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

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1577 by gezelter, Wed Jun 8 20:26:56 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"
#	Line 47 | Line 48 | namespace OpenMD {
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		*/
54	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96		ff_ = info_->getForceField();
97		nLocal_ = snap_->getNumberOfAtoms();
98	<
98	>
99		nGroups_ = info_->getNLocalCutoffGroups();
100		// gather the information for atomtype IDs (atids):
101	<	identsLocal = info_->getIdentArray();
101	>	idents = info_->getIdentArray();
102	>	regions = info_->getRegions();
103		AtomLocalToGlobal = info_->getGlobalAtomIndices();
104		cgLocalToGlobal = info_->getGlobalGroupIndices();
105		vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67	–	vector<RealType> massFactorsLocal = info_->getMassFactors();
68	–	PairList excludes = info_->getExcludedInteractions();
69	–	PairList oneTwo = info_->getOneTwoInteractions();
70	–	PairList oneThree = info_->getOneThreeInteractions();
71	–	PairList oneFour = info_->getOneFourInteractions();
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	+	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	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
123	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
77	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
78	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
79	<	AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
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_);
129	<	AtomCommPotColumn = new Communicator<Column,potVec>(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	<	nAtomsInRow_ = AtomCommIntRow->getSize();
138	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
139	<	nGroupsInRow_ = cgCommIntRow->getSize();
140	<	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_);
149		atomRowData.setStorageLayout(storageLayout_);
#	Line 102 | Line 152 | namespace OpenMD {
152		cgRowData.resize(nGroupsInRow_);
153		cgRowData.setStorageLayout(DataStorage::dslPosition);
154		cgColData.resize(nGroupsInCol_);
155	<	cgColData.setStorageLayout(DataStorage::dslPosition);
156	<
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	<	AtomCommIntRow->gather(identsLocal, identsRow);
166	<	AtomCommIntColumn->gather(identsLocal, identsCol);
165	>	AtomPlanIntRow->gather(idents, identsRow);
166	>	AtomPlanIntColumn->gather(idents, identsCol);
167	>
168	>	regionsRow.resize(nAtomsInRow_);
169	>	regionsCol.resize(nAtomsInCol_);
170
171	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
172	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
171	>	AtomPlanIntRow->gather(regions, regionsRow);
172	>	AtomPlanIntColumn->gather(regions, regionsCol);
173
174	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
174	>	// allocate memory for the parallel objects
175	>	atypesRow.resize(nAtomsInRow_);
176	>	atypesCol.resize(nAtomsInCol_);
177
178	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
179	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
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++) {
#	Line 141 | Line 223 | namespace OpenMD {
223		}
224		}
225
226	<	skipsForRowAtom.clear();
227	<	skipsForRowAtom.resize(nAtomsInRow_);
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	<	if (excludes.hasPair(iglob, jglob))
238	<	skipsForRowAtom[i].push_back(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	<	toposForRowAtom.clear();
259	<	toposForRowAtom.resize(nAtomsInRow_);
260	<	for (int i = 0; i < nAtomsInRow_; i++) {
261	<	int iglob = AtomRowToGlobal[i];
262	<	int nTopos = 0;
263	<	for (int j = 0; j < nAtomsInCol_; j++) {
264	<	int jglob = AtomColToGlobal[j];
265	<	if (oneTwo.hasPair(iglob, jglob)) {
266	<	toposForRowAtom[i].push_back(j);
267	<	topoDistRow[i][nTopos] = 1;
268	<	nTopos++;
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		}
167	–	if (oneThree.hasPair(iglob, jglob)) {
168	–	toposForRowAtom[i].push_back(j);
169	–	topoDistRow[i][nTopos] = 2;
170	–	nTopos++;
171	–	}
172	–	if (oneFour.hasPair(iglob, jglob)) {
173	–	toposForRowAtom[i].push_back(j);
174	–	topoDistRow[i][nTopos] = 3;
175	–	nTopos++;
176	–	}
289		}
290		}
179	–
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++) {
#	Line 186 | Line 304 | namespace OpenMD {
304		int aid = AtomLocalToGlobal[j];
305		if (globalGroupMembership[aid] == gid) {
306		groupList_[i].push_back(j);
189	–
307		}
308		}
309		}
310
194	–	skipsForLocalAtom.clear();
195	–	skipsForLocalAtom.resize(nLocal_);
311
312	<	for (int i = 0; i < nLocal_; i++) {
198	<	int iglob = AtomLocalToGlobal[i];
199	<	for (int j = 0; j < nLocal_; j++) {
200	<	int jglob = AtomLocalToGlobal[j];
201	<	if (excludes.hasPair(iglob, jglob))
202	<	skipsForLocalAtom[i].push_back(j);
203	<	}
204	<	}
205	<	toposForLocalAtom.clear();
206	<	toposForLocalAtom.resize(nLocal_);
207	<	for (int i = 0; i < nLocal_; i++) {
208	<	int iglob = AtomLocalToGlobal[i];
209	<	int nTopos = 0;
210	<	for (int j = 0; j < nLocal_; j++) {
211	<	int jglob = AtomLocalToGlobal[j];
212	<	if (oneTwo.hasPair(iglob, jglob)) {
213	<	toposForLocalAtom[i].push_back(j);
214	<	topoDistLocal[i][nTopos] = 1;
215	<	nTopos++;
216	<	}
217	<	if (oneThree.hasPair(iglob, jglob)) {
218	<	toposForLocalAtom[i].push_back(j);
219	<	topoDistLocal[i][nTopos] = 2;
220	<	nTopos++;
221	<	}
222	<	if (oneFour.hasPair(iglob, jglob)) {
223	<	toposForLocalAtom[i].push_back(j);
224	<	topoDistLocal[i][nTopos] = 3;
225	<	nTopos++;
226	<	}
227	<	}
228	<	}
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	<	RealType rc;
323	>	largestRcut_ = 0.0;
324		int atid;
325		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
326	<	vector<RealType> atypeCutoff;
327	<	atypeCutoff.resize( atypes.size() );
328	<
329	<	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
330	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
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	<	atypeCutoff[atid] = rc;
332	>	if (userChoseCutoff_)
333	>	atypeCutoff[atid] = userCutoff_;
334	>	else
335	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
336		}
337	<
337	>
338		vector<RealType> gTypeCutoffs;
248	–
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();
#	Line 275 | Line 366 | namespace OpenMD {
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();
#	Line 298 | Line 390 | namespace OpenMD {
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 = identsLocal[atom1];
403	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
402	>	atid = idents[atom1];
403	>	if (atypeCutoff[atid] > groupCutoff[cg1])
404		groupCutoff[cg1] = atypeCutoff[atid];
311	–	}
405		}
406	<
406	>
407		bool gTypeFound = false;
408	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
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) {
414	>	if (!gTypeFound) {
415		gTypeCutoffs.push_back( groupCutoff[cg1] );
416		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
417		}
#	Line 327 | Line 420 | namespace OpenMD {
420
421		// Now we find the maximum group cutoff value present in the simulation
422
423	<	vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
424	<	RealType groupMax = *groupMaxLoc;
423	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
424	>	gTypeCutoffs.end());
425
426		#ifdef IS_MPI
427	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
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	<	for (int i = 0; i < gTypeCutoffs.size();  i++) {
434	<	for (int j = 0; j < gTypeCutoffs.size();  j++) {
435	<
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();
461	>	simError();
462	>	break;
463		}
464
465	<	pair<int,int> key = make_pair(i,j);
360	<	gTypeCutoffMap[key].first = thisRcut;
361	<
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	<	gTypeCutoffMap[key].second = thisRcut*thisRcut;
471	<
472	<	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
367	<
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(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
476	>	if (abs(GrCut[i][j] - userCutoff_) > 0.0001) {
477		sprintf(painCave.errMsg,
478		"ForceMatrixDecomposition::createGtypeCutoffMap "
479	<	"user-specified rCut does not match computed group Cutoff\n");
479	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
480		painCave.severity = OPENMD_ERROR;
481		painCave.isFatal = 1;
482		simError();
#	Line 381 | Line 486 | namespace OpenMD {
486		}
487		}
488
489	<
490	<	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
386	<	int i, j;
387	<
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	<
499	<	return gTypeCutoffMap[make_pair(i,j)];
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
402	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403	–	longRangePot_[j] = 0.0;
404	–	}
405	–
519		#ifdef IS_MPI
520		if (storageLayout_ & DataStorage::dslForce) {
521		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 418 | Line 531 | namespace OpenMD {
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));
422	–
423	–	pot_local = 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(), 0.0);
544	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
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) {
#	Line 433 | Line 552 | namespace OpenMD {
552		}
553
554		if (storageLayout_ & DataStorage::dslFunctional) {
555	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
556	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
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) {
#	Line 444 | Line 565 | namespace OpenMD {
565		atomColData.functionalDerivative.end(), 0.0);
566		}
567
568	<	#else
569	<
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);
#	Line 455 | Line 605 | namespace OpenMD {
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	<	#endif
619	<
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
#	Line 474 | Line 638 | namespace OpenMD {
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
#	Line 513 | 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		vector<RealType> rho_tmp(n, 0.0);
715	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
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
#	Line 534 | Line 743 | namespace OpenMD {
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 557 | 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		}
795	+
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	+	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	<	AtomCommPotRow->scatter(pot_row, pot_temp);
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	<	pot_local += pot_temp[ii];
876	<
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	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
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	<	pot_local += pot_temp[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	<	int ForceMatrixDecomposition::getNAtomsInRow() {
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_;
#	Line 618 | Line 1003 | namespace OpenMD {
1003		/**
1004		* returns the list of atoms belonging to this group.
1005		*/
1006	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
1006	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
1007		#ifdef IS_MPI
1008		return groupListRow_[cg1];
1009		#else
#	Line 626 | Line 1011 | namespace OpenMD {
1011		#endif
1012		}
1013
1014	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
1014	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
1015		#ifdef IS_MPI
1016		return groupListCol_[cg2];
1017		#else
#	Line 643 | 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 657 | 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 670 | 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) {
1083	>	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1084		#ifdef IS_MPI
1085		return massFactorsRow[atom1];
1086		#else
1087	<	return massFactorsLocal[atom1];
1087	>	return massFactors[atom1];
1088		#endif
1089		}
1090
1091	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1091	>	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1092		#ifdef IS_MPI
1093		return massFactorsCol[atom2];
1094		#else
1095	<	return massFactorsLocal[atom2];
1095	>	return massFactors[atom2];
1096		#endif
1097
1098		}
#	Line 700 | 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::getSkipsForRowAtom(int atom1) {
1115	<	#ifdef IS_MPI
710	<	return skipsForRowAtom[atom1];
711	<	#else
712	<	return skipsForLocalAtom[atom1];
713	<	#endif
1114	>	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1115	>	return excludesForAtom[atom1];
1116		}
1117
1118		/**
1119	<	* There are a number of reasons to skip a pair or a
718	<	* particle. Mostly we do this to exclude atoms who are involved in
719	<	* short range interactions (bonds, bends, torsions), but we also
720	<	* need to exclude some overcounted interactions that result from
1119	>	* We need to exclude some overcounted interactions that result from
1120		* the parallel decomposition.
1121		*/
1122	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1122	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1123		int unique_id_1, unique_id_2;
1124	<
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
731	–	// this situation should only arise in MPI simulations
1138		if (unique_id_1 == unique_id_2) return true;
1139	<
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;
1145	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1146		}
1147	<	#else
1148	<	// in the normal loop, the atom numbers are unique
1149	<	unique_id_1 = atom1;
1150	<	unique_id_2 = atom2;
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	<	#ifdef IS_MPI
747	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748	<	i != skipsForRowAtom[atom1].end(); ++i) {
749	<	if ( (*i) == unique_id_2 ) return true;
750	<	}
751	<	#else
752	<	for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
753	<	i != skipsForLocalAtom[atom1].end(); ++i) {
754	<	if ( (*i) == unique_id_2 ) return true;
755	<	}
756	<	#endif
1155	>	return false;
1156		}
1157
1158	<	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
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	<	#ifdef IS_MPI
1173	<	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
1174	<	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
1172	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1173	>	i != excludesForAtom[atom1].end(); ++i) {
1174	>	if ( (*i) == atom2 ) return true;
1175		}
765	–	#else
766	–	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
767	–	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
768	–	}
769	–	#endif
1176
1177	<	// zero is default for unconnected (i.e. normal) pair interactions
772	<	return 0;
1177	>	return false;
1178		}
1179
1180	+
1181		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1182		#ifdef IS_MPI
1183		atomRowData.force[atom1] += fg;
#	Line 789 | Line 1195 | namespace OpenMD {
1195		}
1196
1197		// filling interaction blocks with pointers
1198	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1199	<	InteractionData idat;
1198	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1199	>	int atom1, int atom2) {
1200
1201	+	idat.excluded = excludeAtomPair(atom1, atom2);
1202	+
1203		#ifdef IS_MPI
1204	<
1205	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1206	<	ff_->getAtomType(identsCol[atom2]) );
1204	>	//idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1205	>	idat.atid1 = identsRow[atom1];
1206	>	idat.atid2 = identsCol[atom2];
1207
1208	<
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]);
1217		}
1218
806	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
807	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
808	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
809	–	}
810	–
1219		if (storageLayout_ & DataStorage::dslTorque) {
1220		idat.t1 = &(atomRowData.torque[atom1]);
1221		idat.t2 = &(atomColData.torque[atom2]);
1222	+	}
1223	+
1224	+	if (storageLayout_ & DataStorage::dslDipole) {
1225	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1226	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1227	+	}
1228	+
1229	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1230	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1231	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1232		}
1233
1234		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 833 | Line 1251 | namespace OpenMD {
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	+	//idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1267	+	idat.atid1 = idents[atom1];
1268	+	idat.atid2 = idents[atom2];
1269
1270	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
1271	<	ff_->getAtomType(identsLocal[atom2]) );
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
846	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
847	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
848	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
849	–	}
850	–
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::dslDensity) {
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		}
#	Line 873 | Line 1313 | namespace OpenMD {
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
877	–	return idat;
1327		}
1328
1329
1330	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
1330	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1331		#ifdef IS_MPI
1332	<	pot_row[atom1] += 0.5 *  *(idat.pot);
1333	<	pot_col[atom2] += 0.5 *  *(idat.pot);
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);
888	–	#else
889	–	longRangePot_ += *(idat.pot);
890	–
891	–	snap_->atomData.force[atom1] += *(idat.f1);
892	–	snap_->atomData.force[atom2] -= *(idat.f1);
893	–	#endif
1339
1340	<	}
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	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1350	>	if (storageLayout_ & DataStorage::dslSitePotential) {
1351	>	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1352	>	atomColData.sitePotential[atom2] += *(idat.sPot2);
1353	>	}
1354
1355	<	InteractionData idat;
1356	<	#ifdef IS_MPI
1357	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
903	<	ff_->getAtomType(identsCol[atom2]) );
1355	>	#else
1356	>	pairwisePot += *(idat.pot);
1357	>	excludedPot += *(idat.excludedPot);
1358
1359	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1360	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1361	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
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	<	if (storageLayout_ & DataStorage::dslTorque) {
1371	<	idat.t1 = &(atomRowData.torque[atom1]);
1372	<	idat.t2 = &(atomColData.torque[atom2]);
1370	>
1371	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1372	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1373	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1374		}
913	–	#else
914	–	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
915	–	ff_->getAtomType(identsLocal[atom2]) );
1375
1376	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1377	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1378	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1376	>	if (storageLayout_ & DataStorage::dslElectricField) {
1377	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1378	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1379		}
1380	<	if (storageLayout_ & DataStorage::dslTorque) {
1381	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1382	<	idat.t2 = &(snap_->atomData.torque[atom2]);
1380	>
1381	>	if (storageLayout_ & DataStorage::dslSitePotential) {
1382	>	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1383	>	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1384		}
1385	<	#endif
1385	>
1386	>	#endif
1387	>
1388		}
1389
1390		/*
#	Line 931 | Line 1393 | namespace OpenMD {
1393		* first element of pair is row-indexed CutoffGroup
1394		* second element of pair is column-indexed CutoffGroup
1395		*/
1396	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1397	<
1398	<	vector<pair<int, int> > neighborList;
1396	>	void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1397	>
1398	>	neighborList.clear();
1399		groupCutoffs cuts;
1400	<	#ifdef IS_MPI
939	<	cellListRow_.clear();
940	<	cellListCol_.clear();
941	<	#else
942	<	cellList_.clear();
943	<	#endif
1400	>	bool doAllPairs = false;
1401
1402		RealType rList_ = (largestRcut_ + skinThickness_);
1403	<	RealType rl2 = rList_ * rList_;
1403	>	RealType rcut, rcutsq, rlistsq;
1404		Snapshot* snap_ = sman_->getCurrentSnapshot();
1405	<	Mat3x3d Hmat = snap_->getHmat();
1406	<	Vector3d Hx = Hmat.getColumn(0);
950	<	Vector3d Hy = Hmat.getColumn(1);
951	<	Vector3d Hz = Hmat.getColumn(2);
1405	>	Mat3x3d box;
1406	>	Mat3x3d invBox;
1407
953	–	nCells_.x() = (int) ( Hx.length() )/ rList_;
954	–	nCells_.y() = (int) ( Hy.length() )/ rList_;
955	–	nCells_.z() = (int) ( Hz.length() )/ rList_;
956	–
957	–	Mat3x3d invHmat = snap_->getInvHmat();
1408		Vector3d rs, scaled, dr;
1409		Vector3i whichCell;
1410		int cellIndex;
1411
1412		#ifdef IS_MPI
1413	<	for (int i = 0; i < nGroupsInRow_; i++) {
1414	<	rs = cgRowData.position[i];
1415	<	// scaled positions relative to the box vectors
1416	<	scaled = invHmat * rs;
1417	<	// wrap the vector back into the unit box by subtracting integer box
1418	<	// numbers
1419	<	for (int j = 0; j < 3; j++)
1420	<	scaled[j] -= roundMe(scaled[j]);
1421	<
1422	<	// find xyz-indices of cell that cutoffGroup is in.
1423	<	whichCell.x() = nCells_.x() * scaled.x();
1424	<	whichCell.y() = nCells_.y() * scaled.y();
975	<	whichCell.z() = nCells_.z() * scaled.z();
976	<
977	<	// find single index of this cell:
978	<	cellIndex = Vlinear(whichCell, nCells_);
979	<	// add this cutoff group to the list of groups in this cell;
980	<	cellListRow_[cellIndex].push_back(i);
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	<	for (int i = 0; i < nGroupsInCol_; i++) {
1428	<	rs = cgColData.position[i];
1429	<	// scaled positions relative to the box vectors
1430	<	scaled = invHmat * rs;
1431	<	// wrap the vector back into the unit box by subtracting integer box
1432	<	// numbers
1433	<	for (int j = 0; j < 3; j++)
1434	<	scaled[j] -= roundMe(scaled[j]);
1435	<
1436	<	// find xyz-indices of cell that cutoffGroup is in.
1437	<	whichCell.x() = nCells_.x() * scaled.x();
1438	<	whichCell.y() = nCells_.y() * scaled.y();
1439	<	whichCell.z() = nCells_.z() * scaled.z();
1440	<
1441	<	// find single index of this cell:
1442	<	cellIndex = Vlinear(whichCell, nCells_);
1443	<	// add this cutoff group to the list of groups in this cell;
1444	<	cellListCol_[cellIndex].push_back(i);
1445	<	}
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	<	for (int i = 0; i < nGroups_; i++) {
1448	<	rs = snap_->cgData.position[i];
1449	<	// scaled positions relative to the box vectors
1450	<	scaled = invHmat * rs;
1451	<	// wrap the vector back into the unit box by subtracting integer box
1452	<	// numbers
1453	<	for (int j = 0; j < 3; j++)
1454	<	scaled[j] -= roundMe(scaled[j]);
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
1012	–	// find xyz-indices of cell that cutoffGroup is in.
1013	–	whichCell.x() = nCells_.x() * scaled.x();
1014	–	whichCell.y() = nCells_.y() * scaled.y();
1015	–	whichCell.z() = nCells_.z() * scaled.z();
1016	–
1017	–	// find single index of this cell:
1018	–	cellIndex = Vlinear(whichCell, nCells_);
1019	–	// add this cutoff group to the list of groups in this cell;
1020	–	cellList_[cellIndex].push_back(i);
1021	–	}
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_);
1029	<
1030	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1031	<	os != cellOffsets_.end(); ++os) {
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	<	Vector3i m2v = m1v + (*os);
1549	<
1550	<	if (m2v.x() >= nCells_.x()) {
1551	<	m2v.x() = 0;
1552	<	} else if (m2v.x() < 0) {
1038	<	m2v.x() = nCells_.x() - 1;
1039	<	}
1040	<
1041	<	if (m2v.y() >= nCells_.y()) {
1042	<	m2v.y() = 0;
1043	<	} else if (m2v.y() < 0) {
1044	<	m2v.y() = nCells_.y() - 1;
1045	<	}
1046	<
1047	<	if (m2v.z() >= nCells_.z()) {
1048	<	m2v.z() = 0;
1049	<	} else if (m2v.z() < 0) {
1050	<	m2v.z() = nCells_.z() - 1;
1051	<	}
1052	<
1053	<	int m2 = Vlinear (m2v, nCells_);
1548	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1549	>	os != cellOffsets_.end(); ++os) {
1550	>
1551	>	Vector3i m2v = m1v + (*os);
1552	>
1553
1554	<	#ifdef IS_MPI
1555	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1556	<	j1 != cellListRow_[m1].end(); ++j1) {
1557	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1558	<	j2 != cellListCol_[m2].end(); ++j2) {
1559	<
1560	<	// Always do this if we're in different cells or if
1561	<	// we're in the same cell and the global index of the
1562	<	// j2 cutoff group is less than the j1 cutoff group
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	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
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	<	snap_->wrapVector(dr);
1585	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1069	<	if (dr.lengthSquare() < cuts.third) {
1070	<	neighborList.push_back(make_pair((*j1), (*j2)));
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		}
1074	–	}
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 the
1601	<	// j2 cutoff group is less than the j1 cutoff group
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	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1610	<	snap_->wrapVector(dr);
1611	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1612	<	if (dr.lengthSquare() < cuts.third) {
1613	<	neighborList.push_back(make_pair((*j1), (*j2)));
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		}
1094	–	}
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	<
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]);
1106	–
1107	–	return neighborList;
1664		}
1665		} //end namespace OpenMD

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