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

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1895 by gezelter, Mon Jul 1 21:09:37 2013 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/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	<	nGroups_ = snap_->getNumberOfCutoffGroups();
99	<
98	>
99	>	nGroups_ = info_->getNLocalCutoffGroups();
100		// gather the information for atomtype IDs (atids):
101	<	identsLocal = info_->getIdentArray();
101	>	idents = info_->getIdentArray();
102		AtomLocalToGlobal = info_->getGlobalAtomIndices();
103		cgLocalToGlobal = info_->getGlobalGroupIndices();
104		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();
105
106	+	massFactors = info_->getMassFactors();
107	+
108	+	PairList* excludes = info_->getExcludedInteractions();
109	+	PairList* oneTwo = info_->getOneTwoInteractions();
110	+	PairList* oneThree = info_->getOneThreeInteractions();
111	+	PairList* oneFour = info_->getOneFourInteractions();
112	+
113	+	if (needVelocities_)
114	+	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
115	+	DataStorage::dslVelocity);
116	+	else
117	+	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118	+
119		#ifdef IS_MPI
120
121	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
122	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
77	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
78	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
79	<	AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
121	>	MPI::Intracomm row = rowComm.getComm();
122	>	MPI::Intracomm col = colComm.getComm();
123
124	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
125	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
126	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
127	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
128	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
124	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
125	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
126	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
127	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
128	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
129
130	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
131	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
132	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
133	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
130	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
131	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
132	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
133	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
134	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
135
136	<	nAtomsInRow_ = AtomCommIntRow->getSize();
137	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
138	<	nGroupsInRow_ = cgCommIntRow->getSize();
139	<	nGroupsInCol_ = cgCommIntColumn->getSize();
136	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
137	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
138	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
139	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
140
141	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
142	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
143	+	nGroupsInRow_ = cgPlanIntRow->getSize();
144	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
145	+
146		// Modify the data storage objects with the correct layouts and sizes:
147		atomRowData.resize(nAtomsInRow_);
148		atomRowData.setStorageLayout(storageLayout_);
#	Line 102 | Line 151 | namespace OpenMD {
151		cgRowData.resize(nGroupsInRow_);
152		cgRowData.setStorageLayout(DataStorage::dslPosition);
153		cgColData.resize(nGroupsInCol_);
154	<	cgColData.setStorageLayout(DataStorage::dslPosition);
155	<
156	<	identsRow.reserve(nAtomsInRow_);
157	<	identsCol.reserve(nAtomsInCol_);
154	>	if (needVelocities_)
155	>	// we only need column velocities if we need them.
156	>	cgColData.setStorageLayout(DataStorage::dslPosition |
157	>	DataStorage::dslVelocity);
158	>	else
159	>	cgColData.setStorageLayout(DataStorage::dslPosition);
160	>
161	>	identsRow.resize(nAtomsInRow_);
162	>	identsCol.resize(nAtomsInCol_);
163
164	<	AtomCommIntRow->gather(identsLocal, identsRow);
165	<	AtomCommIntColumn->gather(identsLocal, identsCol);
164	>	AtomPlanIntRow->gather(idents, identsRow);
165	>	AtomPlanIntColumn->gather(idents, identsCol);
166
167	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
168	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
169	<
116	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
117	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
167	>	// allocate memory for the parallel objects
168	>	atypesRow.resize(nAtomsInRow_);
169	>	atypesCol.resize(nAtomsInCol_);
170
171	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
172	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
171	>	for (int i = 0; i < nAtomsInRow_; i++)
172	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
173	>	for (int i = 0; i < nAtomsInCol_; i++)
174	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
175
176	+	pot_row.resize(nAtomsInRow_);
177	+	pot_col.resize(nAtomsInCol_);
178	+
179	+	expot_row.resize(nAtomsInRow_);
180	+	expot_col.resize(nAtomsInCol_);
181	+
182	+	AtomRowToGlobal.resize(nAtomsInRow_);
183	+	AtomColToGlobal.resize(nAtomsInCol_);
184	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
185	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
186	+
187	+	cgRowToGlobal.resize(nGroupsInRow_);
188	+	cgColToGlobal.resize(nGroupsInCol_);
189	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
190	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
191	+
192	+	massFactorsRow.resize(nAtomsInRow_);
193	+	massFactorsCol.resize(nAtomsInCol_);
194	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
195	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
196	+
197		groupListRow_.clear();
198	<	groupListRow_.reserve(nGroupsInRow_);
198	>	groupListRow_.resize(nGroupsInRow_);
199		for (int i = 0; i < nGroupsInRow_; i++) {
200		int gid = cgRowToGlobal[i];
201		for (int j = 0; j < nAtomsInRow_; j++) {
#	Line 131 | Line 206 | namespace OpenMD {
206		}
207
208		groupListCol_.clear();
209	<	groupListCol_.reserve(nGroupsInCol_);
209	>	groupListCol_.resize(nGroupsInCol_);
210		for (int i = 0; i < nGroupsInCol_; i++) {
211		int gid = cgColToGlobal[i];
212		for (int j = 0; j < nAtomsInCol_; j++) {
#	Line 141 | Line 216 | namespace OpenMD {
216		}
217		}
218
219	<	skipsForRowAtom.clear();
220	<	skipsForRowAtom.reserve(nAtomsInRow_);
219	>	excludesForAtom.clear();
220	>	excludesForAtom.resize(nAtomsInRow_);
221	>	toposForAtom.clear();
222	>	toposForAtom.resize(nAtomsInRow_);
223	>	topoDist.clear();
224	>	topoDist.resize(nAtomsInRow_);
225		for (int i = 0; i < nAtomsInRow_; i++) {
226		int iglob = AtomRowToGlobal[i];
227	+
228		for (int j = 0; j < nAtomsInCol_; j++) {
229	<	int jglob = AtomColToGlobal[j];
230	<	if (excludes.hasPair(iglob, jglob))
231	<	skipsForRowAtom[i].push_back(j);
229	>	int jglob = AtomColToGlobal[j];
230	>
231	>	if (excludes->hasPair(iglob, jglob))
232	>	excludesForAtom[i].push_back(j);
233	>
234	>	if (oneTwo->hasPair(iglob, jglob)) {
235	>	toposForAtom[i].push_back(j);
236	>	topoDist[i].push_back(1);
237	>	} else {
238	>	if (oneThree->hasPair(iglob, jglob)) {
239	>	toposForAtom[i].push_back(j);
240	>	topoDist[i].push_back(2);
241	>	} else {
242	>	if (oneFour->hasPair(iglob, jglob)) {
243	>	toposForAtom[i].push_back(j);
244	>	topoDist[i].push_back(3);
245	>	}
246	>	}
247	>	}
248		}
249		}
250
251	<	toposForRowAtom.clear();
252	<	toposForRowAtom.reserve(nAtomsInRow_);
253	<	for (int i = 0; i < nAtomsInRow_; i++) {
254	<	int iglob = AtomRowToGlobal[i];
255	<	int nTopos = 0;
256	<	for (int j = 0; j < nAtomsInCol_; j++) {
257	<	int jglob = AtomColToGlobal[j];
258	<	if (oneTwo.hasPair(iglob, jglob)) {
259	<	toposForRowAtom[i].push_back(j);
260	<	topoDistRow[i][nTopos] = 1;
261	<	nTopos++;
251	>	#else
252	>	excludesForAtom.clear();
253	>	excludesForAtom.resize(nLocal_);
254	>	toposForAtom.clear();
255	>	toposForAtom.resize(nLocal_);
256	>	topoDist.clear();
257	>	topoDist.resize(nLocal_);
258	>
259	>	for (int i = 0; i < nLocal_; i++) {
260	>	int iglob = AtomLocalToGlobal[i];
261	>
262	>	for (int j = 0; j < nLocal_; j++) {
263	>	int jglob = AtomLocalToGlobal[j];
264	>
265	>	if (excludes->hasPair(iglob, jglob))
266	>	excludesForAtom[i].push_back(j);
267	>
268	>	if (oneTwo->hasPair(iglob, jglob)) {
269	>	toposForAtom[i].push_back(j);
270	>	topoDist[i].push_back(1);
271	>	} else {
272	>	if (oneThree->hasPair(iglob, jglob)) {
273	>	toposForAtom[i].push_back(j);
274	>	topoDist[i].push_back(2);
275	>	} else {
276	>	if (oneFour->hasPair(iglob, jglob)) {
277	>	toposForAtom[i].push_back(j);
278	>	topoDist[i].push_back(3);
279	>	}
280	>	}
281		}
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	–	}
282		}
283		}
179	–
284		#endif
285
286	+	// allocate memory for the parallel objects
287	+	atypesLocal.resize(nLocal_);
288	+
289	+	for (int i = 0; i < nLocal_; i++)
290	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
291	+
292		groupList_.clear();
293	<	groupList_.reserve(nGroups_);
293	>	groupList_.resize(nGroups_);
294		for (int i = 0; i < nGroups_; i++) {
295		int gid = cgLocalToGlobal[i];
296		for (int j = 0; j < nLocal_; j++) {
297		int aid = AtomLocalToGlobal[j];
298	<	if (globalGroupMembership[aid] == gid)
298	>	if (globalGroupMembership[aid] == gid) {
299		groupList_[i].push_back(j);
300	+	}
301		}
302		}
303
193	–	skipsForLocalAtom.clear();
194	–	skipsForLocalAtom.reserve(nLocal_);
304
305	<	for (int i = 0; i < nLocal_; i++) {
197	<	int iglob = AtomLocalToGlobal[i];
198	<	for (int j = 0; j < nLocal_; j++) {
199	<	int jglob = AtomLocalToGlobal[j];
200	<	if (excludes.hasPair(iglob, jglob))
201	<	skipsForLocalAtom[i].push_back(j);
202	<	}
203	<	}
305	>	createGtypeCutoffMap();
306
205	–	toposForLocalAtom.clear();
206	–	toposForLocalAtom.reserve(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	–	}
229	–
307		}
308
309		void ForceMatrixDecomposition::createGtypeCutoffMap() {
310	<
310	>
311		RealType tol = 1e-6;
312	<	RealType rc;
312	>	largestRcut_ = 0.0;
313		int atid;
314		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315	<	vector<RealType> atypeCutoff;
316	<	atypeCutoff.reserve( atypes.size() );
317	<
318	<	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
319	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
315	>
316	>	map<int, RealType> atypeCutoff;
317	>
318	>	for (set<AtomType*>::iterator at = atypes.begin();
319	>	at != atypes.end(); ++at){
320		atid = (*at)->getIdent();
321	<	atypeCutoff[atid] = rc;
321	>	if (userChoseCutoff_)
322	>	atypeCutoff[atid] = userCutoff_;
323	>	else
324	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
325		}
326	<
326	>
327		vector<RealType> gTypeCutoffs;
248	–
328		// first we do a single loop over the cutoff groups to find the
329		// largest cutoff for any atypes present in this group.
330		#ifdef IS_MPI
331		vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
332	+	groupRowToGtype.resize(nGroupsInRow_);
333		for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
334		vector<int> atomListRow = getAtomsInGroupRow(cg1);
335		for (vector<int>::iterator ia = atomListRow.begin();
#	Line 275 | Line 355 | namespace OpenMD {
355
356		}
357		vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
358	+	groupColToGtype.resize(nGroupsInCol_);
359		for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
360		vector<int> atomListCol = getAtomsInGroupColumn(cg2);
361		for (vector<int>::iterator jb = atomListCol.begin();
#	Line 298 | Line 379 | namespace OpenMD {
379		}
380		}
381		#else
382	+
383		vector<RealType> groupCutoff(nGroups_, 0.0);
384	+	groupToGtype.resize(nGroups_);
385		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
386		groupCutoff[cg1] = 0.0;
387		vector<int> atomList = getAtomsInGroupRow(cg1);
388		for (vector<int>::iterator ia = atomList.begin();
389		ia != atomList.end(); ++ia) {
390		int atom1 = (*ia);
391	<	atid = identsLocal[atom1];
392	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
391	>	atid = idents[atom1];
392	>	if (atypeCutoff[atid] > groupCutoff[cg1])
393		groupCutoff[cg1] = atypeCutoff[atid];
311	–	}
394		}
395	<
395	>
396		bool gTypeFound = false;
397	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
397	>	for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
398		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
399		groupToGtype[cg1] = gt;
400		gTypeFound = true;
401		}
402		}
403	<	if (!gTypeFound) {
403	>	if (!gTypeFound) {
404		gTypeCutoffs.push_back( groupCutoff[cg1] );
405		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
406		}
#	Line 327 | Line 409 | namespace OpenMD {
409
410		// Now we find the maximum group cutoff value present in the simulation
411
412	<	vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
413	<	RealType groupMax = *groupMaxLoc;
412	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
413	>	gTypeCutoffs.end());
414
415		#ifdef IS_MPI
416	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
416	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
417	>	MPI::MAX);
418		#endif
419
420		RealType tradRcut = groupMax;
421
422	<	for (int i = 0; i < gTypeCutoffs.size();  i++) {
423	<	for (int j = 0; j < gTypeCutoffs.size();  j++) {
341	<
422	>	for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
423	>	for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {
424		RealType thisRcut;
425		switch(cutoffPolicy_) {
426		case TRADITIONAL:
427		thisRcut = tradRcut;
428	+	break;
429		case MIX:
430		thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
431	+	break;
432		case MAX:
433		thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
434	+	break;
435		default:
436		sprintf(painCave.errMsg,
437		"ForceMatrixDecomposition::createGtypeCutoffMap "
438		"hit an unknown cutoff policy!\n");
439		painCave.severity = OPENMD_ERROR;
440		painCave.isFatal = 1;
441	<	simError();
441	>	simError();
442	>	break;
443		}
444
445		pair<int,int> key = make_pair(i,j);
446		gTypeCutoffMap[key].first = thisRcut;
361	–
447		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
363	–
448		gTypeCutoffMap[key].second = thisRcut*thisRcut;
365	–
449		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
367	–
450		// sanity check
451
452		if (userChoseCutoff_) {
453		if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
454		sprintf(painCave.errMsg,
455		"ForceMatrixDecomposition::createGtypeCutoffMap "
456	<	"user-specified rCut does not match computed group Cutoff\n");
456	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
457		painCave.severity = OPENMD_ERROR;
458		painCave.isFatal = 1;
459		simError();
#	Line 381 | Line 463 | namespace OpenMD {
463		}
464		}
465
384	–
466		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467	<	int i, j;
387	<
467	>	int i, j;
468		#ifdef IS_MPI
469		i = groupRowToGtype[cg1];
470		j = groupColToGtype[cg2];
471		#else
472		i = groupToGtype[cg1];
473		j = groupToGtype[cg2];
474	<	#endif
395	<
474	>	#endif
475		return gTypeCutoffMap[make_pair(i,j)];
476		}
477
478	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
479	+	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
480	+	if (toposForAtom[atom1][j] == atom2)
481	+	return topoDist[atom1][j];
482	+	}
483	+	return 0;
484	+	}
485
486		void ForceMatrixDecomposition::zeroWorkArrays() {
487	+	pairwisePot = 0.0;
488	+	embeddingPot = 0.0;
489	+	excludedPot = 0.0;
490	+	excludedSelfPot = 0.0;
491
402	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403	–	longRangePot_[j] = 0.0;
404	–	}
405	–
492		#ifdef IS_MPI
493		if (storageLayout_ & DataStorage::dslForce) {
494		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 418 | Line 504 | namespace OpenMD {
504		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
505
506		fill(pot_col.begin(), pot_col.end(),
507	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
508	+
509	+	fill(expot_row.begin(), expot_row.end(),
510		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422	–
423	–	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
511
512	+	fill(expot_col.begin(), expot_col.end(),
513	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
514	+
515		if (storageLayout_ & DataStorage::dslParticlePot) {
516	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
517	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
516	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
517	>	0.0);
518	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
519	>	0.0);
520		}
521
522		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 433 | Line 525 | namespace OpenMD {
525		}
526
527		if (storageLayout_ & DataStorage::dslFunctional) {
528	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
529	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
528	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
529	>	0.0);
530	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
531	>	0.0);
532		}
533
534		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 444 | Line 538 | namespace OpenMD {
538		atomColData.functionalDerivative.end(), 0.0);
539		}
540
541	<	#else
542	<
541	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
542	>	fill(atomRowData.skippedCharge.begin(),
543	>	atomRowData.skippedCharge.end(), 0.0);
544	>	fill(atomColData.skippedCharge.begin(),
545	>	atomColData.skippedCharge.end(), 0.0);
546	>	}
547	>
548	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
549	>	fill(atomRowData.flucQFrc.begin(),
550	>	atomRowData.flucQFrc.end(), 0.0);
551	>	fill(atomColData.flucQFrc.begin(),
552	>	atomColData.flucQFrc.end(), 0.0);
553	>	}
554	>
555	>	if (storageLayout_ & DataStorage::dslElectricField) {
556	>	fill(atomRowData.electricField.begin(),
557	>	atomRowData.electricField.end(), V3Zero);
558	>	fill(atomColData.electricField.begin(),
559	>	atomColData.electricField.end(), V3Zero);
560	>	}
561	>
562	>	#endif
563	>	// even in parallel, we need to zero out the local arrays:
564	>
565		if (storageLayout_ & DataStorage::dslParticlePot) {
566		fill(snap_->atomData.particlePot.begin(),
567		snap_->atomData.particlePot.end(), 0.0);
#	Line 455 | Line 571 | namespace OpenMD {
571		fill(snap_->atomData.density.begin(),
572		snap_->atomData.density.end(), 0.0);
573		}
574	+
575		if (storageLayout_ & DataStorage::dslFunctional) {
576		fill(snap_->atomData.functional.begin(),
577		snap_->atomData.functional.end(), 0.0);
578		}
579	+
580		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
581		fill(snap_->atomData.functionalDerivative.begin(),
582		snap_->atomData.functionalDerivative.end(), 0.0);
583		}
584	<	#endif
585	<
584	>
585	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
586	>	fill(snap_->atomData.skippedCharge.begin(),
587	>	snap_->atomData.skippedCharge.end(), 0.0);
588	>	}
589	>
590	>	if (storageLayout_ & DataStorage::dslElectricField) {
591	>	fill(snap_->atomData.electricField.begin(),
592	>	snap_->atomData.electricField.end(), V3Zero);
593	>	}
594		}
595
596
#	Line 474 | Line 600 | namespace OpenMD {
600		#ifdef IS_MPI
601
602		// gather up the atomic positions
603	<	AtomCommVectorRow->gather(snap_->atomData.position,
603	>	AtomPlanVectorRow->gather(snap_->atomData.position,
604		atomRowData.position);
605	<	AtomCommVectorColumn->gather(snap_->atomData.position,
605	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
606		atomColData.position);
607
608		// gather up the cutoff group positions
609	<	cgCommVectorRow->gather(snap_->cgData.position,
609	>
610	>	cgPlanVectorRow->gather(snap_->cgData.position,
611		cgRowData.position);
612	<	cgCommVectorColumn->gather(snap_->cgData.position,
612	>
613	>	cgPlanVectorColumn->gather(snap_->cgData.position,
614		cgColData.position);
615	+
616	+
617	+
618	+	if (needVelocities_) {
619	+	// gather up the atomic velocities
620	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
621	+	atomColData.velocity);
622	+
623	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
624	+	cgColData.velocity);
625	+	}
626	+
627
628		// if needed, gather the atomic rotation matrices
629		if (storageLayout_ & DataStorage::dslAmat) {
630	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
630	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
631		atomRowData.aMat);
632	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
632	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
633		atomColData.aMat);
634		}
635	<
636	<	// if needed, gather the atomic eletrostatic frames
637	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
638	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
639	<	atomRowData.electroFrame);
640	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
641	<	atomColData.electroFrame);
635	>
636	>	// if needed, gather the atomic eletrostatic information
637	>	if (storageLayout_ & DataStorage::dslDipole) {
638	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
639	>	atomRowData.dipole);
640	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
641	>	atomColData.dipole);
642		}
643	+
644	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
645	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
646	+	atomRowData.quadrupole);
647	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
648	+	atomColData.quadrupole);
649	+	}
650	+
651	+	// if needed, gather the atomic fluctuating charge values
652	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
653	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
654	+	atomRowData.flucQPos);
655	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
656	+	atomColData.flucQPos);
657	+	}
658	+
659		#endif
660		}
661
#	Line 513 | Line 669 | namespace OpenMD {
669
670		if (storageLayout_ & DataStorage::dslDensity) {
671
672	<	AtomCommRealRow->scatter(atomRowData.density,
672	>	AtomPlanRealRow->scatter(atomRowData.density,
673		snap_->atomData.density);
674
675		int n = snap_->atomData.density.size();
676		vector<RealType> rho_tmp(n, 0.0);
677	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
677	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
678		for (int i = 0; i < n; i++)
679		snap_->atomData.density[i] += rho_tmp[i];
680		}
681	+
682	+	// this isn't necessary if we don't have polarizable atoms, but
683	+	// we'll leave it here for now.
684	+	if (storageLayout_ & DataStorage::dslElectricField) {
685	+
686	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
687	+	snap_->atomData.electricField);
688	+
689	+	int n = snap_->atomData.electricField.size();
690	+	vector<Vector3d> field_tmp(n, V3Zero);
691	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
692	+	field_tmp);
693	+	for (int i = 0; i < n; i++)
694	+	snap_->atomData.electricField[i] += field_tmp[i];
695	+	}
696		#endif
697		}
698
#	Line 534 | Line 705 | namespace OpenMD {
705		storageLayout_ = sman_->getStorageLayout();
706		#ifdef IS_MPI
707		if (storageLayout_ & DataStorage::dslFunctional) {
708	<	AtomCommRealRow->gather(snap_->atomData.functional,
708	>	AtomPlanRealRow->gather(snap_->atomData.functional,
709		atomRowData.functional);
710	<	AtomCommRealColumn->gather(snap_->atomData.functional,
710	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
711		atomColData.functional);
712		}
713
714		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
715	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
715	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
716		atomRowData.functionalDerivative);
717	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
717	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
718		atomColData.functionalDerivative);
719		}
720		#endif
#	Line 557 | Line 728 | namespace OpenMD {
728		int n = snap_->atomData.force.size();
729		vector<Vector3d> frc_tmp(n, V3Zero);
730
731	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
731	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
732		for (int i = 0; i < n; i++) {
733		snap_->atomData.force[i] += frc_tmp[i];
734		frc_tmp[i] = 0.0;
735		}
736
737	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
738	<	for (int i = 0; i < n; i++)
737	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
738	>	for (int i = 0; i < n; i++) {
739		snap_->atomData.force[i] += frc_tmp[i];
740	<
741	<
740	>	}
741	>
742		if (storageLayout_ & DataStorage::dslTorque) {
743
744	<	int nt = snap_->atomData.force.size();
744	>	int nt = snap_->atomData.torque.size();
745		vector<Vector3d> trq_tmp(nt, V3Zero);
746
747	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
748	<	for (int i = 0; i < n; i++) {
747	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
748	>	for (int i = 0; i < nt; i++) {
749		snap_->atomData.torque[i] += trq_tmp[i];
750		trq_tmp[i] = 0.0;
751		}
752
753	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
754	<	for (int i = 0; i < n; i++)
753	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
754	>	for (int i = 0; i < nt; i++)
755		snap_->atomData.torque[i] += trq_tmp[i];
756		}
757	+
758	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
759	+
760	+	int ns = snap_->atomData.skippedCharge.size();
761	+	vector<RealType> skch_tmp(ns, 0.0);
762	+
763	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
764	+	for (int i = 0; i < ns; i++) {
765	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
766	+	skch_tmp[i] = 0.0;
767	+	}
768	+
769	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
770	+	for (int i = 0; i < ns; i++)
771	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
772	+
773	+	}
774
775	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
776	+
777	+	int nq = snap_->atomData.flucQFrc.size();
778	+	vector<RealType> fqfrc_tmp(nq, 0.0);
779	+
780	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
781	+	for (int i = 0; i < nq; i++) {
782	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
783	+	fqfrc_tmp[i] = 0.0;
784	+	}
785	+
786	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
787	+	for (int i = 0; i < nq; i++)
788	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
789	+
790	+	}
791	+
792	+	if (storageLayout_ & DataStorage::dslElectricField) {
793	+
794	+	int nef = snap_->atomData.electricField.size();
795	+	vector<Vector3d> efield_tmp(nef, V3Zero);
796	+
797	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
798	+	for (int i = 0; i < nef; i++) {
799	+	snap_->atomData.electricField[i] += efield_tmp[i];
800	+	efield_tmp[i] = 0.0;
801	+	}
802	+
803	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
804	+	for (int i = 0; i < nef; i++)
805	+	snap_->atomData.electricField[i] += efield_tmp[i];
806	+	}
807	+
808	+
809		nLocal_ = snap_->getNumberOfAtoms();
810
811		vector<potVec> pot_temp(nLocal_,
812		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
813	+	vector<potVec> expot_temp(nLocal_,
814	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
815
816		// scatter/gather pot_row into the members of my column
817
818	<	AtomCommPotRow->scatter(pot_row, pot_temp);
818	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
819	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
820
821	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
822	<	pot_local += pot_temp[ii];
823	<
821	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
822	>	pairwisePot += pot_temp[ii];
823	>
824	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
825	>	excludedPot += expot_temp[ii];
826	>
827	>	if (storageLayout_ & DataStorage::dslParticlePot) {
828	>	// This is the pairwise contribution to the particle pot.  The
829	>	// embedding contribution is added in each of the low level
830	>	// non-bonded routines.  In single processor, this is done in
831	>	// unpackInteractionData, not in collectData.
832	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
833	>	for (int i = 0; i < nLocal_; i++) {
834	>	// factor of two is because the total potential terms are divided
835	>	// by 2 in parallel due to row/ column scatter
836	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
837	>	}
838	>	}
839	>	}
840	>
841		fill(pot_temp.begin(), pot_temp.end(),
842		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
843	+	fill(expot_temp.begin(), expot_temp.end(),
844	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
845
846	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
846	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
847	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
848
849		for (int ii = 0;  ii < pot_temp.size(); ii++ )
850	<	pot_local += pot_temp[ii];
850	>	pairwisePot += pot_temp[ii];
851	>
852	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
853	>	excludedPot += expot_temp[ii];
854	>
855	>	if (storageLayout_ & DataStorage::dslParticlePot) {
856	>	// This is the pairwise contribution to the particle pot.  The
857	>	// embedding contribution is added in each of the low level
858	>	// non-bonded routines.  In single processor, this is done in
859	>	// unpackInteractionData, not in collectData.
860	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
861	>	for (int i = 0; i < nLocal_; i++) {
862	>	// factor of two is because the total potential terms are divided
863	>	// by 2 in parallel due to row/ column scatter
864	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
865	>	}
866	>	}
867	>	}
868
869	+	if (storageLayout_ & DataStorage::dslParticlePot) {
870	+	int npp = snap_->atomData.particlePot.size();
871	+	vector<RealType> ppot_temp(npp, 0.0);
872	+
873	+	// This is the direct or embedding contribution to the particle
874	+	// pot.
875	+
876	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
877	+	for (int i = 0; i < npp; i++) {
878	+	snap_->atomData.particlePot[i] += ppot_temp[i];
879	+	}
880	+
881	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
882	+
883	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
884	+	for (int i = 0; i < npp; i++) {
885	+	snap_->atomData.particlePot[i] += ppot_temp[i];
886	+	}
887	+	}
888	+
889	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
890	+	RealType ploc1 = pairwisePot[ii];
891	+	RealType ploc2 = 0.0;
892	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
893	+	pairwisePot[ii] = ploc2;
894	+	}
895	+
896	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
897	+	RealType ploc1 = excludedPot[ii];
898	+	RealType ploc2 = 0.0;
899	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
900	+	excludedPot[ii] = ploc2;
901	+	}
902	+
903	+	// Here be dragons.
904	+	MPI::Intracomm col = colComm.getComm();
905	+
906	+	col.Allreduce(MPI::IN_PLACE,
907	+	&snap_->frameData.conductiveHeatFlux[0], 3,
908	+	MPI::REALTYPE, MPI::SUM);
909	+
910	+
911		#endif
912	+
913		}
914
915	<	int ForceMatrixDecomposition::getNAtomsInRow() {
915	>	/**
916	>	* Collects information obtained during the post-pair (and embedding
917	>	* functional) loops onto local data structures.
918	>	*/
919	>	void ForceMatrixDecomposition::collectSelfData() {
920	>	snap_ = sman_->getCurrentSnapshot();
921	>	storageLayout_ = sman_->getStorageLayout();
922	>
923	>	#ifdef IS_MPI
924	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
925	>	RealType ploc1 = embeddingPot[ii];
926	>	RealType ploc2 = 0.0;
927	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
928	>	embeddingPot[ii] = ploc2;
929	>	}
930	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
931	>	RealType ploc1 = excludedSelfPot[ii];
932	>	RealType ploc2 = 0.0;
933	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
934	>	excludedSelfPot[ii] = ploc2;
935	>	}
936	>	#endif
937	>
938	>	}
939	>
940	>
941	>
942	>	int& ForceMatrixDecomposition::getNAtomsInRow() {
943		#ifdef IS_MPI
944		return nAtomsInRow_;
945		#else
#	Line 618 | Line 950 | namespace OpenMD {
950		/**
951		* returns the list of atoms belonging to this group.
952		*/
953	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
953	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
954		#ifdef IS_MPI
955		return groupListRow_[cg1];
956		#else
#	Line 626 | Line 958 | namespace OpenMD {
958		#endif
959		}
960
961	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
961	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
962		#ifdef IS_MPI
963		return groupListCol_[cg2];
964		#else
#	Line 643 | Line 975 | namespace OpenMD {
975		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
976		#endif
977
978	<	snap_->wrapVector(d);
978	>	if (usePeriodicBoundaryConditions_) {
979	>	snap_->wrapVector(d);
980	>	}
981		return d;
982		}
983
984	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
985	+	#ifdef IS_MPI
986	+	return cgColData.velocity[cg2];
987	+	#else
988	+	return snap_->cgData.velocity[cg2];
989	+	#endif
990	+	}
991
992	+	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
993	+	#ifdef IS_MPI
994	+	return atomColData.velocity[atom2];
995	+	#else
996	+	return snap_->atomData.velocity[atom2];
997	+	#endif
998	+	}
999	+
1000	+
1001		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
1002
1003		Vector3d d;
#	Line 657 | Line 1007 | namespace OpenMD {
1007		#else
1008		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1009		#endif
1010	<
1011	<	snap_->wrapVector(d);
1010	>	if (usePeriodicBoundaryConditions_) {
1011	>	snap_->wrapVector(d);
1012	>	}
1013		return d;
1014		}
1015
#	Line 670 | Line 1021 | namespace OpenMD {
1021		#else
1022		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1023		#endif
1024	<
1025	<	snap_->wrapVector(d);
1024	>	if (usePeriodicBoundaryConditions_) {
1025	>	snap_->wrapVector(d);
1026	>	}
1027		return d;
1028		}
1029
1030	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1030	>	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1031		#ifdef IS_MPI
1032		return massFactorsRow[atom1];
1033		#else
1034	<	return massFactorsLocal[atom1];
1034	>	return massFactors[atom1];
1035		#endif
1036		}
1037
1038	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1038	>	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1039		#ifdef IS_MPI
1040		return massFactorsCol[atom2];
1041		#else
1042	<	return massFactorsLocal[atom2];
1042	>	return massFactors[atom2];
1043		#endif
1044
1045		}
#	Line 700 | Line 1052 | namespace OpenMD {
1052		#else
1053		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1054		#endif
1055	<
1056	<	snap_->wrapVector(d);
1055	>	if (usePeriodicBoundaryConditions_) {
1056	>	snap_->wrapVector(d);
1057	>	}
1058		return d;
1059		}
1060
1061	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
1062	<	#ifdef IS_MPI
710	<	return skipsForRowAtom[atom1];
711	<	#else
712	<	return skipsForLocalAtom[atom1];
713	<	#endif
1061	>	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1062	>	return excludesForAtom[atom1];
1063		}
1064
1065		/**
1066	<	* 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
1066	>	* We need to exclude some overcounted interactions that result from
1067		* the parallel decomposition.
1068		*/
1069	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1069	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1070		int unique_id_1, unique_id_2;
1071	<
1071	>
1072		#ifdef IS_MPI
1073		// in MPI, we have to look up the unique IDs for each atom
1074		unique_id_1 = AtomRowToGlobal[atom1];
1075		unique_id_2 = AtomColToGlobal[atom2];
1076	+	// group1 = cgRowToGlobal[cg1];
1077	+	// group2 = cgColToGlobal[cg2];
1078	+	#else
1079	+	unique_id_1 = AtomLocalToGlobal[atom1];
1080	+	unique_id_2 = AtomLocalToGlobal[atom2];
1081	+	int group1 = cgLocalToGlobal[cg1];
1082	+	int group2 = cgLocalToGlobal[cg2];
1083	+	#endif
1084
731	–	// this situation should only arise in MPI simulations
1085		if (unique_id_1 == unique_id_2) return true;
1086	<
1086	>
1087	>	#ifdef IS_MPI
1088		// this prevents us from doing the pair on multiple processors
1089		if (unique_id_1 < unique_id_2) {
1090		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1091		} else {
1092	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1092	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1093		}
1094	<	#else
1095	<	// in the normal loop, the atom numbers are unique
1096	<	unique_id_1 = atom1;
1097	<	unique_id_2 = atom2;
1094	>	#endif
1095	>
1096	>	#ifndef IS_MPI
1097	>	if (group1 == group2) {
1098	>	if (unique_id_1 < unique_id_2) return true;
1099	>	}
1100		#endif
1101
1102	<	#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
1102	>	return false;
1103		}
1104
1105	<	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
1105	>	/**
1106	>	* We need to handle the interactions for atoms who are involved in
1107	>	* the same rigid body as well as some short range interactions
1108	>	* (bonds, bends, torsions) differently from other interactions.
1109	>	* We'll still visit the pairwise routines, but with a flag that
1110	>	* tells those routines to exclude the pair from direct long range
1111	>	* interactions.  Some indirect interactions (notably reaction
1112	>	* field) must still be handled for these pairs.
1113	>	*/
1114	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1115	>
1116	>	// excludesForAtom was constructed to use row/column indices in the MPI
1117	>	// version, and to use local IDs in the non-MPI version:
1118
1119	<	#ifdef IS_MPI
1120	<	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
1121	<	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
1119	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1120	>	i != excludesForAtom[atom1].end(); ++i) {
1121	>	if ( (*i) == atom2 ) return true;
1122		}
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
1123
1124	<	// zero is default for unconnected (i.e. normal) pair interactions
772	<	return 0;
1124	>	return false;
1125		}
1126
1127	+
1128		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1129		#ifdef IS_MPI
1130		atomRowData.force[atom1] += fg;
#	Line 789 | Line 1142 | namespace OpenMD {
1142		}
1143
1144		// filling interaction blocks with pointers
1145	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1146	<	InteractionData idat;
1145	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1146	>	int atom1, int atom2) {
1147
1148	+	idat.excluded = excludeAtomPair(atom1, atom2);
1149	+
1150		#ifdef IS_MPI
1151	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1152	+	idat.atid1 = identsRow[atom1];
1153	+	idat.atid2 = identsCol[atom2];
1154	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1155	+	//                         ff_->getAtomType(identsCol[atom2]) );
1156
797	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
798	–	ff_->getAtomType(identsCol[atom2]) );
799	–
800	–
1157		if (storageLayout_ & DataStorage::dslAmat) {
1158		idat.A1 = &(atomRowData.aMat[atom1]);
1159		idat.A2 = &(atomColData.aMat[atom2]);
1160		}
1161
806	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
807	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
808	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
809	–	}
810	–
1162		if (storageLayout_ & DataStorage::dslTorque) {
1163		idat.t1 = &(atomRowData.torque[atom1]);
1164		idat.t2 = &(atomColData.torque[atom2]);
1165	+	}
1166	+
1167	+	if (storageLayout_ & DataStorage::dslDipole) {
1168	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1169	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1170	+	}
1171	+
1172	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1173	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1174	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1175		}
1176
1177		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 833 | Line 1194 | namespace OpenMD {
1194		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1195		}
1196
1197	<	#else
1197	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1198	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1199	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1200	>	}
1201
1202	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
1203	<	ff_->getAtomType(identsLocal[atom2]) );
1202	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1203	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1204	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1205	>	}
1206
1207	+	#else
1208	+
1209	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1210	+	idat.atid1 = idents[atom1];
1211	+	idat.atid2 = idents[atom2];
1212	+
1213		if (storageLayout_ & DataStorage::dslAmat) {
1214		idat.A1 = &(snap_->atomData.aMat[atom1]);
1215		idat.A2 = &(snap_->atomData.aMat[atom2]);
1216		}
1217
846	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
847	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
848	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
849	–	}
850	–
1218		if (storageLayout_ & DataStorage::dslTorque) {
1219		idat.t1 = &(snap_->atomData.torque[atom1]);
1220		idat.t2 = &(snap_->atomData.torque[atom2]);
1221		}
1222
1223	<	if (storageLayout_ & DataStorage::dslDensity) {
1223	>	if (storageLayout_ & DataStorage::dslDipole) {
1224	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1225	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1226	>	}
1227	>
1228	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1229	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1230	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1231	>	}
1232	>
1233	>	if (storageLayout_ & DataStorage::dslDensity) {
1234		idat.rho1 = &(snap_->atomData.density[atom1]);
1235		idat.rho2 = &(snap_->atomData.density[atom2]);
1236		}
#	Line 873 | Line 1250 | namespace OpenMD {
1250		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1251		}
1252
1253	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1254	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1255	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1256	+	}
1257	+
1258	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1259	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1260	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1261	+	}
1262	+
1263		#endif
877	–	return idat;
1264		}
1265
1266
1267	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
1267	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1268		#ifdef IS_MPI
1269	<	pot_row[atom1] += 0.5 *  *(idat.pot);
1270	<	pot_col[atom2] += 0.5 *  *(idat.pot);
1269	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1270	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1271	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1272	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1273
1274		atomRowData.force[atom1] += *(idat.f1);
1275		atomColData.force[atom2] -= *(idat.f1);
888	–	#else
889	–	longRangePot_ += *(idat.pot);
890	–
891	–	snap_->atomData.force[atom1] += *(idat.f1);
892	–	snap_->atomData.force[atom2] -= *(idat.f1);
893	–	#endif
1276
1277	<	}
1277	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1278	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1279	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1280	>	}
1281
1282	+	if (storageLayout_ & DataStorage::dslElectricField) {
1283	+	atomRowData.electricField[atom1] += *(idat.eField1);
1284	+	atomColData.electricField[atom2] += *(idat.eField2);
1285	+	}
1286
1287	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1287	>	#else
1288	>	pairwisePot += *(idat.pot);
1289	>	excludedPot += *(idat.excludedPot);
1290
1291	<	InteractionData idat;
1292	<	#ifdef IS_MPI
902	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
903	<	ff_->getAtomType(identsCol[atom2]) );
1291	>	snap_->atomData.force[atom1] += *(idat.f1);
1292	>	snap_->atomData.force[atom2] -= *(idat.f1);
1293
1294	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1295	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1296	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1294	>	if (idat.doParticlePot) {
1295	>	// This is the pairwise contribution to the particle pot.  The
1296	>	// embedding contribution is added in each of the low level
1297	>	// non-bonded routines.  In parallel, this calculation is done
1298	>	// in collectData, not in unpackInteractionData.
1299	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1300	>	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1301		}
1302	<	if (storageLayout_ & DataStorage::dslTorque) {
1303	<	idat.t1 = &(atomRowData.torque[atom1]);
1304	<	idat.t2 = &(atomColData.torque[atom2]);
1302	>
1303	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1304	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1305	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1306		}
913	–	#else
914	–	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
915	–	ff_->getAtomType(identsLocal[atom2]) );
1307
1308	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1309	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1310	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1308	>	if (storageLayout_ & DataStorage::dslElectricField) {
1309	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1310	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1311		}
1312	<	if (storageLayout_ & DataStorage::dslTorque) {
1313	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1314	<	idat.t2 = &(snap_->atomData.torque[atom2]);
924	<	}
925	<	#endif
1312	>
1313	>	#endif
1314	>
1315		}
1316
1317		/*
#	Line 931 | Line 1320 | namespace OpenMD {
1320		* first element of pair is row-indexed CutoffGroup
1321		* second element of pair is column-indexed CutoffGroup
1322		*/
1323	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1324	<
1325	<	vector<pair<int, int> > neighborList;
1323	>	void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1324	>
1325	>	neighborList.clear();
1326		groupCutoffs cuts;
1327	<	#ifdef IS_MPI
939	<	cellListRow_.clear();
940	<	cellListCol_.clear();
941	<	#else
942	<	cellList_.clear();
943	<	#endif
1327	>	bool doAllPairs = false;
1328
1329		RealType rList_ = (largestRcut_ + skinThickness_);
946	–	RealType rl2 = rList_ * rList_;
1330		Snapshot* snap_ = sman_->getCurrentSnapshot();
1331	<	Mat3x3d Hmat = snap_->getHmat();
1332	<	Vector3d Hx = Hmat.getColumn(0);
950	<	Vector3d Hy = Hmat.getColumn(1);
951	<	Vector3d Hz = Hmat.getColumn(2);
1331	>	Mat3x3d box;
1332	>	Mat3x3d invBox;
1333
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();
1334		Vector3d rs, scaled, dr;
1335		Vector3i whichCell;
1336		int cellIndex;
1337
1338		#ifdef IS_MPI
1339	<	for (int i = 0; i < nGroupsInRow_; i++) {
1340	<	rs = cgRowData.position[i];
1341	<	// scaled positions relative to the box vectors
1342	<	scaled = invHmat * rs;
1343	<	// wrap the vector back into the unit box by subtracting integer box
1344	<	// numbers
1345	<	for (int j = 0; j < 3; j++)
1346	<	scaled[j] -= roundMe(scaled[j]);
1347	<
1348	<	// find xyz-indices of cell that cutoffGroup is in.
1349	<	whichCell.x() = nCells_.x() * scaled.x();
1350	<	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);
1339	>	cellListRow_.clear();
1340	>	cellListCol_.clear();
1341	>	#else
1342	>	cellList_.clear();
1343	>	#endif
1344	>
1345	>	if (!usePeriodicBoundaryConditions_) {
1346	>	box = snap_->getBoundingBox();
1347	>	invBox = snap_->getInvBoundingBox();
1348	>	} else {
1349	>	box = snap_->getHmat();
1350	>	invBox = snap_->getInvHmat();
1351		}
1352	<
1353	<	for (int i = 0; i < nGroupsInCol_; i++) {
1354	<	rs = cgColData.position[i];
1355	<	// scaled positions relative to the box vectors
1356	<	scaled = invHmat * rs;
1357	<	// wrap the vector back into the unit box by subtracting integer box
1358	<	// numbers
1359	<	for (int j = 0; j < 3; j++)
1360	<	scaled[j] -= roundMe(scaled[j]);
1361	<
1362	<	// find xyz-indices of cell that cutoffGroup is in.
1363	<	whichCell.x() = nCells_.x() * scaled.x();
1364	<	whichCell.y() = nCells_.y() * scaled.y();
1365	<	whichCell.z() = nCells_.z() * scaled.z();
1366	<
1367	<	// find single index of this cell:
1368	<	cellIndex = Vlinear(whichCell, nCells_);
1369	<	// add this cutoff group to the list of groups in this cell;
1370	<	cellListCol_[cellIndex].push_back(i);
1371	<	}
1352	>
1353	>	Vector3d boxX = box.getColumn(0);
1354	>	Vector3d boxY = box.getColumn(1);
1355	>	Vector3d boxZ = box.getColumn(2);
1356	>
1357	>	nCells_.x() = (int) ( boxX.length() )/ rList_;
1358	>	nCells_.y() = (int) ( boxY.length() )/ rList_;
1359	>	nCells_.z() = (int) ( boxZ.length() )/ rList_;
1360	>
1361	>	// handle small boxes where the cell offsets can end up repeating cells
1362	>
1363	>	if (nCells_.x() < 3) doAllPairs = true;
1364	>	if (nCells_.y() < 3) doAllPairs = true;
1365	>	if (nCells_.z() < 3) doAllPairs = true;
1366	>
1367	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1368	>
1369	>	#ifdef IS_MPI
1370	>	cellListRow_.resize(nCtot);
1371	>	cellListCol_.resize(nCtot);
1372		#else
1373	<	for (int i = 0; i < nGroups_; i++) {
1374	<	rs = snap_->cgData.position[i];
1375	<	// scaled positions relative to the box vectors
1376	<	scaled = invHmat * rs;
1377	<	// wrap the vector back into the unit box by subtracting integer box
1378	<	// numbers
1379	<	for (int j = 0; j < 3; j++)
1380	<	scaled[j] -= roundMe(scaled[j]);
1373	>	cellList_.resize(nCtot);
1374	>	#endif
1375	>
1376	>	if (!doAllPairs) {
1377	>	#ifdef IS_MPI
1378	>
1379	>	for (int i = 0; i < nGroupsInRow_; i++) {
1380	>	rs = cgRowData.position[i];
1381	>
1382	>	// scaled positions relative to the box vectors
1383	>	scaled = invBox * rs;
1384	>
1385	>	// wrap the vector back into the unit box by subtracting integer box
1386	>	// numbers
1387	>	for (int j = 0; j < 3; j++) {
1388	>	scaled[j] -= roundMe(scaled[j]);
1389	>	scaled[j] += 0.5;
1390	>	// Handle the special case when an object is exactly on the
1391	>	// boundary (a scaled coordinate of 1.0 is the same as
1392	>	// scaled coordinate of 0.0)
1393	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1394	>	}
1395	>
1396	>	// find xyz-indices of cell that cutoffGroup is in.
1397	>	whichCell.x() = nCells_.x() * scaled.x();
1398	>	whichCell.y() = nCells_.y() * scaled.y();
1399	>	whichCell.z() = nCells_.z() * scaled.z();
1400	>
1401	>	// find single index of this cell:
1402	>	cellIndex = Vlinear(whichCell, nCells_);
1403	>
1404	>	// add this cutoff group to the list of groups in this cell;
1405	>	cellListRow_[cellIndex].push_back(i);
1406	>	}
1407	>	for (int i = 0; i < nGroupsInCol_; i++) {
1408	>	rs = cgColData.position[i];
1409	>
1410	>	// scaled positions relative to the box vectors
1411	>	scaled = invBox * rs;
1412	>
1413	>	// wrap the vector back into the unit box by subtracting integer box
1414	>	// numbers
1415	>	for (int j = 0; j < 3; j++) {
1416	>	scaled[j] -= roundMe(scaled[j]);
1417	>	scaled[j] += 0.5;
1418	>	// Handle the special case when an object is exactly on the
1419	>	// boundary (a scaled coordinate of 1.0 is the same as
1420	>	// scaled coordinate of 0.0)
1421	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1422	>	}
1423	>
1424	>	// find xyz-indices of cell that cutoffGroup is in.
1425	>	whichCell.x() = nCells_.x() * scaled.x();
1426	>	whichCell.y() = nCells_.y() * scaled.y();
1427	>	whichCell.z() = nCells_.z() * scaled.z();
1428	>
1429	>	// find single index of this cell:
1430	>	cellIndex = Vlinear(whichCell, nCells_);
1431	>
1432	>	// add this cutoff group to the list of groups in this cell;
1433	>	cellListCol_[cellIndex].push_back(i);
1434	>	}
1435	>
1436	>	#else
1437	>	for (int i = 0; i < nGroups_; i++) {
1438	>	rs = snap_->cgData.position[i];
1439	>
1440	>	// scaled positions relative to the box vectors
1441	>	scaled = invBox * rs;
1442	>
1443	>	// wrap the vector back into the unit box by subtracting integer box
1444	>	// numbers
1445	>	for (int j = 0; j < 3; j++) {
1446	>	scaled[j] -= roundMe(scaled[j]);
1447	>	scaled[j] += 0.5;
1448	>	// Handle the special case when an object is exactly on the
1449	>	// boundary (a scaled coordinate of 1.0 is the same as
1450	>	// scaled coordinate of 0.0)
1451	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1452	>	}
1453	>
1454	>	// find xyz-indices of cell that cutoffGroup is in.
1455	>	whichCell.x() = nCells_.x() * scaled.x();
1456	>	whichCell.y() = nCells_.y() * scaled.y();
1457	>	whichCell.z() = nCells_.z() * scaled.z();
1458	>
1459	>	// find single index of this cell:
1460	>	cellIndex = Vlinear(whichCell, nCells_);
1461	>
1462	>	// add this cutoff group to the list of groups in this cell;
1463	>	cellList_[cellIndex].push_back(i);
1464	>	}
1465
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	–	}
1466		#endif
1467
1468	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1469	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1470	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1471	<	Vector3i m1v(m1x, m1y, m1z);
1472	<	int m1 = Vlinear(m1v, nCells_);
1029	<
1030	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1031	<	os != cellOffsets_.end(); ++os) {
1468	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1469	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1470	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1471	>	Vector3i m1v(m1x, m1y, m1z);
1472	>	int m1 = Vlinear(m1v, nCells_);
1473
1474	<	Vector3i m2v = m1v + (*os);
1475	<
1476	<	if (m2v.x() >= nCells_.x()) {
1477	<	m2v.x() = 0;
1478	<	} 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_);
1474	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1475	>	os != cellOffsets_.end(); ++os) {
1476	>
1477	>	Vector3i m2v = m1v + (*os);
1478	>
1479
1480	<	#ifdef IS_MPI
1481	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1482	<	j1 != cellListRow_[m1].end(); ++j1) {
1483	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1484	<	j2 != cellListCol_[m2].end(); ++j2) {
1485	<
1486	<	// Always do this if we're in different cells or if
1487	<	// we're in the same cell and the global index of the
1488	<	// j2 cutoff group is less than the j1 cutoff group
1480	>	if (m2v.x() >= nCells_.x()) {
1481	>	m2v.x() = 0;
1482	>	} else if (m2v.x() < 0) {
1483	>	m2v.x() = nCells_.x() - 1;
1484	>	}
1485	>
1486	>	if (m2v.y() >= nCells_.y()) {
1487	>	m2v.y() = 0;
1488	>	} else if (m2v.y() < 0) {
1489	>	m2v.y() = nCells_.y() - 1;
1490	>	}
1491	>
1492	>	if (m2v.z() >= nCells_.z()) {
1493	>	m2v.z() = 0;
1494	>	} else if (m2v.z() < 0) {
1495	>	m2v.z() = nCells_.z() - 1;
1496	>	}
1497
1498	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1498	>	int m2 = Vlinear (m2v, nCells_);
1499	>
1500	>	#ifdef IS_MPI
1501	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1502	>	j1 != cellListRow_[m1].end(); ++j1) {
1503	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1504	>	j2 != cellListCol_[m2].end(); ++j2) {
1505	>
1506	>	// In parallel, we need to visit *all* pairs of row
1507	>	// & column indicies and will divide labor in the
1508	>	// force evaluation later.
1509		dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1510	<	snap_->wrapVector(dr);
1510	>	if (usePeriodicBoundaryConditions_) {
1511	>	snap_->wrapVector(dr);
1512	>	}
1513		cuts = getGroupCutoffs( (*j1), (*j2) );
1514		if (dr.lengthSquare() < cuts.third) {
1515		neighborList.push_back(make_pair((*j1), (*j2)));
1516	<	}
1516	>	}
1517		}
1518		}
1074	–	}
1519		#else
1520	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1521	<	j1 != cellList_[m1].end(); ++j1) {
1522	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1523	<	j2 != cellList_[m2].end(); ++j2) {
1524	<
1525	<	// Always do this if we're in different cells or if
1526	<	// we're in the same cell and the global index of the
1527	<	// j2 cutoff group is less than the j1 cutoff group
1520	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1521	>	j1 != cellList_[m1].end(); ++j1) {
1522	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1523	>	j2 != cellList_[m2].end(); ++j2) {
1524	>
1525	>	// Always do this if we're in different cells or if
1526	>	// we're in the same cell and the global index of
1527	>	// the j2 cutoff group is greater than or equal to
1528	>	// the j1 cutoff group.  Note that Rappaport's code
1529	>	// has a "less than" conditional here, but that
1530	>	// deals with atom-by-atom computation.  OpenMD
1531	>	// allows atoms within a single cutoff group to
1532	>	// interact with each other.
1533
1534	<	if (m2 != m1 || (*j2) < (*j1)) {
1535	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1536	<	snap_->wrapVector(dr);
1537	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1538	<	if (dr.lengthSquare() < cuts.third) {
1539	<	neighborList.push_back(make_pair((*j1), (*j2)));
1534	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1535	>
1536	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1537	>	if (usePeriodicBoundaryConditions_) {
1538	>	snap_->wrapVector(dr);
1539	>	}
1540	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1541	>	if (dr.lengthSquare() < cuts.third) {
1542	>	neighborList.push_back(make_pair((*j1), (*j2)));
1543	>	}
1544		}
1545		}
1546		}
1094	–	}
1547		#endif
1548	+	}
1549		}
1550		}
1551		}
1552	+	} else {
1553	+	// branch to do all cutoff group pairs
1554	+	#ifdef IS_MPI
1555	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1556	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1557	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1558	+	if (usePeriodicBoundaryConditions_) {
1559	+	snap_->wrapVector(dr);
1560	+	}
1561	+	cuts = getGroupCutoffs( j1, j2 );
1562	+	if (dr.lengthSquare() < cuts.third) {
1563	+	neighborList.push_back(make_pair(j1, j2));
1564	+	}
1565	+	}
1566	+	}
1567	+	#else
1568	+	// include all groups here.
1569	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1570	+	// include self group interactions j2 == j1
1571	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1572	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1573	+	if (usePeriodicBoundaryConditions_) {
1574	+	snap_->wrapVector(dr);
1575	+	}
1576	+	cuts = getGroupCutoffs( j1, j2 );
1577	+	if (dr.lengthSquare() < cuts.third) {
1578	+	neighborList.push_back(make_pair(j1, j2));
1579	+	}
1580	+	}
1581	+	}
1582	+	#endif
1583		}
1584	<
1584	>
1585		// save the local cutoff group positions for the check that is
1586		// done on each loop:
1587		saved_CG_positions_.clear();
1588		for (int i = 0; i < nGroups_; i++)
1589		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1106	–
1107	–	return neighborList;
1590		}
1591		} //end namespace OpenMD

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