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

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1551 by gezelter, Thu Apr 28 18:38:21 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
44		#include "nonbonded/NonBondedInteraction.hpp"
45		#include "brains/SnapshotManager.hpp"
46	+	#include "brains/PairList.hpp"
47
48		using namespace std;
49		namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	+
53	+	// In a parallel computation, row and colum scans must visit all
54	+	// surrounding cells (not just the 14 upper triangular blocks that
55	+	// are used when the processor can see all pairs)
56	+	#ifdef IS_MPI
57	+	cellOffsets_.clear();
58	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
66	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	+	#endif
86	+	}
87	+
88	+
89		/**
90		* distributeInitialData is essentially a copy of the older fortran
91		* SimulationSetup
92		*/
53	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96	<	#ifdef IS_MPI
97	<	int nLocal = snap_->getNumberOfAtoms();
98	<	int nGroups = snap_->getNumberOfCutoffGroups();
96	>	ff_ = info_->getForceField();
97	>	nLocal_ = snap_->getNumberOfAtoms();
98	>
99	>	nGroups_ = info_->getNLocalCutoffGroups();
100	>	// gather the information for atomtype IDs (atids):
101	>	idents = info_->getIdentArray();
102	>	regions = info_->getRegions();
103	>	AtomLocalToGlobal = info_->getGlobalAtomIndices();
104	>	cgLocalToGlobal = info_->getGlobalGroupIndices();
105	>	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
106	>
107	>	massFactors = info_->getMassFactors();
108	>
109	>	PairList* excludes = info_->getExcludedInteractions();
110	>	PairList* oneTwo = info_->getOneTwoInteractions();
111	>	PairList* oneThree = info_->getOneThreeInteractions();
112	>	PairList* oneFour = info_->getOneFourInteractions();
113
114	<	AtomCommIntRow = new Communicator<Row,int>(nLocal);
115	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
116	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
117	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
114	>	if (needVelocities_)
115	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
116	>	DataStorage::dslVelocity);
117	>	else
118	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
119	>
120	>	#ifdef IS_MPI
121	>
122	>	MPI_Comm row = rowComm.getComm();
123	>	MPI_Comm col = colComm.getComm();
124
125	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal);
126	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
127	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
128	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
125	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
126	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
127	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
128	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
129	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
130
131	<	cgCommIntRow = new Communicator<Row,int>(nGroups);
132	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
133	<	cgCommIntColumn = new Communicator<Column,int>(nGroups);
134	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
131	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
132	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
133	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
134	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
135	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
136
137	<	int nAtomsInRow = AtomCommIntRow->getSize();
138	<	int nAtomsInCol = AtomCommIntColumn->getSize();
139	<	int nGroupsInRow = cgCommIntRow->getSize();
140	<	int nGroupsInCol = cgCommIntColumn->getSize();
137	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
138	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
139	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
140	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
141
142	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
143	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
144	+	nGroupsInRow_ = cgPlanIntRow->getSize();
145	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
146	+
147		// Modify the data storage objects with the correct layouts and sizes:
148	<	atomRowData.resize(nAtomsInRow);
148	>	atomRowData.resize(nAtomsInRow_);
149		atomRowData.setStorageLayout(storageLayout_);
150	<	atomColData.resize(nAtomsInCol);
150	>	atomColData.resize(nAtomsInCol_);
151		atomColData.setStorageLayout(storageLayout_);
152	<	cgRowData.resize(nGroupsInRow);
152	>	cgRowData.resize(nGroupsInRow_);
153		cgRowData.setStorageLayout(DataStorage::dslPosition);
154	<	cgColData.resize(nGroupsInCol);
155	<	cgColData.setStorageLayout(DataStorage::dslPosition);
154	>	cgColData.resize(nGroupsInCol_);
155	>	if (needVelocities_)
156	>	// we only need column velocities if we need them.
157	>	cgColData.setStorageLayout(DataStorage::dslPosition |
158	>	DataStorage::dslVelocity);
159	>	else
160	>	cgColData.setStorageLayout(DataStorage::dslPosition);
161	>
162	>	identsRow.resize(nAtomsInRow_);
163	>	identsCol.resize(nAtomsInCol_);
164
165	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
166	<	vector<RealType> (nAtomsInRow, 0.0));
93	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
94	<	vector<RealType> (nAtomsInCol, 0.0));
165	>	AtomPlanIntRow->gather(idents, identsRow);
166	>	AtomPlanIntColumn->gather(idents, identsCol);
167
168	<
169	<	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
168	>	regionsRow.resize(nAtomsInRow_);
169	>	regionsCol.resize(nAtomsInCol_);
170
171	<	// gather the information for atomtype IDs (atids):
172	<	vector<int> identsLocal = info_->getIdentArray();
101	<	identsRow.reserve(nAtomsInRow);
102	<	identsCol.reserve(nAtomsInCol);
171	>	AtomPlanIntRow->gather(regions, regionsRow);
172	>	AtomPlanIntColumn->gather(regions, regionsCol);
173
174	<	AtomCommIntRow->gather(identsLocal, identsRow);
175	<	AtomCommIntColumn->gather(identsLocal, identsCol);
176	<
107	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
108	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
109	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
110	<
111	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
112	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
113	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
174	>	// allocate memory for the parallel objects
175	>	atypesRow.resize(nAtomsInRow_);
176	>	atypesCol.resize(nAtomsInCol_);
177
178	<	// still need:
179	<	// topoDist
180	<	// exclude
178	>	for (int i = 0; i < nAtomsInRow_; i++)
179	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
180	>	for (int i = 0; i < nAtomsInCol_; i++)
181	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
182	>
183	>	pot_row.resize(nAtomsInRow_);
184	>	pot_col.resize(nAtomsInCol_);
185	>
186	>	expot_row.resize(nAtomsInRow_);
187	>	expot_col.resize(nAtomsInCol_);
188	>
189	>	AtomRowToGlobal.resize(nAtomsInRow_);
190	>	AtomColToGlobal.resize(nAtomsInCol_);
191	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
192	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
193	>
194	>	cgRowToGlobal.resize(nGroupsInRow_);
195	>	cgColToGlobal.resize(nGroupsInCol_);
196	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
197	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
198	>
199	>	massFactorsRow.resize(nAtomsInRow_);
200	>	massFactorsCol.resize(nAtomsInCol_);
201	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
202	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
203	>
204	>	groupListRow_.clear();
205	>	groupListRow_.resize(nGroupsInRow_);
206	>	for (int i = 0; i < nGroupsInRow_; i++) {
207	>	int gid = cgRowToGlobal[i];
208	>	for (int j = 0; j < nAtomsInRow_; j++) {
209	>	int aid = AtomRowToGlobal[j];
210	>	if (globalGroupMembership[aid] == gid)
211	>	groupListRow_[i].push_back(j);
212	>	}
213	>	}
214	>
215	>	groupListCol_.clear();
216	>	groupListCol_.resize(nGroupsInCol_);
217	>	for (int i = 0; i < nGroupsInCol_; i++) {
218	>	int gid = cgColToGlobal[i];
219	>	for (int j = 0; j < nAtomsInCol_; j++) {
220	>	int aid = AtomColToGlobal[j];
221	>	if (globalGroupMembership[aid] == gid)
222	>	groupListCol_[i].push_back(j);
223	>	}
224	>	}
225	>
226	>	excludesForAtom.clear();
227	>	excludesForAtom.resize(nAtomsInRow_);
228	>	toposForAtom.clear();
229	>	toposForAtom.resize(nAtomsInRow_);
230	>	topoDist.clear();
231	>	topoDist.resize(nAtomsInRow_);
232	>	for (int i = 0; i < nAtomsInRow_; i++) {
233	>	int iglob = AtomRowToGlobal[i];
234	>
235	>	for (int j = 0; j < nAtomsInCol_; j++) {
236	>	int jglob = AtomColToGlobal[j];
237	>
238	>	if (excludes->hasPair(iglob, jglob))
239	>	excludesForAtom[i].push_back(j);
240	>
241	>	if (oneTwo->hasPair(iglob, jglob)) {
242	>	toposForAtom[i].push_back(j);
243	>	topoDist[i].push_back(1);
244	>	} else {
245	>	if (oneThree->hasPair(iglob, jglob)) {
246	>	toposForAtom[i].push_back(j);
247	>	topoDist[i].push_back(2);
248	>	} else {
249	>	if (oneFour->hasPair(iglob, jglob)) {
250	>	toposForAtom[i].push_back(j);
251	>	topoDist[i].push_back(3);
252	>	}
253	>	}
254	>	}
255	>	}
256	>	}
257	>
258	>	#else
259	>	excludesForAtom.clear();
260	>	excludesForAtom.resize(nLocal_);
261	>	toposForAtom.clear();
262	>	toposForAtom.resize(nLocal_);
263	>	topoDist.clear();
264	>	topoDist.resize(nLocal_);
265	>
266	>	for (int i = 0; i < nLocal_; i++) {
267	>	int iglob = AtomLocalToGlobal[i];
268	>
269	>	for (int j = 0; j < nLocal_; j++) {
270	>	int jglob = AtomLocalToGlobal[j];
271	>
272	>	if (excludes->hasPair(iglob, jglob))
273	>	excludesForAtom[i].push_back(j);
274	>
275	>	if (oneTwo->hasPair(iglob, jglob)) {
276	>	toposForAtom[i].push_back(j);
277	>	topoDist[i].push_back(1);
278	>	} else {
279	>	if (oneThree->hasPair(iglob, jglob)) {
280	>	toposForAtom[i].push_back(j);
281	>	topoDist[i].push_back(2);
282	>	} else {
283	>	if (oneFour->hasPair(iglob, jglob)) {
284	>	toposForAtom[i].push_back(j);
285	>	topoDist[i].push_back(3);
286	>	}
287	>	}
288	>	}
289	>	}
290	>	}
291	>	#endif
292	>
293	>	// allocate memory for the parallel objects
294	>	atypesLocal.resize(nLocal_);
295	>
296	>	for (int i = 0; i < nLocal_; i++)
297	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
298	>
299	>	groupList_.clear();
300	>	groupList_.resize(nGroups_);
301	>	for (int i = 0; i < nGroups_; i++) {
302	>	int gid = cgLocalToGlobal[i];
303	>	for (int j = 0; j < nLocal_; j++) {
304	>	int aid = AtomLocalToGlobal[j];
305	>	if (globalGroupMembership[aid] == gid) {
306	>	groupList_[i].push_back(j);
307	>	}
308	>	}
309	>	}
310	>
311	>
312	>	createGtypeCutoffMap();
313	>
314	>	}
315	>
316	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
317	>
318	>	GrCut.clear();
319	>	GrCutSq.clear();
320	>	GrlistSq.clear();
321	>
322	>	RealType tol = 1e-6;
323	>	largestRcut_ = 0.0;
324	>	int atid;
325	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
326	>
327	>	map<int, RealType> atypeCutoff;
328	>
329	>	for (set<AtomType*>::iterator at = atypes.begin();
330	>	at != atypes.end(); ++at){
331	>	atid = (*at)->getIdent();
332	>	if (userChoseCutoff_)
333	>	atypeCutoff[atid] = userCutoff_;
334	>	else
335	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
336	>	}
337	>
338	>	vector<RealType> gTypeCutoffs;
339	>	// first we do a single loop over the cutoff groups to find the
340	>	// largest cutoff for any atypes present in this group.
341	>	#ifdef IS_MPI
342	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
343	>	groupRowToGtype.resize(nGroupsInRow_);
344	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
345	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
346	>	for (vector<int>::iterator ia = atomListRow.begin();
347	>	ia != atomListRow.end(); ++ia) {
348	>	int atom1 = (*ia);
349	>	atid = identsRow[atom1];
350	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
351	>	groupCutoffRow[cg1] = atypeCutoff[atid];
352	>	}
353	>	}
354	>
355	>	bool gTypeFound = false;
356	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
357	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
358	>	groupRowToGtype[cg1] = gt;
359	>	gTypeFound = true;
360	>	}
361	>	}
362	>	if (!gTypeFound) {
363	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
364	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
365	>	}
366	>
367	>	}
368	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
369	>	groupColToGtype.resize(nGroupsInCol_);
370	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
371	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
372	>	for (vector<int>::iterator jb = atomListCol.begin();
373	>	jb != atomListCol.end(); ++jb) {
374	>	int atom2 = (*jb);
375	>	atid = identsCol[atom2];
376	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
377	>	groupCutoffCol[cg2] = atypeCutoff[atid];
378	>	}
379	>	}
380	>	bool gTypeFound = false;
381	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
382	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
383	>	groupColToGtype[cg2] = gt;
384	>	gTypeFound = true;
385	>	}
386	>	}
387	>	if (!gTypeFound) {
388	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
389	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
390	>	}
391	>	}
392	>	#else
393	>
394	>	vector<RealType> groupCutoff(nGroups_, 0.0);
395	>	groupToGtype.resize(nGroups_);
396	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
397	>	groupCutoff[cg1] = 0.0;
398	>	vector<int> atomList = getAtomsInGroupRow(cg1);
399	>	for (vector<int>::iterator ia = atomList.begin();
400	>	ia != atomList.end(); ++ia) {
401	>	int atom1 = (*ia);
402	>	atid = idents[atom1];
403	>	if (atypeCutoff[atid] > groupCutoff[cg1])
404	>	groupCutoff[cg1] = atypeCutoff[atid];
405	>	}
406	>
407	>	bool gTypeFound = false;
408	>	for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
409	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
410	>	groupToGtype[cg1] = gt;
411	>	gTypeFound = true;
412	>	}
413	>	}
414	>	if (!gTypeFound) {
415	>	gTypeCutoffs.push_back( groupCutoff[cg1] );
416	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
417	>	}
418	>	}
419	>	#endif
420	>
421	>	// Now we find the maximum group cutoff value present in the simulation
422	>
423	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
424	>	gTypeCutoffs.end());
425	>
426	>	#ifdef IS_MPI
427	>	MPI_Allreduce(MPI_IN_PLACE, &groupMax, 1, MPI_REALTYPE,
428	>	MPI_MAX, MPI_COMM_WORLD);
429		#endif
430	+
431	+	RealType tradRcut = groupMax;
432	+
433	+	GrCut.resize( gTypeCutoffs.size() );
434	+	GrCutSq.resize( gTypeCutoffs.size() );
435	+	GrlistSq.resize( gTypeCutoffs.size() );
436	+
437	+
438	+	for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
439	+	GrCut[i].resize( gTypeCutoffs.size() , 0.0);
440	+	GrCutSq[i].resize( gTypeCutoffs.size(), 0.0 );
441	+	GrlistSq[i].resize( gTypeCutoffs.size(), 0.0 );
442	+
443	+	for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {
444	+	RealType thisRcut;
445	+	switch(cutoffPolicy_) {
446	+	case TRADITIONAL:
447	+	thisRcut = tradRcut;
448	+	break;
449	+	case MIX:
450	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
451	+	break;
452	+	case MAX:
453	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
454	+	break;
455	+	default:
456	+	sprintf(painCave.errMsg,
457	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
458	+	"hit an unknown cutoff policy!\n");
459	+	painCave.severity = OPENMD_ERROR;
460	+	painCave.isFatal = 1;
461	+	simError();
462	+	break;
463	+	}
464	+
465	+	GrCut[i][j] = thisRcut;
466	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
467	+	GrCutSq[i][j] = thisRcut * thisRcut;
468	+	GrlistSq[i][j] = pow(thisRcut + skinThickness_, 2);
469	+
470	+	// pair<int,int> key = make_pair(i,j);
471	+	// gTypeCutoffMap[key].first = thisRcut;
472	+	// gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
473	+	// sanity check
474	+
475	+	if (userChoseCutoff_) {
476	+	if (abs(GrCut[i][j] - userCutoff_) > 0.0001) {
477	+	sprintf(painCave.errMsg,
478	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
479	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
480	+	painCave.severity = OPENMD_ERROR;
481	+	painCave.isFatal = 1;
482	+	simError();
483	+	}
484	+	}
485	+	}
486	+	}
487		}
488	+
489	+	void ForceMatrixDecomposition::getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) {
490	+	int i, j;
491	+	#ifdef IS_MPI
492	+	i = groupRowToGtype[cg1];
493	+	j = groupColToGtype[cg2];
494	+	#else
495	+	i = groupToGtype[cg1];
496	+	j = groupToGtype[cg2];
497	+	#endif
498	+	rcut = GrCut[i][j];
499	+	rcutsq = GrCutSq[i][j];
500	+	rlistsq = GrlistSq[i][j];
501	+	return;
502	+	//return gTypeCutoffMap[make_pair(i,j)];
503	+	}
504	+
505	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
506	+	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
507	+	if (toposForAtom[atom1][j] == atom2)
508	+	return topoDist[atom1][j];
509	+	}
510	+	return 0;
511	+	}
512	+
513	+	void ForceMatrixDecomposition::zeroWorkArrays() {
514	+	pairwisePot = 0.0;
515	+	embeddingPot = 0.0;
516	+	excludedPot = 0.0;
517	+	excludedSelfPot = 0.0;
518	+
519	+	#ifdef IS_MPI
520	+	if (storageLayout_ & DataStorage::dslForce) {
521	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
522	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
523	+	}
524	+
525	+	if (storageLayout_ & DataStorage::dslTorque) {
526	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
527	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
528	+	}
529
530	+	fill(pot_row.begin(), pot_row.end(),
531	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
532
533	+	fill(pot_col.begin(), pot_col.end(),
534	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
535
536	+	fill(expot_row.begin(), expot_row.end(),
537	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
538	+
539	+	fill(expot_col.begin(), expot_col.end(),
540	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
541	+
542	+	if (storageLayout_ & DataStorage::dslParticlePot) {
543	+	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
544	+	0.0);
545	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
546	+	0.0);
547	+	}
548	+
549	+	if (storageLayout_ & DataStorage::dslDensity) {
550	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
551	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
552	+	}
553	+
554	+	if (storageLayout_ & DataStorage::dslFunctional) {
555	+	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
556	+	0.0);
557	+	fill(atomColData.functional.begin(), atomColData.functional.end(),
558	+	0.0);
559	+	}
560	+
561	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
562	+	fill(atomRowData.functionalDerivative.begin(),
563	+	atomRowData.functionalDerivative.end(), 0.0);
564	+	fill(atomColData.functionalDerivative.begin(),
565	+	atomColData.functionalDerivative.end(), 0.0);
566	+	}
567	+
568	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
569	+	fill(atomRowData.skippedCharge.begin(),
570	+	atomRowData.skippedCharge.end(), 0.0);
571	+	fill(atomColData.skippedCharge.begin(),
572	+	atomColData.skippedCharge.end(), 0.0);
573	+	}
574	+
575	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
576	+	fill(atomRowData.flucQFrc.begin(),
577	+	atomRowData.flucQFrc.end(), 0.0);
578	+	fill(atomColData.flucQFrc.begin(),
579	+	atomColData.flucQFrc.end(), 0.0);
580	+	}
581	+
582	+	if (storageLayout_ & DataStorage::dslElectricField) {
583	+	fill(atomRowData.electricField.begin(),
584	+	atomRowData.electricField.end(), V3Zero);
585	+	fill(atomColData.electricField.begin(),
586	+	atomColData.electricField.end(), V3Zero);
587	+	}
588	+
589	+	if (storageLayout_ & DataStorage::dslSitePotential) {
590	+	fill(atomRowData.sitePotential.begin(),
591	+	atomRowData.sitePotential.end(), 0.0);
592	+	fill(atomColData.sitePotential.begin(),
593	+	atomColData.sitePotential.end(), 0.0);
594	+	}
595	+
596	+	#endif
597	+	// even in parallel, we need to zero out the local arrays:
598	+
599	+	if (storageLayout_ & DataStorage::dslParticlePot) {
600	+	fill(snap_->atomData.particlePot.begin(),
601	+	snap_->atomData.particlePot.end(), 0.0);
602	+	}
603	+
604	+	if (storageLayout_ & DataStorage::dslDensity) {
605	+	fill(snap_->atomData.density.begin(),
606	+	snap_->atomData.density.end(), 0.0);
607	+	}
608	+
609	+	if (storageLayout_ & DataStorage::dslFunctional) {
610	+	fill(snap_->atomData.functional.begin(),
611	+	snap_->atomData.functional.end(), 0.0);
612	+	}
613	+
614	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
615	+	fill(snap_->atomData.functionalDerivative.begin(),
616	+	snap_->atomData.functionalDerivative.end(), 0.0);
617	+	}
618	+
619	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
620	+	fill(snap_->atomData.skippedCharge.begin(),
621	+	snap_->atomData.skippedCharge.end(), 0.0);
622	+	}
623	+
624	+	if (storageLayout_ & DataStorage::dslElectricField) {
625	+	fill(snap_->atomData.electricField.begin(),
626	+	snap_->atomData.electricField.end(), V3Zero);
627	+	}
628	+	if (storageLayout_ & DataStorage::dslSitePotential) {
629	+	fill(snap_->atomData.sitePotential.begin(),
630	+	snap_->atomData.sitePotential.end(), 0.0);
631	+	}
632	+	}
633	+
634	+
635		void ForceMatrixDecomposition::distributeData()  {
636		snap_ = sman_->getCurrentSnapshot();
637		storageLayout_ = sman_->getStorageLayout();
638		#ifdef IS_MPI
639
640		// gather up the atomic positions
641	<	AtomCommVectorRow->gather(snap_->atomData.position,
641	>	AtomPlanVectorRow->gather(snap_->atomData.position,
642		atomRowData.position);
643	<	AtomCommVectorColumn->gather(snap_->atomData.position,
643	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
644		atomColData.position);
645
646		// gather up the cutoff group positions
647	<	cgCommVectorRow->gather(snap_->cgData.position,
647	>
648	>	cgPlanVectorRow->gather(snap_->cgData.position,
649		cgRowData.position);
650	<	cgCommVectorColumn->gather(snap_->cgData.position,
650	>
651	>	cgPlanVectorColumn->gather(snap_->cgData.position,
652		cgColData.position);
653	+
654	+
655	+
656	+	if (needVelocities_) {
657	+	// gather up the atomic velocities
658	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
659	+	atomColData.velocity);
660	+
661	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
662	+	cgColData.velocity);
663	+	}
664	+
665
666		// if needed, gather the atomic rotation matrices
667		if (storageLayout_ & DataStorage::dslAmat) {
668	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
668	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
669		atomRowData.aMat);
670	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
670	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
671		atomColData.aMat);
672		}
673	<
674	<	// if needed, gather the atomic eletrostatic frames
675	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
676	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
677	<	atomRowData.electroFrame);
678	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
679	<	atomColData.electroFrame);
673	>
674	>	// if needed, gather the atomic eletrostatic information
675	>	if (storageLayout_ & DataStorage::dslDipole) {
676	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
677	>	atomRowData.dipole);
678	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
679	>	atomColData.dipole);
680		}
681	+
682	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
683	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
684	+	atomRowData.quadrupole);
685	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
686	+	atomColData.quadrupole);
687	+	}
688	+
689	+	// if needed, gather the atomic fluctuating charge values
690	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
691	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
692	+	atomRowData.flucQPos);
693	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
694	+	atomColData.flucQPos);
695	+	}
696	+
697		#endif
698		}
699
700	+	/* collects information obtained during the pre-pair loop onto local
701	+	* data structures.
702	+	*/
703		void ForceMatrixDecomposition::collectIntermediateData() {
704		snap_ = sman_->getCurrentSnapshot();
705		storageLayout_ = sman_->getStorageLayout();
#	Line 162 | Line 707 | namespace OpenMD {
707
708		if (storageLayout_ & DataStorage::dslDensity) {
709
710	<	AtomCommRealRow->scatter(atomRowData.density,
710	>	AtomPlanRealRow->scatter(atomRowData.density,
711		snap_->atomData.density);
712
713		int n = snap_->atomData.density.size();
714	<	std::vector<RealType> rho_tmp(n, 0.0);
715	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
714	>	vector<RealType> rho_tmp(n, 0.0);
715	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
716		for (int i = 0; i < n; i++)
717		snap_->atomData.density[i] += rho_tmp[i];
718		}
719	+
720	+	// this isn't necessary if we don't have polarizable atoms, but
721	+	// we'll leave it here for now.
722	+	if (storageLayout_ & DataStorage::dslElectricField) {
723	+
724	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
725	+	snap_->atomData.electricField);
726	+
727	+	int n = snap_->atomData.electricField.size();
728	+	vector<Vector3d> field_tmp(n, V3Zero);
729	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
730	+	field_tmp);
731	+	for (int i = 0; i < n; i++)
732	+	snap_->atomData.electricField[i] += field_tmp[i];
733	+	}
734		#endif
735		}
736	<
736	>
737	>	/*
738	>	* redistributes information obtained during the pre-pair loop out to
739	>	* row and column-indexed data structures
740	>	*/
741		void ForceMatrixDecomposition::distributeIntermediateData() {
742		snap_ = sman_->getCurrentSnapshot();
743		storageLayout_ = sman_->getStorageLayout();
744		#ifdef IS_MPI
745		if (storageLayout_ & DataStorage::dslFunctional) {
746	<	AtomCommRealRow->gather(snap_->atomData.functional,
746	>	AtomPlanRealRow->gather(snap_->atomData.functional,
747		atomRowData.functional);
748	<	AtomCommRealColumn->gather(snap_->atomData.functional,
748	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
749		atomColData.functional);
750		}
751
752		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
753	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
753	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
754		atomRowData.functionalDerivative);
755	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
755	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
756		atomColData.functionalDerivative);
757		}
758		#endif
#	Line 202 | Line 766 | namespace OpenMD {
766		int n = snap_->atomData.force.size();
767		vector<Vector3d> frc_tmp(n, V3Zero);
768
769	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
769	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
770		for (int i = 0; i < n; i++) {
771		snap_->atomData.force[i] += frc_tmp[i];
772		frc_tmp[i] = 0.0;
773		}
774
775	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
776	<	for (int i = 0; i < n; i++)
775	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
776	>	for (int i = 0; i < n; i++) {
777		snap_->atomData.force[i] += frc_tmp[i];
778	<
779	<
778	>	}
779	>
780		if (storageLayout_ & DataStorage::dslTorque) {
781
782	<	int nt = snap_->atomData.force.size();
782	>	int nt = snap_->atomData.torque.size();
783		vector<Vector3d> trq_tmp(nt, V3Zero);
784
785	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
786	<	for (int i = 0; i < n; i++) {
785	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
786	>	for (int i = 0; i < nt; i++) {
787		snap_->atomData.torque[i] += trq_tmp[i];
788		trq_tmp[i] = 0.0;
789		}
790
791	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
792	<	for (int i = 0; i < n; i++)
791	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
792	>	for (int i = 0; i < nt; i++)
793		snap_->atomData.torque[i] += trq_tmp[i];
794		}
231	–
232	–	int nLocal = snap_->getNumberOfAtoms();
795
796	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
797	<	vector<RealType> (nLocal, 0.0));
796	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
797	>
798	>	int ns = snap_->atomData.skippedCharge.size();
799	>	vector<RealType> skch_tmp(ns, 0.0);
800	>
801	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
802	>	for (int i = 0; i < ns; i++) {
803	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
804	>	skch_tmp[i] = 0.0;
805	>	}
806	>
807	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
808	>	for (int i = 0; i < ns; i++)
809	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
810	>
811	>	}
812
813	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
814	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
815	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
816	<	pot_local[i] += pot_temp[i][ii];
813	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
814	>
815	>	int nq = snap_->atomData.flucQFrc.size();
816	>	vector<RealType> fqfrc_tmp(nq, 0.0);
817	>
818	>	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
819	>	for (int i = 0; i < nq; i++) {
820	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
821	>	fqfrc_tmp[i] = 0.0;
822		}
823	+
824	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
825	+	for (int i = 0; i < nq; i++)
826	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
827	+
828		}
829	+
830	+	if (storageLayout_ & DataStorage::dslElectricField) {
831	+
832	+	int nef = snap_->atomData.electricField.size();
833	+	vector<Vector3d> efield_tmp(nef, V3Zero);
834	+
835	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
836	+	for (int i = 0; i < nef; i++) {
837	+	snap_->atomData.electricField[i] += efield_tmp[i];
838	+	efield_tmp[i] = 0.0;
839	+	}
840	+
841	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
842	+	for (int i = 0; i < nef; i++)
843	+	snap_->atomData.electricField[i] += efield_tmp[i];
844	+	}
845	+
846	+	if (storageLayout_ & DataStorage::dslSitePotential) {
847	+
848	+	int nsp = snap_->atomData.sitePotential.size();
849	+	vector<RealType> sp_tmp(nsp, 0.0);
850	+
851	+	AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
852	+	for (int i = 0; i < nsp; i++) {
853	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
854	+	sp_tmp[i] = 0.0;
855	+	}
856	+
857	+	AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
858	+	for (int i = 0; i < nsp; i++)
859	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
860	+	}
861	+
862	+	nLocal_ = snap_->getNumberOfAtoms();
863	+
864	+	vector<potVec> pot_temp(nLocal_,
865	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
866	+	vector<potVec> expot_temp(nLocal_,
867	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
868	+
869	+	// scatter/gather pot_row into the members of my column
870	+
871	+	AtomPlanPotRow->scatter(pot_row, pot_temp);
872	+	AtomPlanPotRow->scatter(expot_row, expot_temp);
873	+
874	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
875	+	pairwisePot += pot_temp[ii];
876	+
877	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
878	+	excludedPot += expot_temp[ii];
879	+
880	+	if (storageLayout_ & DataStorage::dslParticlePot) {
881	+	// This is the pairwise contribution to the particle pot.  The
882	+	// embedding contribution is added in each of the low level
883	+	// non-bonded routines.  In single processor, this is done in
884	+	// unpackInteractionData, not in collectData.
885	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
886	+	for (int i = 0; i < nLocal_; i++) {
887	+	// factor of two is because the total potential terms are divided
888	+	// by 2 in parallel due to row/ column scatter
889	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
890	+	}
891	+	}
892	+	}
893	+
894	+	fill(pot_temp.begin(), pot_temp.end(),
895	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
896	+	fill(expot_temp.begin(), expot_temp.end(),
897	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
898	+
899	+	AtomPlanPotColumn->scatter(pot_col, pot_temp);
900	+	AtomPlanPotColumn->scatter(expot_col, expot_temp);
901	+
902	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
903	+	pairwisePot += pot_temp[ii];
904	+
905	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
906	+	excludedPot += expot_temp[ii];
907	+
908	+	if (storageLayout_ & DataStorage::dslParticlePot) {
909	+	// This is the pairwise contribution to the particle pot.  The
910	+	// embedding contribution is added in each of the low level
911	+	// non-bonded routines.  In single processor, this is done in
912	+	// unpackInteractionData, not in collectData.
913	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
914	+	for (int i = 0; i < nLocal_; i++) {
915	+	// factor of two is because the total potential terms are divided
916	+	// by 2 in parallel due to row/ column scatter
917	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
918	+	}
919	+	}
920	+	}
921	+
922	+	if (storageLayout_ & DataStorage::dslParticlePot) {
923	+	int npp = snap_->atomData.particlePot.size();
924	+	vector<RealType> ppot_temp(npp, 0.0);
925	+
926	+	// This is the direct or embedding contribution to the particle
927	+	// pot.
928	+
929	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
930	+	for (int i = 0; i < npp; i++) {
931	+	snap_->atomData.particlePot[i] += ppot_temp[i];
932	+	}
933	+
934	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
935	+
936	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
937	+	for (int i = 0; i < npp; i++) {
938	+	snap_->atomData.particlePot[i] += ppot_temp[i];
939	+	}
940	+	}
941	+
942	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
943	+	RealType ploc1 = pairwisePot[ii];
944	+	RealType ploc2 = 0.0;
945	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
946	+	pairwisePot[ii] = ploc2;
947	+	}
948	+
949	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
950	+	RealType ploc1 = excludedPot[ii];
951	+	RealType ploc2 = 0.0;
952	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
953	+	excludedPot[ii] = ploc2;
954	+	}
955	+
956	+	// Here be dragons.
957	+	MPI_Comm col = colComm.getComm();
958	+
959	+	MPI_Allreduce(MPI_IN_PLACE,
960	+	&snap_->frameData.conductiveHeatFlux[0], 3,
961	+	MPI_REALTYPE, MPI_SUM, col);
962	+
963	+
964		#endif
965	+
966		}
967
968	+	/**
969	+	* Collects information obtained during the post-pair (and embedding
970	+	* functional) loops onto local data structures.
971	+	*/
972	+	void ForceMatrixDecomposition::collectSelfData() {
973	+	snap_ = sman_->getCurrentSnapshot();
974	+	storageLayout_ = sman_->getStorageLayout();
975	+
976	+	#ifdef IS_MPI
977	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
978	+	RealType ploc1 = embeddingPot[ii];
979	+	RealType ploc2 = 0.0;
980	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
981	+	embeddingPot[ii] = ploc2;
982	+	}
983	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
984	+	RealType ploc1 = excludedSelfPot[ii];
985	+	RealType ploc2 = 0.0;
986	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
987	+	excludedSelfPot[ii] = ploc2;
988	+	}
989	+	#endif
990	+
991	+	}
992	+
993	+
994	+
995	+	int& ForceMatrixDecomposition::getNAtomsInRow() {
996	+	#ifdef IS_MPI
997	+	return nAtomsInRow_;
998	+	#else
999	+	return nLocal_;
1000	+	#endif
1001	+	}
1002	+
1003	+	/**
1004	+	* returns the list of atoms belonging to this group.
1005	+	*/
1006	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
1007	+	#ifdef IS_MPI
1008	+	return groupListRow_[cg1];
1009	+	#else
1010	+	return groupList_[cg1];
1011	+	#endif
1012	+	}
1013	+
1014	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
1015	+	#ifdef IS_MPI
1016	+	return groupListCol_[cg2];
1017	+	#else
1018	+	return groupList_[cg2];
1019	+	#endif
1020	+	}
1021
1022		Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
1023		Vector3d d;
#	Line 253 | Line 1028 | namespace OpenMD {
1028		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
1029		#endif
1030
1031	<	snap_->wrapVector(d);
1031	>	if (usePeriodicBoundaryConditions_) {
1032	>	snap_->wrapVector(d);
1033	>	}
1034		return d;
1035		}
1036
1037	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
1038	+	#ifdef IS_MPI
1039	+	return cgColData.velocity[cg2];
1040	+	#else
1041	+	return snap_->cgData.velocity[cg2];
1042	+	#endif
1043	+	}
1044
1045	+	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
1046	+	#ifdef IS_MPI
1047	+	return atomColData.velocity[atom2];
1048	+	#else
1049	+	return snap_->atomData.velocity[atom2];
1050	+	#endif
1051	+	}
1052	+
1053	+
1054		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
1055
1056		Vector3d d;
#	Line 267 | Line 1060 | namespace OpenMD {
1060		#else
1061		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1062		#endif
1063	<
1064	<	snap_->wrapVector(d);
1063	>	if (usePeriodicBoundaryConditions_) {
1064	>	snap_->wrapVector(d);
1065	>	}
1066		return d;
1067		}
1068
#	Line 280 | Line 1074 | namespace OpenMD {
1074		#else
1075		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1076		#endif
1077	<
1078	<	snap_->wrapVector(d);
1077	>	if (usePeriodicBoundaryConditions_) {
1078	>	snap_->wrapVector(d);
1079	>	}
1080		return d;
1081		}
1082	+
1083	+	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1084	+	#ifdef IS_MPI
1085	+	return massFactorsRow[atom1];
1086	+	#else
1087	+	return massFactors[atom1];
1088	+	#endif
1089	+	}
1090	+
1091	+	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1092	+	#ifdef IS_MPI
1093	+	return massFactorsCol[atom2];
1094	+	#else
1095	+	return massFactors[atom2];
1096	+	#endif
1097	+
1098	+	}
1099
1100		Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
1101		Vector3d d;
#	Line 293 | Line 1105 | namespace OpenMD {
1105		#else
1106		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1107		#endif
1108	<
1109	<	snap_->wrapVector(d);
1108	>	if (usePeriodicBoundaryConditions_) {
1109	>	snap_->wrapVector(d);
1110	>	}
1111		return d;
1112		}
1113
1114	+	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1115	+	return excludesForAtom[atom1];
1116	+	}
1117	+
1118	+	/**
1119	+	* We need to exclude some overcounted interactions that result from
1120	+	* the parallel decomposition.
1121	+	*/
1122	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1123	+	int unique_id_1, unique_id_2;
1124	+
1125	+	#ifdef IS_MPI
1126	+	// in MPI, we have to look up the unique IDs for each atom
1127	+	unique_id_1 = AtomRowToGlobal[atom1];
1128	+	unique_id_2 = AtomColToGlobal[atom2];
1129	+	// group1 = cgRowToGlobal[cg1];
1130	+	// group2 = cgColToGlobal[cg2];
1131	+	#else
1132	+	unique_id_1 = AtomLocalToGlobal[atom1];
1133	+	unique_id_2 = AtomLocalToGlobal[atom2];
1134	+	int group1 = cgLocalToGlobal[cg1];
1135	+	int group2 = cgLocalToGlobal[cg2];
1136	+	#endif
1137	+
1138	+	if (unique_id_1 == unique_id_2) return true;
1139	+
1140	+	#ifdef IS_MPI
1141	+	// this prevents us from doing the pair on multiple processors
1142	+	if (unique_id_1 < unique_id_2) {
1143	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1144	+	} else {
1145	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1146	+	}
1147	+	#endif
1148	+
1149	+	#ifndef IS_MPI
1150	+	if (group1 == group2) {
1151	+	if (unique_id_1 < unique_id_2) return true;
1152	+	}
1153	+	#endif
1154	+
1155	+	return false;
1156	+	}
1157	+
1158	+	/**
1159	+	* We need to handle the interactions for atoms who are involved in
1160	+	* the same rigid body as well as some short range interactions
1161	+	* (bonds, bends, torsions) differently from other interactions.
1162	+	* We'll still visit the pairwise routines, but with a flag that
1163	+	* tells those routines to exclude the pair from direct long range
1164	+	* interactions.  Some indirect interactions (notably reaction
1165	+	* field) must still be handled for these pairs.
1166	+	*/
1167	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1168	+
1169	+	// excludesForAtom was constructed to use row/column indices in the MPI
1170	+	// version, and to use local IDs in the non-MPI version:
1171	+
1172	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1173	+	i != excludesForAtom[atom1].end(); ++i) {
1174	+	if ( (*i) == atom2 ) return true;
1175	+	}
1176	+
1177	+	return false;
1178	+	}
1179	+
1180	+
1181		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1182		#ifdef IS_MPI
1183		atomRowData.force[atom1] += fg;
#	Line 312 | Line 1192 | namespace OpenMD {
1192		#else
1193		snap_->atomData.force[atom2] += fg;
1194		#endif
315	–
1195		}
1196
1197		// filling interaction blocks with pointers
1198	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1198	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1199	>	int atom1, int atom2) {
1200
1201	<	InteractionData idat;
1201	>	idat.excluded = excludeAtomPair(atom1, atom2);
1202	>
1203		#ifdef IS_MPI
1204	+	//idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1205	+	idat.atid1 = identsRow[atom1];
1206	+	idat.atid2 = identsCol[atom2];
1207	+
1208	+	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1209	+	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1210	+	} else {
1211	+	idat.sameRegion = false;
1212	+	}
1213	+
1214		if (storageLayout_ & DataStorage::dslAmat) {
1215	<	idat.A1 = atomRowData.aMat[atom1];
1216	<	idat.A2 = atomColData.aMat[atom2];
1215	>	idat.A1 = &(atomRowData.aMat[atom1]);
1216	>	idat.A2 = &(atomColData.aMat[atom2]);
1217		}
1218	+
1219	+	if (storageLayout_ & DataStorage::dslTorque) {
1220	+	idat.t1 = &(atomRowData.torque[atom1]);
1221	+	idat.t2 = &(atomColData.torque[atom2]);
1222	+	}
1223
1224	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1225	<	idat.eFrame1 = atomRowData.electroFrame[atom1];
1226	<	idat.eFrame2 = atomColData.electroFrame[atom2];
1224	>	if (storageLayout_ & DataStorage::dslDipole) {
1225	>	idat.dipole1 = &(atomRowData.dipole[atom1]);
1226	>	idat.dipole2 = &(atomColData.dipole[atom2]);
1227		}
1228
1229	<	if (storageLayout_ & DataStorage::dslTorque) {
1230	<	idat.t1 = atomRowData.torque[atom1];
1231	<	idat.t2 = atomColData.torque[atom2];
1229	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1230	>	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1231	>	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1232		}
1233
1234		if (storageLayout_ & DataStorage::dslDensity) {
1235	<	idat.rho1 = atomRowData.density[atom1];
1236	<	idat.rho2 = atomColData.density[atom2];
1235	>	idat.rho1 = &(atomRowData.density[atom1]);
1236	>	idat.rho2 = &(atomColData.density[atom2]);
1237		}
1238
1239	+	if (storageLayout_ & DataStorage::dslFunctional) {
1240	+	idat.frho1 = &(atomRowData.functional[atom1]);
1241	+	idat.frho2 = &(atomColData.functional[atom2]);
1242	+	}
1243	+
1244		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1245	<	idat.dfrho1 = atomRowData.functionalDerivative[atom1];
1246	<	idat.dfrho2 = atomColData.functionalDerivative[atom2];
1245	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1246	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1247		}
1248	<	#endif
1248	>
1249	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1250	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1251	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1252	>	}
1253	>
1254	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1255	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1256	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1257	>	}
1258	>
1259	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1260	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1261	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1262	>	}
1263	>
1264	>	#else
1265
1266	<	}
1267	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1268	<	}
1269	<	SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
1266	>	//idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1267	>	idat.atid1 = idents[atom1];
1268	>	idat.atid2 = idents[atom2];
1269	>
1270	>	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1271	>	idat.sameRegion = (regions[atom1] == regions[atom2]);
1272	>	} else {
1273	>	idat.sameRegion = false;
1274	>	}
1275	>
1276	>	if (storageLayout_ & DataStorage::dslAmat) {
1277	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1278	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1279	>	}
1280	>
1281	>	if (storageLayout_ & DataStorage::dslTorque) {
1282	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1283	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1284	>	}
1285	>
1286	>	if (storageLayout_ & DataStorage::dslDipole) {
1287	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1288	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1289	>	}
1290	>
1291	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1292	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1293	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1294	>	}
1295	>
1296	>	if (storageLayout_ & DataStorage::dslDensity) {
1297	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1298	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1299	>	}
1300	>
1301	>	if (storageLayout_ & DataStorage::dslFunctional) {
1302	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1303	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1304	>	}
1305	>
1306	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1307	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1308	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1309	>	}
1310	>
1311	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1312	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1313	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1314	>	}
1315	>
1316	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1317	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1318	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1319	>	}
1320	>
1321	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1322	>	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1323	>	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1324	>	}
1325	>
1326	>	#endif
1327		}
1328
1329
1330	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1331	+	#ifdef IS_MPI
1332	+	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1333	+	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1334	+	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1335	+	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1336	+
1337	+	atomRowData.force[atom1] += *(idat.f1);
1338	+	atomColData.force[atom2] -= *(idat.f1);
1339	+
1340	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1341	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1342	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1343	+	}
1344	+
1345	+	if (storageLayout_ & DataStorage::dslElectricField) {
1346	+	atomRowData.electricField[atom1] += *(idat.eField1);
1347	+	atomColData.electricField[atom2] += *(idat.eField2);
1348	+	}
1349	+
1350	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1351	+	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1352	+	atomColData.sitePotential[atom2] += *(idat.sPot2);
1353	+	}
1354	+
1355	+	#else
1356	+	pairwisePot += *(idat.pot);
1357	+	excludedPot += *(idat.excludedPot);
1358	+
1359	+	snap_->atomData.force[atom1] += *(idat.f1);
1360	+	snap_->atomData.force[atom2] -= *(idat.f1);
1361	+
1362	+	if (idat.doParticlePot) {
1363	+	// This is the pairwise contribution to the particle pot.  The
1364	+	// embedding contribution is added in each of the low level
1365	+	// non-bonded routines.  In parallel, this calculation is done
1366	+	// in collectData, not in unpackInteractionData.
1367	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1368	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1369	+	}
1370	+
1371	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1372	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1373	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1374	+	}
1375	+
1376	+	if (storageLayout_ & DataStorage::dslElectricField) {
1377	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1378	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1379	+	}
1380	+
1381	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1382	+	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1383	+	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1384	+	}
1385	+
1386	+	#endif
1387	+
1388	+	}
1389	+
1390	+	/*
1391	+	* buildNeighborList
1392	+	*
1393	+	* first element of pair is row-indexed CutoffGroup
1394	+	* second element of pair is column-indexed CutoffGroup
1395	+	*/
1396	+	void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1397	+
1398	+	neighborList.clear();
1399	+	groupCutoffs cuts;
1400	+	bool doAllPairs = false;
1401	+
1402	+	RealType rList_ = (largestRcut_ + skinThickness_);
1403	+	RealType rcut, rcutsq, rlistsq;
1404	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1405	+	Mat3x3d box;
1406	+	Mat3x3d invBox;
1407	+
1408	+	Vector3d rs, scaled, dr;
1409	+	Vector3i whichCell;
1410	+	int cellIndex;
1411	+
1412	+	#ifdef IS_MPI
1413	+	cellListRow_.clear();
1414	+	cellListCol_.clear();
1415	+	#else
1416	+	cellList_.clear();
1417	+	#endif
1418	+
1419	+	if (!usePeriodicBoundaryConditions_) {
1420	+	box = snap_->getBoundingBox();
1421	+	invBox = snap_->getInvBoundingBox();
1422	+	} else {
1423	+	box = snap_->getHmat();
1424	+	invBox = snap_->getInvHmat();
1425	+	}
1426	+
1427	+	Vector3d boxX = box.getColumn(0);
1428	+	Vector3d boxY = box.getColumn(1);
1429	+	Vector3d boxZ = box.getColumn(2);
1430	+
1431	+	nCells_.x() = int( boxX.length() / rList_ );
1432	+	nCells_.y() = int( boxY.length() / rList_ );
1433	+	nCells_.z() = int( boxZ.length() / rList_ );
1434	+
1435	+	// handle small boxes where the cell offsets can end up repeating cells
1436	+
1437	+	if (nCells_.x() < 3) doAllPairs = true;
1438	+	if (nCells_.y() < 3) doAllPairs = true;
1439	+	if (nCells_.z() < 3) doAllPairs = true;
1440	+
1441	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1442	+
1443	+	#ifdef IS_MPI
1444	+	cellListRow_.resize(nCtot);
1445	+	cellListCol_.resize(nCtot);
1446	+	#else
1447	+	cellList_.resize(nCtot);
1448	+	#endif
1449	+
1450	+	if (!doAllPairs) {
1451	+	#ifdef IS_MPI
1452	+
1453	+	for (int i = 0; i < nGroupsInRow_; i++) {
1454	+	rs = cgRowData.position[i];
1455	+
1456	+	// scaled positions relative to the box vectors
1457	+	scaled = invBox * rs;
1458	+
1459	+	// wrap the vector back into the unit box by subtracting integer box
1460	+	// numbers
1461	+	for (int j = 0; j < 3; j++) {
1462	+	scaled[j] -= roundMe(scaled[j]);
1463	+	scaled[j] += 0.5;
1464	+	// Handle the special case when an object is exactly on the
1465	+	// boundary (a scaled coordinate of 1.0 is the same as
1466	+	// scaled coordinate of 0.0)
1467	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1468	+	}
1469	+
1470	+	// find xyz-indices of cell that cutoffGroup is in.
1471	+	whichCell.x() = nCells_.x() * scaled.x();
1472	+	whichCell.y() = nCells_.y() * scaled.y();
1473	+	whichCell.z() = nCells_.z() * scaled.z();
1474	+
1475	+	// find single index of this cell:
1476	+	cellIndex = Vlinear(whichCell, nCells_);
1477	+
1478	+	// add this cutoff group to the list of groups in this cell;
1479	+	cellListRow_[cellIndex].push_back(i);
1480	+	}
1481	+	for (int i = 0; i < nGroupsInCol_; i++) {
1482	+	rs = cgColData.position[i];
1483	+
1484	+	// scaled positions relative to the box vectors
1485	+	scaled = invBox * rs;
1486	+
1487	+	// wrap the vector back into the unit box by subtracting integer box
1488	+	// numbers
1489	+	for (int j = 0; j < 3; j++) {
1490	+	scaled[j] -= roundMe(scaled[j]);
1491	+	scaled[j] += 0.5;
1492	+	// Handle the special case when an object is exactly on the
1493	+	// boundary (a scaled coordinate of 1.0 is the same as
1494	+	// scaled coordinate of 0.0)
1495	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1496	+	}
1497	+
1498	+	// find xyz-indices of cell that cutoffGroup is in.
1499	+	whichCell.x() = nCells_.x() * scaled.x();
1500	+	whichCell.y() = nCells_.y() * scaled.y();
1501	+	whichCell.z() = nCells_.z() * scaled.z();
1502	+
1503	+	// find single index of this cell:
1504	+	cellIndex = Vlinear(whichCell, nCells_);
1505	+
1506	+	// add this cutoff group to the list of groups in this cell;
1507	+	cellListCol_[cellIndex].push_back(i);
1508	+	}
1509	+
1510	+	#else
1511	+	for (int i = 0; i < nGroups_; i++) {
1512	+	rs = snap_->cgData.position[i];
1513	+
1514	+	// scaled positions relative to the box vectors
1515	+	scaled = invBox * rs;
1516	+
1517	+	// wrap the vector back into the unit box by subtracting integer box
1518	+	// numbers
1519	+	for (int j = 0; j < 3; j++) {
1520	+	scaled[j] -= roundMe(scaled[j]);
1521	+	scaled[j] += 0.5;
1522	+	// Handle the special case when an object is exactly on the
1523	+	// boundary (a scaled coordinate of 1.0 is the same as
1524	+	// scaled coordinate of 0.0)
1525	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1526	+	}
1527	+
1528	+	// find xyz-indices of cell that cutoffGroup is in.
1529	+	whichCell.x() = int(nCells_.x() * scaled.x());
1530	+	whichCell.y() = int(nCells_.y() * scaled.y());
1531	+	whichCell.z() = int(nCells_.z() * scaled.z());
1532	+
1533	+	// find single index of this cell:
1534	+	cellIndex = Vlinear(whichCell, nCells_);
1535	+
1536	+	// add this cutoff group to the list of groups in this cell;
1537	+	cellList_[cellIndex].push_back(i);
1538	+	}
1539	+
1540	+	#endif
1541	+
1542	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1543	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1544	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1545	+	Vector3i m1v(m1x, m1y, m1z);
1546	+	int m1 = Vlinear(m1v, nCells_);
1547	+
1548	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1549	+	os != cellOffsets_.end(); ++os) {
1550	+
1551	+	Vector3i m2v = m1v + (*os);
1552	+
1553	+
1554	+	if (m2v.x() >= nCells_.x()) {
1555	+	m2v.x() = 0;
1556	+	} else if (m2v.x() < 0) {
1557	+	m2v.x() = nCells_.x() - 1;
1558	+	}
1559	+
1560	+	if (m2v.y() >= nCells_.y()) {
1561	+	m2v.y() = 0;
1562	+	} else if (m2v.y() < 0) {
1563	+	m2v.y() = nCells_.y() - 1;
1564	+	}
1565	+
1566	+	if (m2v.z() >= nCells_.z()) {
1567	+	m2v.z() = 0;
1568	+	} else if (m2v.z() < 0) {
1569	+	m2v.z() = nCells_.z() - 1;
1570	+	}
1571	+
1572	+	int m2 = Vlinear (m2v, nCells_);
1573	+
1574	+	#ifdef IS_MPI
1575	+	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1576	+	j1 != cellListRow_[m1].end(); ++j1) {
1577	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1578	+	j2 != cellListCol_[m2].end(); ++j2) {
1579	+
1580	+	// In parallel, we need to visit *all* pairs of row
1581	+	// & column indicies and will divide labor in the
1582	+	// force evaluation later.
1583	+	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1584	+	if (usePeriodicBoundaryConditions_) {
1585	+	snap_->wrapVector(dr);
1586	+	}
1587	+	getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1588	+	if (dr.lengthSquare() < rlistsq) {
1589	+	neighborList.push_back(make_pair((*j1), (*j2)));
1590	+	}
1591	+	}
1592	+	}
1593	+	#else
1594	+	for (vector<int>::iterator j1 = cellList_[m1].begin();
1595	+	j1 != cellList_[m1].end(); ++j1) {
1596	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1597	+	j2 != cellList_[m2].end(); ++j2) {
1598	+
1599	+	// Always do this if we're in different cells or if
1600	+	// we're in the same cell and the global index of
1601	+	// the j2 cutoff group is greater than or equal to
1602	+	// the j1 cutoff group.  Note that Rappaport's code
1603	+	// has a "less than" conditional here, but that
1604	+	// deals with atom-by-atom computation.  OpenMD
1605	+	// allows atoms within a single cutoff group to
1606	+	// interact with each other.
1607	+
1608	+	if (m2 != m1 || (*j2) >= (*j1) ) {
1609	+
1610	+	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1611	+	if (usePeriodicBoundaryConditions_) {
1612	+	snap_->wrapVector(dr);
1613	+	}
1614	+	getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1615	+	if (dr.lengthSquare() < rlistsq) {
1616	+	neighborList.push_back(make_pair((*j1), (*j2)));
1617	+	}
1618	+	}
1619	+	}
1620	+	}
1621	+	#endif
1622	+	}
1623	+	}
1624	+	}
1625	+	}
1626	+	} else {
1627	+	// branch to do all cutoff group pairs
1628	+	#ifdef IS_MPI
1629	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1630	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1631	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1632	+	if (usePeriodicBoundaryConditions_) {
1633	+	snap_->wrapVector(dr);
1634	+	}
1635	+	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1636	+	if (dr.lengthSquare() < rlistsq) {
1637	+	neighborList.push_back(make_pair(j1, j2));
1638	+	}
1639	+	}
1640	+	}
1641	+	#else
1642	+	// include all groups here.
1643	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1644	+	// include self group interactions j2 == j1
1645	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1646	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1647	+	if (usePeriodicBoundaryConditions_) {
1648	+	snap_->wrapVector(dr);
1649	+	}
1650	+	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1651	+	if (dr.lengthSquare() < rlistsq) {
1652	+	neighborList.push_back(make_pair(j1, j2));
1653	+	}
1654	+	}
1655	+	}
1656	+	#endif
1657	+	}
1658	+
1659	+	// save the local cutoff group positions for the check that is
1660	+	// done on each loop:
1661	+	saved_CG_positions_.clear();
1662	+	for (int i = 0; i < nGroups_; i++)
1663	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1664	+	}
1665		} //end namespace OpenMD

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