2];
1078	+	#else
1079	+	unique_id_1 = AtomLocalToGlobal[atom1];
1080	+	unique_id_2 = AtomLocalToGlobal[atom2];
1081	+	int group1 = cgLocalToGlobal[cg1];
1082	+	int group2 = cgLocalToGlobal[cg2];
1083	+	#endif
1084	+
1085	+	if (unique_id_1 == unique_id_2) return true;
1086	+
1087	+	#ifdef IS_MPI
1088	+	// this prevents us from doing the pair on multiple processors
1089	+	if (unique_id_1 < unique_id_2) {
1090	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1091	+	} else {
1092	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1093	+	}
1094	+	#endif
1095	+
1096	+	#ifndef IS_MPI
1097	+	if (group1 == group2) {
1098	+	if (unique_id_1 < unique_id_2) return true;
1099	+	}
1100	+	#endif
1101	+
1102	+	return false;
1103	+	}
1104	+
1105	+	/**
1106	+	* We need to handle the interactions for atoms who are involved in
1107	+	* the same rigid body as well as some short range interactions
1108	+	* (bonds, bends, torsions) differently from other interactions.
1109	+	* We'll still visit the pairwise routines, but with a flag that
1110	+	* tells those routines to exclude the pair from direct long range
1111	+	* interactions.  Some indirect interactions (notably reaction
1112	+	* field) must still be handled for these pairs.
1113	+	*/
1114	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1115	+
1116	+	// excludesForAtom was constructed to use row/column indices in the MPI
1117	+	// version, and to use local IDs in the non-MPI version:
1118	+
1119	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1120	+	i != excludesForAtom[atom1].end(); ++i) {
1121	+	if ( (*i) == atom2 ) return true;
1122	+	}
1123	+
1124	+	return false;
1125	+	}
1126	+
1127	+
1128		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1129		#ifdef IS_MPI
1130		atomRowData.force[atom1] += fg;
#	Line 391 | Line 1142 | namespace OpenMD {
1142		}
1143
1144		// filling interaction blocks with pointers
1145	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1146	<	InteractionData idat;
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.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1153	+	//                         ff_->getAtomType(identsCol[atom2]) );
1154	+
1155		if (storageLayout_ & DataStorage::dslAmat) {
1156		idat.A1 = &(atomRowData.aMat[atom1]);
1157		idat.A2 = &(atomColData.aMat[atom2]);
1158		}
1159
403	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
404	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
405	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
406	–	}
407	–
1160		if (storageLayout_ & DataStorage::dslTorque) {
1161		idat.t1 = &(atomRowData.torque[atom1]);
1162		idat.t2 = &(atomColData.torque[atom2]);
1163		}
1164
1165	+	if (storageLayout_ & DataStorage::dslDipole) {
1166	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1167	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1168	+	}
1169	+
1170	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1171	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1172	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1173	+	}
1174	+
1175		if (storageLayout_ & DataStorage::dslDensity) {
1176		idat.rho1 = &(atomRowData.density[atom1]);
1177		idat.rho2 = &(atomColData.density[atom2]);
1178		}
1179
1180	+	if (storageLayout_ & DataStorage::dslFunctional) {
1181	+	idat.frho1 = &(atomRowData.functional[atom1]);
1182	+	idat.frho2 = &(atomColData.functional[atom2]);
1183	+	}
1184	+
1185		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1186		idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1187		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1188		}
1189	+
1190	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1191	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1192	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1193	+	}
1194	+
1195	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1196	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1197	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1198	+	}
1199	+
1200	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1201	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1202	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1203	+	}
1204	+
1205		#else
1206	+
1207	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1208	+
1209		if (storageLayout_ & DataStorage::dslAmat) {
1210		idat.A1 = &(snap_->atomData.aMat[atom1]);
1211		idat.A2 = &(snap_->atomData.aMat[atom2]);
1212		}
1213
428	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
429	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
430	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
431	–	}
432	–
1214		if (storageLayout_ & DataStorage::dslTorque) {
1215		idat.t1 = &(snap_->atomData.torque[atom1]);
1216		idat.t2 = &(snap_->atomData.torque[atom2]);
1217		}
1218
1219	<	if (storageLayout_ & DataStorage::dslDensity) {
1219	>	if (storageLayout_ & DataStorage::dslDipole) {
1220	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1221	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1222	>	}
1223	>
1224	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1225	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1226	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1227	>	}
1228	>
1229	>	if (storageLayout_ & DataStorage::dslDensity) {
1230		idat.rho1 = &(snap_->atomData.density[atom1]);
1231		idat.rho2 = &(snap_->atomData.density[atom2]);
1232		}
1233
1234	+	if (storageLayout_ & DataStorage::dslFunctional) {
1235	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1236	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1237	+	}
1238	+
1239		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1240		idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1241		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1242		}
1243	+
1244	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1245	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1246	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1247	+	}
1248	+
1249	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1250	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1251	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1252	+	}
1253	+
1254	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1255	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1256	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1257	+	}
1258	+
1259		#endif
448	–	return idat;
1260		}
1261
1262	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1263	<
453	<	InteractionData idat;
1262	>
1263	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1264		#ifdef IS_MPI
1265	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1266	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1267	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1265	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1266	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1267	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1268	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1269	>
1270	>	atomRowData.force[atom1] += *(idat.f1);
1271	>	atomColData.force[atom2] -= *(idat.f1);
1272	>
1273	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1274	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1275	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1276		}
1277	<	if (storageLayout_ & DataStorage::dslTorque) {
1278	<	idat.t1 = &(atomRowData.torque[atom1]);
1279	<	idat.t2 = &(atomColData.torque[atom2]);
1277	>
1278	>	if (storageLayout_ & DataStorage::dslElectricField) {
1279	>	atomRowData.electricField[atom1] += *(idat.eField1);
1280	>	atomColData.electricField[atom2] += *(idat.eField2);
1281		}
1282	<	if (storageLayout_ & DataStorage::dslForce) {
464	<	idat.t1 = &(atomRowData.force[atom1]);
465	<	idat.t2 = &(atomColData.force[atom2]);
466	<	}
1282	>
1283		#else
1284	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1285	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1286	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1284	>	pairwisePot += *(idat.pot);
1285	>	excludedPot += *(idat.excludedPot);
1286	>
1287	>	snap_->atomData.force[atom1] += *(idat.f1);
1288	>	snap_->atomData.force[atom2] -= *(idat.f1);
1289	>
1290	>	if (idat.doParticlePot) {
1291	>	// This is the pairwise contribution to the particle pot.  The
1292	>	// embedding contribution is added in each of the low level
1293	>	// non-bonded routines.  In parallel, this calculation is done
1294	>	// in collectData, not in unpackInteractionData.
1295	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1296	>	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1297		}
1298	<	if (storageLayout_ & DataStorage::dslTorque) {
1299	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1300	<	idat.t2 = &(snap_->atomData.torque[atom2]);
1298	>
1299	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1300	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1301	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1302		}
1303	<	if (storageLayout_ & DataStorage::dslForce) {
1304	<	idat.t1 = &(snap_->atomData.force[atom1]);
1305	<	idat.t2 = &(snap_->atomData.force[atom2]);
1303	>
1304	>	if (storageLayout_ & DataStorage::dslElectricField) {
1305	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1306	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1307		}
1308	+
1309		#endif
1310
1311		}
1312
484	–
485	–
486	–
1313		/*
1314		* buildNeighborList
1315		*
#	Line 493 | Line 1319 | namespace OpenMD {
1319		vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1320
1321		vector<pair<int, int> > neighborList;
1322	<	#ifdef IS_MPI
1323	<	cellListRow_.clear();
498	<	cellListCol_.clear();
499	<	#else
500	<	cellList_.clear();
501	<	#endif
1322	>	groupCutoffs cuts;
1323	>	bool doAllPairs = false;
1324
1325	<	// dangerous to not do error checking.
504	<	RealType rCut_;
505	<
506	<	RealType rList_ = (rCut_ + skinThickness_);
507	<	RealType rl2 = rList_ * rList_;
1325	>	RealType rList_ = (largestRcut_ + skinThickness_);
1326		Snapshot* snap_ = sman_->getCurrentSnapshot();
1327	<	Mat3x3d Hmat = snap_->getHmat();
1328	<	Vector3d Hx = Hmat.getColumn(0);
511	<	Vector3d Hy = Hmat.getColumn(1);
512	<	Vector3d Hz = Hmat.getColumn(2);
1327	>	Mat3x3d box;
1328	>	Mat3x3d invBox;
1329
514	–	nCells_.x() = (int) ( Hx.length() )/ rList_;
515	–	nCells_.y() = (int) ( Hy.length() )/ rList_;
516	–	nCells_.z() = (int) ( Hz.length() )/ rList_;
517	–
518	–	Mat3x3d invHmat = snap_->getInvHmat();
1330		Vector3d rs, scaled, dr;
1331		Vector3i whichCell;
1332		int cellIndex;
1333
1334		#ifdef IS_MPI
1335	<	for (int i = 0; i < nGroupsInRow_; i++) {
1336	<	rs = cgRowData.position[i];
1337	<	// scaled positions relative to the box vectors
1338	<	scaled = invHmat * rs;
1339	<	// wrap the vector back into the unit box by subtracting integer box
1340	<	// numbers
1341	<	for (int j = 0; j < 3; j++)
1342	<	scaled[j] -= roundMe(scaled[j]);
1343	<
1344	<	// find xyz-indices of cell that cutoffGroup is in.
1345	<	whichCell.x() = nCells_.x() * scaled.x();
1346	<	whichCell.y() = nCells_.y() * scaled.y();
536	<	whichCell.z() = nCells_.z() * scaled.z();
537	<
538	<	// find single index of this cell:
539	<	cellIndex = Vlinear(whichCell, nCells_);
540	<	// add this cutoff group to the list of groups in this cell;
541	<	cellListRow_[cellIndex].push_back(i);
1335	>	cellListRow_.clear();
1336	>	cellListCol_.clear();
1337	>	#else
1338	>	cellList_.clear();
1339	>	#endif
1340	>
1341	>	if (!usePeriodicBoundaryConditions_) {
1342	>	box = snap_->getBoundingBox();
1343	>	invBox = snap_->getInvBoundingBox();
1344	>	} else {
1345	>	box = snap_->getHmat();
1346	>	invBox = snap_->getInvHmat();
1347		}
1348	<
1349	<	for (int i = 0; i < nGroupsInCol_; i++) {
1350	<	rs = cgColData.position[i];
1351	<	// scaled positions relative to the box vectors
1352	<	scaled = invHmat * rs;
1353	<	// wrap the vector back into the unit box by subtracting integer box
1354	<	// numbers
1355	<	for (int j = 0; j < 3; j++)
1356	<	scaled[j] -= roundMe(scaled[j]);
1357	<
1358	<	// find xyz-indices of cell that cutoffGroup is in.
1359	<	whichCell.x() = nCells_.x() * scaled.x();
1360	<	whichCell.y() = nCells_.y() * scaled.y();
1361	<	whichCell.z() = nCells_.z() * scaled.z();
1362	<
1363	<	// find single index of this cell:
1364	<	cellIndex = Vlinear(whichCell, nCells_);
1365	<	// add this cutoff group to the list of groups in this cell;
1366	<	cellListCol_[cellIndex].push_back(i);
1367	<	}
1348	>
1349	>	Vector3d boxX = box.getColumn(0);
1350	>	Vector3d boxY = box.getColumn(1);
1351	>	Vector3d boxZ = box.getColumn(2);
1352	>
1353	>	nCells_.x() = (int) ( boxX.length() )/ rList_;
1354	>	nCells_.y() = (int) ( boxY.length() )/ rList_;
1355	>	nCells_.z() = (int) ( boxZ.length() )/ rList_;
1356	>
1357	>	// handle small boxes where the cell offsets can end up repeating cells
1358	>
1359	>	if (nCells_.x() < 3) doAllPairs = true;
1360	>	if (nCells_.y() < 3) doAllPairs = true;
1361	>	if (nCells_.z() < 3) doAllPairs = true;
1362	>
1363	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1364	>
1365	>	#ifdef IS_MPI
1366	>	cellListRow_.resize(nCtot);
1367	>	cellListCol_.resize(nCtot);
1368		#else
1369	<	for (int i = 0; i < nGroups_; i++) {
1370	<	rs = snap_->cgData.position[i];
1371	<	// scaled positions relative to the box vectors
1372	<	scaled = invHmat * rs;
1373	<	// wrap the vector back into the unit box by subtracting integer box
1374	<	// numbers
1375	<	for (int j = 0; j < 3; j++)
1376	<	scaled[j] -= roundMe(scaled[j]);
1369	>	cellList_.resize(nCtot);
1370	>	#endif
1371	>
1372	>	if (!doAllPairs) {
1373	>	#ifdef IS_MPI
1374	>
1375	>	for (int i = 0; i < nGroupsInRow_; i++) {
1376	>	rs = cgRowData.position[i];
1377	>
1378	>	// scaled positions relative to the box vectors
1379	>	scaled = invBox * rs;
1380	>
1381	>	// wrap the vector back into the unit box by subtracting integer box
1382	>	// numbers
1383	>	for (int j = 0; j < 3; j++) {
1384	>	scaled[j] -= roundMe(scaled[j]);
1385	>	scaled[j] += 0.5;
1386	>	// Handle the special case when an object is exactly on the
1387	>	// boundary (a scaled coordinate of 1.0 is the same as
1388	>	// scaled coordinate of 0.0)
1389	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1390	>	}
1391	>
1392	>	// find xyz-indices of cell that cutoffGroup is in.
1393	>	whichCell.x() = nCells_.x() * scaled.x();
1394	>	whichCell.y() = nCells_.y() * scaled.y();
1395	>	whichCell.z() = nCells_.z() * scaled.z();
1396	>
1397	>	// find single index of this cell:
1398	>	cellIndex = Vlinear(whichCell, nCells_);
1399	>
1400	>	// add this cutoff group to the list of groups in this cell;
1401	>	cellListRow_[cellIndex].push_back(i);
1402	>	}
1403	>	for (int i = 0; i < nGroupsInCol_; i++) {
1404	>	rs = cgColData.position[i];
1405	>
1406	>	// scaled positions relative to the box vectors
1407	>	scaled = invBox * rs;
1408	>
1409	>	// wrap the vector back into the unit box by subtracting integer box
1410	>	// numbers
1411	>	for (int j = 0; j < 3; j++) {
1412	>	scaled[j] -= roundMe(scaled[j]);
1413	>	scaled[j] += 0.5;
1414	>	// Handle the special case when an object is exactly on the
1415	>	// boundary (a scaled coordinate of 1.0 is the same as
1416	>	// scaled coordinate of 0.0)
1417	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1418	>	}
1419	>
1420	>	// find xyz-indices of cell that cutoffGroup is in.
1421	>	whichCell.x() = nCells_.x() * scaled.x();
1422	>	whichCell.y() = nCells_.y() * scaled.y();
1423	>	whichCell.z() = nCells_.z() * scaled.z();
1424	>
1425	>	// find single index of this cell:
1426	>	cellIndex = Vlinear(whichCell, nCells_);
1427	>
1428	>	// add this cutoff group to the list of groups in this cell;
1429	>	cellListCol_[cellIndex].push_back(i);
1430	>	}
1431	>
1432	>	#else
1433	>	for (int i = 0; i < nGroups_; i++) {
1434	>	rs = snap_->cgData.position[i];
1435	>
1436	>	// scaled positions relative to the box vectors
1437	>	scaled = invBox * rs;
1438	>
1439	>	// wrap the vector back into the unit box by subtracting integer box
1440	>	// numbers
1441	>	for (int j = 0; j < 3; j++) {
1442	>	scaled[j] -= roundMe(scaled[j]);
1443	>	scaled[j] += 0.5;
1444	>	// Handle the special case when an object is exactly on the
1445	>	// boundary (a scaled coordinate of 1.0 is the same as
1446	>	// scaled coordinate of 0.0)
1447	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1448	>	}
1449	>
1450	>	// find xyz-indices of cell that cutoffGroup is in.
1451	>	whichCell.x() = nCells_.x() * scaled.x();
1452	>	whichCell.y() = nCells_.y() * scaled.y();
1453	>	whichCell.z() = nCells_.z() * scaled.z();
1454	>
1455	>	// find single index of this cell:
1456	>	cellIndex = Vlinear(whichCell, nCells_);
1457	>
1458	>	// add this cutoff group to the list of groups in this cell;
1459	>	cellList_[cellIndex].push_back(i);
1460	>	}
1461
573	–	// find xyz-indices of cell that cutoffGroup is in.
574	–	whichCell.x() = nCells_.x() * scaled.x();
575	–	whichCell.y() = nCells_.y() * scaled.y();
576	–	whichCell.z() = nCells_.z() * scaled.z();
577	–
578	–	// find single index of this cell:
579	–	cellIndex = Vlinear(whichCell, nCells_);
580	–	// add this cutoff group to the list of groups in this cell;
581	–	cellList_[cellIndex].push_back(i);
582	–	}
1462		#endif
1463
1464	<
1465	<
1466	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1467	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1468	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
590	<	Vector3i m1v(m1x, m1y, m1z);
591	<	int m1 = Vlinear(m1v, nCells_);
592	<
593	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
594	<	os != cellOffsets_.end(); ++os) {
1464	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1465	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1466	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1467	>	Vector3i m1v(m1x, m1y, m1z);
1468	>	int m1 = Vlinear(m1v, nCells_);
1469
1470	<	Vector3i m2v = m1v + (*os);
1471	<
1472	<	if (m2v.x() >= nCells_.x()) {
1473	<	m2v.x() = 0;
1474	<	} else if (m2v.x() < 0) {
601	<	m2v.x() = nCells_.x() - 1;
602	<	}
603	<
604	<	if (m2v.y() >= nCells_.y()) {
605	<	m2v.y() = 0;
606	<	} else if (m2v.y() < 0) {
607	<	m2v.y() = nCells_.y() - 1;
608	<	}
609	<
610	<	if (m2v.z() >= nCells_.z()) {
611	<	m2v.z() = 0;
612	<	} else if (m2v.z() < 0) {
613	<	m2v.z() = nCells_.z() - 1;
614	<	}
615	<
616	<	int m2 = Vlinear (m2v, nCells_);
1470	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1471	>	os != cellOffsets_.end(); ++os) {
1472	>
1473	>	Vector3i m2v = m1v + (*os);
1474	>
1475
1476	<	#ifdef IS_MPI
1477	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1478	<	j1 != cellListRow_[m1].end(); ++j1) {
1479	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1480	<	j2 != cellListCol_[m2].end(); ++j2) {
1481	<
1482	<	// Always do this if we're in different cells or if
1483	<	// we're in the same cell and the global index of the
1484	<	// j2 cutoff group is less than the j1 cutoff group
1476	>	if (m2v.x() >= nCells_.x()) {
1477	>	m2v.x() = 0;
1478	>	} else if (m2v.x() < 0) {
1479	>	m2v.x() = nCells_.x() - 1;
1480	>	}
1481	>
1482	>	if (m2v.y() >= nCells_.y()) {
1483	>	m2v.y() = 0;
1484	>	} else if (m2v.y() < 0) {
1485	>	m2v.y() = nCells_.y() - 1;
1486	>	}
1487	>
1488	>	if (m2v.z() >= nCells_.z()) {
1489	>	m2v.z() = 0;
1490	>	} else if (m2v.z() < 0) {
1491	>	m2v.z() = nCells_.z() - 1;
1492	>	}
1493
1494	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1494	>	int m2 = Vlinear (m2v, nCells_);
1495	>
1496	>	#ifdef IS_MPI
1497	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1498	>	j1 != cellListRow_[m1].end(); ++j1) {
1499	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1500	>	j2 != cellListCol_[m2].end(); ++j2) {
1501	>
1502	>	// In parallel, we need to visit *all* pairs of row
1503	>	// & column indicies and will divide labor in the
1504	>	// force evaluation later.
1505		dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1506	<	snap_->wrapVector(dr);
1507	<	if (dr.lengthSquare() < rl2) {
632	<	neighborList.push_back(make_pair((*j1), (*j2)));
1506	>	if (usePeriodicBoundaryConditions_) {
1507	>	snap_->wrapVector(dr);
1508		}
1509	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1510	+	if (dr.lengthSquare() < cuts.third) {
1511	+	neighborList.push_back(make_pair((*j1), (*j2)));
1512	+	}
1513		}
1514		}
636	–	}
1515		#else
1516	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1517	<	j1 != cellList_[m1].end(); ++j1) {
1518	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1519	<	j2 != cellList_[m2].end(); ++j2) {
1520	<
1521	<	// Always do this if we're in different cells or if
1522	<	// we're in the same cell and the global index of the
1523	<	// j2 cutoff group is less than the j1 cutoff group
1516	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1517	>	j1 != cellList_[m1].end(); ++j1) {
1518	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1519	>	j2 != cellList_[m2].end(); ++j2) {
1520	>
1521	>	// Always do this if we're in different cells or if
1522	>	// we're in the same cell and the global index of
1523	>	// the j2 cutoff group is greater than or equal to
1524	>	// the j1 cutoff group.  Note that Rappaport's code
1525	>	// has a "less than" conditional here, but that
1526	>	// deals with atom-by-atom computation.  OpenMD
1527	>	// allows atoms within a single cutoff group to
1528	>	// interact with each other.
1529
1530	<	if (m2 != m1 || (*j2) < (*j1)) {
1531	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1532	<	snap_->wrapVector(dr);
1533	<	if (dr.lengthSquare() < rl2) {
1534	<	neighborList.push_back(make_pair((*j1), (*j2)));
1530	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1531	>
1532	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1533	>	if (usePeriodicBoundaryConditions_) {
1534	>	snap_->wrapVector(dr);
1535	>	}
1536	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1537	>	if (dr.lengthSquare() < cuts.third) {
1538	>	neighborList.push_back(make_pair((*j1), (*j2)));
1539	>	}
1540		}
1541		}
1542		}
655	–	}
1543		#endif
1544	+	}
1545		}
1546		}
1547		}
1548	+	} else {
1549	+	// branch to do all cutoff group pairs
1550	+	#ifdef IS_MPI
1551	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1552	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1553	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1554	+	if (usePeriodicBoundaryConditions_) {
1555	+	snap_->wrapVector(dr);
1556	+	}
1557	+	cuts = getGroupCutoffs( j1, j2 );
1558	+	if (dr.lengthSquare() < cuts.third) {
1559	+	neighborList.push_back(make_pair(j1, j2));
1560	+	}
1561	+	}
1562	+	}
1563	+	#else
1564	+	// include all groups here.
1565	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1566	+	// include self group interactions j2 == j1
1567	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1568	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1569	+	if (usePeriodicBoundaryConditions_) {
1570	+	snap_->wrapVector(dr);
1571	+	}
1572	+	cuts = getGroupCutoffs( j1, j2 );
1573	+	if (dr.lengthSquare() < cuts.third) {
1574	+	neighborList.push_back(make_pair(j1, j2));
1575	+	}
1576	+	}
1577	+	}
1578	+	#endif
1579		}
1580	<
1580	>
1581		// save the local cutoff group positions for the check that is
1582		// done on each loop:
1583		saved_CG_positions_.clear();
1584		for (int i = 0; i < nGroups_; i++)
1585		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1586	<
1586	>
1587		return neighborList;
1588		}
1589		} //end namespace OpenMD

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