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

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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1547 by gezelter, Mon Apr 11 18:44:16 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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/ForceDecomposition.hpp"
42	>	#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
44		#include "nonbonded/NonBondedInteraction.hpp"
45		#include "brains/SnapshotManager.hpp"
46	+	#include "brains/PairList.hpp"
47
48		using namespace std;
49		namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	+
53	+	// Row and colum scans must visit all surrounding cells
54	+	cellOffsets_.clear();
55	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
56	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
57	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
58	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
65	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
66	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
67	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
74	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
75	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
76	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
82	+	}
83	+
84	+
85		/**
86		* distributeInitialData is essentially a copy of the older fortran
87		* SimulationSetup
88		*/
89	<
90	<	void ForceDecomposition::distributeInitialData() {
91	<	#ifdef IS_MPI
92	<	Snapshot* snap = sman_->getCurrentSnapshot();
93	<	int nLocal = snap->getNumberOfAtoms();
94	<	int nGroups = snap->getNumberOfCutoffGroups();
89	>	void ForceMatrixDecomposition::distributeInitialData() {
90	>	snap_ = sman_->getCurrentSnapshot();
91	>	storageLayout_ = sman_->getStorageLayout();
92	>	ff_ = info_->getForceField();
93	>	nLocal_ = snap_->getNumberOfAtoms();
94	>
95	>	nGroups_ = info_->getNLocalCutoffGroups();
96	>	// gather the information for atomtype IDs (atids):
97	>	idents = info_->getIdentArray();
98	>	regions = info_->getRegions();
99	>	AtomLocalToGlobal = info_->getGlobalAtomIndices();
100	>	cgLocalToGlobal = info_->getGlobalGroupIndices();
101	>	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
102
103	<	AtomCommIntI = new Communicator<Row,int>(nLocal);
61	<	AtomCommRealI = new Communicator<Row,RealType>(nLocal);
62	<	AtomCommVectorI = new Communicator<Row,Vector3d>(nLocal);
63	<	AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nLocal);
103	>	massFactors = info_->getMassFactors();
104
105	<	AtomCommIntJ = new Communicator<Column,int>(nLocal);
106	<	AtomCommRealJ = new Communicator<Column,RealType>(nLocal);
107	<	AtomCommVectorJ = new Communicator<Column,Vector3d>(nLocal);
108	<	AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nLocal);
105	>	PairList* excludes = info_->getExcludedInteractions();
106	>	PairList* oneTwo = info_->getOneTwoInteractions();
107	>	PairList* oneThree = info_->getOneThreeInteractions();
108	>	PairList* oneFour = info_->getOneFourInteractions();
109	>
110	>	if (needVelocities_)
111	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
112	>	DataStorage::dslVelocity);
113	>	else
114	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
115	>
116	>	#ifdef IS_MPI
117	>
118	>	MPI_Comm row = rowComm.getComm();
119	>	MPI_Comm col = colComm.getComm();
120
121	<	cgCommIntI = new Communicator<Row,int>(nGroups);
122	<	cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
123	<	cgCommIntJ = new Communicator<Column,int>(nGroups);
124	<	cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
121	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
122	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
123	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
124	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
125	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
126
127	<	int nAtomsInRow = AtomCommIntI->getSize();
128	<	int nAtomsInCol = AtomCommIntJ->getSize();
129	<	int nGroupsInRow = cgCommIntI->getSize();
130	<	int nGroupsInCol = cgCommIntJ->getSize();
127	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
128	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
129	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
130	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
131	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
132
133	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
134	<	vector<RealType> (nAtomsInRow, 0.0));
135	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
136	<	vector<RealType> (nAtomsInCol, 0.0));
133	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
134	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
135	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
136	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
137	>
138	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
139	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
140	>	nGroupsInRow_ = cgPlanIntRow->getSize();
141	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
142	>
143	>	// Modify the data storage objects with the correct layouts and sizes:
144	>	atomRowData.resize(nAtomsInRow_);
145	>	atomRowData.setStorageLayout(storageLayout_);
146	>	atomColData.resize(nAtomsInCol_);
147	>	atomColData.setStorageLayout(storageLayout_);
148	>	cgRowData.resize(nGroupsInRow_);
149	>	cgRowData.setStorageLayout(DataStorage::dslPosition);
150	>	cgColData.resize(nGroupsInCol_);
151	>	if (needVelocities_)
152	>	// we only need column velocities if we need them.
153	>	cgColData.setStorageLayout(DataStorage::dslPosition |
154	>	DataStorage::dslVelocity);
155	>	else
156	>	cgColData.setStorageLayout(DataStorage::dslPosition);
157	>
158	>	identsRow.resize(nAtomsInRow_);
159	>	identsCol.resize(nAtomsInCol_);
160
161	<	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
161	>	AtomPlanIntRow->gather(idents, identsRow);
162	>	AtomPlanIntColumn->gather(idents, identsCol);
163
164	<	// gather the information for atomtype IDs (atids):
165	<	vector<int> identsLocal = info_->getIdentArray();
166	<	identsRow.reserve(nAtomsInRow);
167	<	identsCol.reserve(nAtomsInCol);
164	>	regionsRow.resize(nAtomsInRow_);
165	>	regionsCol.resize(nAtomsInCol_);
166	>
167	>	AtomPlanIntRow->gather(regions, regionsRow);
168	>	AtomPlanIntColumn->gather(regions, regionsCol);
169	>
170	>	// allocate memory for the parallel objects
171	>	atypesRow.resize(nAtomsInRow_);
172	>	atypesCol.resize(nAtomsInCol_);
173
174	<	AtomCommIntI->gather(identsLocal, identsRow);
175	<	AtomCommIntJ->gather(identsLocal, identsCol);
174	>	for (int i = 0; i < nAtomsInRow_; i++)
175	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
176	>	for (int i = 0; i < nAtomsInCol_; i++)
177	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
178
179	<	AtomLocalToGlobal = info_->getLocalToGlobalAtomIndex();
180	<	AtomCommIntI->gather(AtomLocalToGlobal, AtomRowToGlobal);
97	<	AtomCommIntJ->gather(AtomLocalToGlobal, AtomColToGlobal);
179	>	pot_row.resize(nAtomsInRow_);
180	>	pot_col.resize(nAtomsInCol_);
181
182	<	cgLocalToGlobal = info_->getLocalToGlobalCutoffGroupIndex();
183	<	cgCommIntI->gather(cgLocalToGlobal, cgRowToGlobal);
101	<	cgCommIntJ->gather(cgLocalToGlobal, cgColToGlobal);
182	>	expot_row.resize(nAtomsInRow_);
183	>	expot_col.resize(nAtomsInCol_);
184
185	<
185	>	AtomRowToGlobal.resize(nAtomsInRow_);
186	>	AtomColToGlobal.resize(nAtomsInCol_);
187	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
188	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
189
190	<	// still need:
191	<	// topoDist
192	<	// exclude
190	>	cgRowToGlobal.resize(nGroupsInRow_);
191	>	cgColToGlobal.resize(nGroupsInCol_);
192	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
193	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
194	>
195	>	massFactorsRow.resize(nAtomsInRow_);
196	>	massFactorsCol.resize(nAtomsInCol_);
197	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
198	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
199	>
200	>	groupListRow_.clear();
201	>	groupListRow_.resize(nGroupsInRow_);
202	>	for (int i = 0; i < nGroupsInRow_; i++) {
203	>	int gid = cgRowToGlobal[i];
204	>	for (int j = 0; j < nAtomsInRow_; j++) {
205	>	int aid = AtomRowToGlobal[j];
206	>	if (globalGroupMembership[aid] == gid)
207	>	groupListRow_[i].push_back(j);
208	>	}
209	>	}
210	>
211	>	groupListCol_.clear();
212	>	groupListCol_.resize(nGroupsInCol_);
213	>	for (int i = 0; i < nGroupsInCol_; i++) {
214	>	int gid = cgColToGlobal[i];
215	>	for (int j = 0; j < nAtomsInCol_; j++) {
216	>	int aid = AtomColToGlobal[j];
217	>	if (globalGroupMembership[aid] == gid)
218	>	groupListCol_[i].push_back(j);
219	>	}
220	>	}
221	>
222	>	excludesForAtom.clear();
223	>	excludesForAtom.resize(nAtomsInRow_);
224	>	toposForAtom.clear();
225	>	toposForAtom.resize(nAtomsInRow_);
226	>	topoDist.clear();
227	>	topoDist.resize(nAtomsInRow_);
228	>	for (int i = 0; i < nAtomsInRow_; i++) {
229	>	int iglob = AtomRowToGlobal[i];
230	>
231	>	for (int j = 0; j < nAtomsInCol_; j++) {
232	>	int jglob = AtomColToGlobal[j];
233	>
234	>	if (excludes->hasPair(iglob, jglob))
235	>	excludesForAtom[i].push_back(j);
236	>
237	>	if (oneTwo->hasPair(iglob, jglob)) {
238	>	toposForAtom[i].push_back(j);
239	>	topoDist[i].push_back(1);
240	>	} else {
241	>	if (oneThree->hasPair(iglob, jglob)) {
242	>	toposForAtom[i].push_back(j);
243	>	topoDist[i].push_back(2);
244	>	} else {
245	>	if (oneFour->hasPair(iglob, jglob)) {
246	>	toposForAtom[i].push_back(j);
247	>	topoDist[i].push_back(3);
248	>	}
249	>	}
250	>	}
251	>	}
252	>	}
253	>
254	>	#else
255	>	excludesForAtom.clear();
256	>	excludesForAtom.resize(nLocal_);
257	>	toposForAtom.clear();
258	>	toposForAtom.resize(nLocal_);
259	>	topoDist.clear();
260	>	topoDist.resize(nLocal_);
261	>
262	>	for (int i = 0; i < nLocal_; i++) {
263	>	int iglob = AtomLocalToGlobal[i];
264	>
265	>	for (int j = 0; j < nLocal_; j++) {
266	>	int jglob = AtomLocalToGlobal[j];
267	>
268	>	if (excludes->hasPair(iglob, jglob))
269	>	excludesForAtom[i].push_back(j);
270	>
271	>	if (oneTwo->hasPair(iglob, jglob)) {
272	>	toposForAtom[i].push_back(j);
273	>	topoDist[i].push_back(1);
274	>	} else {
275	>	if (oneThree->hasPair(iglob, jglob)) {
276	>	toposForAtom[i].push_back(j);
277	>	topoDist[i].push_back(2);
278	>	} else {
279	>	if (oneFour->hasPair(iglob, jglob)) {
280	>	toposForAtom[i].push_back(j);
281	>	topoDist[i].push_back(3);
282	>	}
283	>	}
284	>	}
285	>	}
286	>	}
287		#endif
288	+
289	+	// allocate memory for the parallel objects
290	+	atypesLocal.resize(nLocal_);
291	+
292	+	for (int i = 0; i < nLocal_; i++)
293	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
294	+
295	+	groupList_.clear();
296	+	groupList_.resize(nGroups_);
297	+	for (int i = 0; i < nGroups_; i++) {
298	+	int gid = cgLocalToGlobal[i];
299	+	for (int j = 0; j < nLocal_; j++) {
300	+	int aid = AtomLocalToGlobal[j];
301	+	if (globalGroupMembership[aid] == gid) {
302	+	groupList_[i].push_back(j);
303	+	}
304	+	}
305	+	}
306		}
307
308	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
309	+	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
310	+	if (toposForAtom[atom1][j] == atom2)
311	+	return topoDist[atom1][j];
312	+	}
313	+	return 0;
314	+	}
315
316	+	void ForceMatrixDecomposition::zeroWorkArrays() {
317	+	pairwisePot = 0.0;
318	+	embeddingPot = 0.0;
319	+	excludedPot = 0.0;
320	+	excludedSelfPot = 0.0;
321
113	–	void ForceDecomposition::distributeData()  {
322		#ifdef IS_MPI
323	<	Snapshot* snap = sman_->getCurrentSnapshot();
323	>	if (storageLayout_ & DataStorage::dslForce) {
324	>	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
325	>	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
326	>	}
327	>
328	>	if (storageLayout_ & DataStorage::dslTorque) {
329	>	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
330	>	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
331	>	}
332	>
333	>	fill(pot_row.begin(), pot_row.end(),
334	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
335	>
336	>	fill(pot_col.begin(), pot_col.end(),
337	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
338	>
339	>	fill(expot_row.begin(), expot_row.end(),
340	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
341	>
342	>	fill(expot_col.begin(), expot_col.end(),
343	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
344	>
345	>	if (storageLayout_ & DataStorage::dslParticlePot) {
346	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
347	>	0.0);
348	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
349	>	0.0);
350	>	}
351	>
352	>	if (storageLayout_ & DataStorage::dslDensity) {
353	>	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
354	>	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
355	>	}
356	>
357	>	if (storageLayout_ & DataStorage::dslFunctional) {
358	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
359	>	0.0);
360	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
361	>	0.0);
362	>	}
363	>
364	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
365	>	fill(atomRowData.functionalDerivative.begin(),
366	>	atomRowData.functionalDerivative.end(), 0.0);
367	>	fill(atomColData.functionalDerivative.begin(),
368	>	atomColData.functionalDerivative.end(), 0.0);
369	>	}
370	>
371	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
372	>	fill(atomRowData.skippedCharge.begin(),
373	>	atomRowData.skippedCharge.end(), 0.0);
374	>	fill(atomColData.skippedCharge.begin(),
375	>	atomColData.skippedCharge.end(), 0.0);
376	>	}
377	>
378	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
379	>	fill(atomRowData.flucQFrc.begin(),
380	>	atomRowData.flucQFrc.end(), 0.0);
381	>	fill(atomColData.flucQFrc.begin(),
382	>	atomColData.flucQFrc.end(), 0.0);
383	>	}
384	>
385	>	if (storageLayout_ & DataStorage::dslElectricField) {
386	>	fill(atomRowData.electricField.begin(),
387	>	atomRowData.electricField.end(), V3Zero);
388	>	fill(atomColData.electricField.begin(),
389	>	atomColData.electricField.end(), V3Zero);
390	>	}
391	>
392	>	if (storageLayout_ & DataStorage::dslSitePotential) {
393	>	fill(atomRowData.sitePotential.begin(),
394	>	atomRowData.sitePotential.end(), 0.0);
395	>	fill(atomColData.sitePotential.begin(),
396	>	atomColData.sitePotential.end(), 0.0);
397	>	}
398	>
399	>	#endif
400	>	// even in parallel, we need to zero out the local arrays:
401	>
402	>	if (storageLayout_ & DataStorage::dslParticlePot) {
403	>	fill(snap_->atomData.particlePot.begin(),
404	>	snap_->atomData.particlePot.end(), 0.0);
405	>	}
406	>
407	>	if (storageLayout_ & DataStorage::dslDensity) {
408	>	fill(snap_->atomData.density.begin(),
409	>	snap_->atomData.density.end(), 0.0);
410	>	}
411	>
412	>	if (storageLayout_ & DataStorage::dslFunctional) {
413	>	fill(snap_->atomData.functional.begin(),
414	>	snap_->atomData.functional.end(), 0.0);
415	>	}
416	>
417	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
418	>	fill(snap_->atomData.functionalDerivative.begin(),
419	>	snap_->atomData.functionalDerivative.end(), 0.0);
420	>	}
421	>
422	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
423	>	fill(snap_->atomData.skippedCharge.begin(),
424	>	snap_->atomData.skippedCharge.end(), 0.0);
425	>	}
426	>
427	>	if (storageLayout_ & DataStorage::dslElectricField) {
428	>	fill(snap_->atomData.electricField.begin(),
429	>	snap_->atomData.electricField.end(), V3Zero);
430	>	}
431	>	if (storageLayout_ & DataStorage::dslSitePotential) {
432	>	fill(snap_->atomData.sitePotential.begin(),
433	>	snap_->atomData.sitePotential.end(), 0.0);
434	>	}
435	>	}
436	>
437	>
438	>	void ForceMatrixDecomposition::distributeData()  {
439	>
440	>	#ifdef IS_MPI
441	>
442	>	snap_ = sman_->getCurrentSnapshot();
443	>	storageLayout_ = sman_->getStorageLayout();
444
445	+	bool needsCG = true;
446	+	if(info_->getNCutoffGroups() != info_->getNAtoms())
447	+	needsCG = false;
448	+
449		// gather up the atomic positions
450	<	AtomCommVectorI->gather(snap->atomData.position,
451	<	snap->atomIData.position);
452	<	AtomCommVectorJ->gather(snap->atomData.position,
453	<	snap->atomJData.position);
450	>	AtomPlanVectorRow->gather(snap_->atomData.position,
451	>	atomRowData.position);
452	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
453	>	atomColData.position);
454
455		// gather up the cutoff group positions
456	<	cgCommVectorI->gather(snap->cgData.position,
457	<	snap->cgIData.position);
458	<	cgCommVectorJ->gather(snap->cgData.position,
459	<	snap->cgJData.position);
456	>
457	>	if (needsCG) {
458	>	cgPlanVectorRow->gather(snap_->cgData.position,
459	>	cgRowData.position);
460	>
461	>	cgPlanVectorColumn->gather(snap_->cgData.position,
462	>	cgColData.position);
463	>	}
464	>
465	>
466	>	if (needVelocities_) {
467	>	// gather up the atomic velocities
468	>	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
469	>	atomColData.velocity);
470	>
471	>	if (needsCG) {
472	>	cgPlanVectorColumn->gather(snap_->cgData.velocity,
473	>	cgColData.velocity);
474	>	}
475	>	}
476	>
477
478		// if needed, gather the atomic rotation matrices
479	<	if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
480	<	AtomCommMatrixI->gather(snap->atomData.aMat,
481	<	snap->atomIData.aMat);
482	<	AtomCommMatrixJ->gather(snap->atomData.aMat,
483	<	snap->atomJData.aMat);
479	>	if (storageLayout_ & DataStorage::dslAmat) {
480	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
481	>	atomRowData.aMat);
482	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
483	>	atomColData.aMat);
484		}
485	<
486	<	// if needed, gather the atomic eletrostatic frames
487	<	if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
488	<	AtomCommMatrixI->gather(snap->atomData.electroFrame,
489	<	snap->atomIData.electroFrame);
490	<	AtomCommMatrixJ->gather(snap->atomData.electroFrame,
491	<	snap->atomJData.electroFrame);
485	>
486	>	// if needed, gather the atomic eletrostatic information
487	>	if (storageLayout_ & DataStorage::dslDipole) {
488	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
489	>	atomRowData.dipole);
490	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
491	>	atomColData.dipole);
492		}
493	+
494	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
495	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
496	+	atomRowData.quadrupole);
497	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
498	+	atomColData.quadrupole);
499	+	}
500	+
501	+	// if needed, gather the atomic fluctuating charge values
502	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
503	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
504	+	atomRowData.flucQPos);
505	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
506	+	atomColData.flucQPos);
507	+	}
508	+
509		#endif
510		}
511
512	<	void ForceDecomposition::collectIntermediateData() {
512	>	/* collects information obtained during the pre-pair loop onto local
513	>	* data structures.
514	>	*/
515	>	void ForceMatrixDecomposition::collectIntermediateData() {
516		#ifdef IS_MPI
149	–	Snapshot* snap = sman_->getCurrentSnapshot();
150	–
151	–	if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
517
518	<	AtomCommRealI->scatter(snap->atomIData.density,
519	<	snap->atomData.density);
518	>	snap_ = sman_->getCurrentSnapshot();
519	>	storageLayout_ = sman_->getStorageLayout();
520
521	<	int n = snap->atomData.density.size();
522	<	std::vector<RealType> rho_tmp(n, 0.0);
523	<	AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
521	>	if (storageLayout_ & DataStorage::dslDensity) {
522	>
523	>	AtomPlanRealRow->scatter(atomRowData.density,
524	>	snap_->atomData.density);
525	>
526	>	int n = snap_->atomData.density.size();
527	>	vector<RealType> rho_tmp(n, 0.0);
528	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
529		for (int i = 0; i < n; i++)
530	<	snap->atomData.density[i] += rho_tmp[i];
530	>	snap_->atomData.density[i] += rho_tmp[i];
531		}
532	+
533	+	// this isn't necessary if we don't have polarizable atoms, but
534	+	// we'll leave it here for now.
535	+	if (storageLayout_ & DataStorage::dslElectricField) {
536	+
537	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
538	+	snap_->atomData.electricField);
539	+
540	+	int n = snap_->atomData.electricField.size();
541	+	vector<Vector3d> field_tmp(n, V3Zero);
542	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
543	+	field_tmp);
544	+	for (int i = 0; i < n; i++)
545	+	snap_->atomData.electricField[i] += field_tmp[i];
546	+	}
547		#endif
548		}
549	<
550	<	void ForceDecomposition::distributeIntermediateData() {
549	>
550	>	/*
551	>	* redistributes information obtained during the pre-pair loop out to
552	>	* row and column-indexed data structures
553	>	*/
554	>	void ForceMatrixDecomposition::distributeIntermediateData() {
555		#ifdef IS_MPI
556	<	Snapshot* snap = sman_->getCurrentSnapshot();
557	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
558	<	AtomCommRealI->gather(snap->atomData.functional,
559	<	snap->atomIData.functional);
560	<	AtomCommRealJ->gather(snap->atomData.functional,
561	<	snap->atomJData.functional);
556	>	snap_ = sman_->getCurrentSnapshot();
557	>	storageLayout_ = sman_->getStorageLayout();
558	>
559	>	if (storageLayout_ & DataStorage::dslFunctional) {
560	>	AtomPlanRealRow->gather(snap_->atomData.functional,
561	>	atomRowData.functional);
562	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
563	>	atomColData.functional);
564		}
565
566	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
567	<	AtomCommRealI->gather(snap->atomData.functionalDerivative,
568	<	snap->atomIData.functionalDerivative);
569	<	AtomCommRealJ->gather(snap->atomData.functionalDerivative,
570	<	snap->atomJData.functionalDerivative);
566	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
567	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
568	>	atomRowData.functionalDerivative);
569	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
570	>	atomColData.functionalDerivative);
571		}
572		#endif
573		}
574
575
576	<	void ForceDecomposition::collectData() {
576	>	void ForceMatrixDecomposition::collectData() {
577		#ifdef IS_MPI
578	<	Snapshot* snap = sman_->getCurrentSnapshot();
579	<
580	<	int n = snap->atomData.force.size();
578	>	snap_ = sman_->getCurrentSnapshot();
579	>	storageLayout_ = sman_->getStorageLayout();
580	>
581	>	int n = snap_->atomData.force.size();
582		vector<Vector3d> frc_tmp(n, V3Zero);
583
584	<	AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
584	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
585		for (int i = 0; i < n; i++) {
586	<	snap->atomData.force[i] += frc_tmp[i];
586	>	snap_->atomData.force[i] += frc_tmp[i];
587		frc_tmp[i] = 0.0;
588		}
589
590	<	AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
591	<	for (int i = 0; i < n; i++)
592	<	snap->atomData.force[i] += frc_tmp[i];
593	<
594	<
595	<	if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
590	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
591	>	for (int i = 0; i < n; i++) {
592	>	snap_->atomData.force[i] += frc_tmp[i];
593	>	}
594	>
595	>	if (storageLayout_ & DataStorage::dslTorque) {
596
597	<	int nt = snap->atomData.force.size();
597	>	int nt = snap_->atomData.torque.size();
598		vector<Vector3d> trq_tmp(nt, V3Zero);
599
600	<	AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
601	<	for (int i = 0; i < n; i++) {
602	<	snap->atomData.torque[i] += trq_tmp[i];
600	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
601	>	for (int i = 0; i < nt; i++) {
602	>	snap_->atomData.torque[i] += trq_tmp[i];
603		trq_tmp[i] = 0.0;
604		}
605
606	<	AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
607	<	for (int i = 0; i < n; i++)
608	<	snap->atomData.torque[i] += trq_tmp[i];
606	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
607	>	for (int i = 0; i < nt; i++)
608	>	snap_->atomData.torque[i] += trq_tmp[i];
609		}
610	+
611	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
612	+
613	+	int ns = snap_->atomData.skippedCharge.size();
614	+	vector<RealType> skch_tmp(ns, 0.0);
615	+
616	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
617	+	for (int i = 0; i < ns; i++) {
618	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
619	+	skch_tmp[i] = 0.0;
620	+	}
621	+
622	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
623	+	for (int i = 0; i < ns; i++)
624	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
625	+
626	+	}
627
628	<	int nLocal = snap->getNumberOfAtoms();
628	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
629
630	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
631	<	vector<RealType> (nLocal, 0.0));
630	>	int nq = snap_->atomData.flucQFrc.size();
631	>	vector<RealType> fqfrc_tmp(nq, 0.0);
632	>
633	>	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
634	>	for (int i = 0; i < nq; i++) {
635	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
636	>	fqfrc_tmp[i] = 0.0;
637	>	}
638	>
639	>	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
640	>	for (int i = 0; i < nq; i++)
641	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
642	>
643	>	}
644	>
645	>	if (storageLayout_ & DataStorage::dslElectricField) {
646	>
647	>	int nef = snap_->atomData.electricField.size();
648	>	vector<Vector3d> efield_tmp(nef, V3Zero);
649	>
650	>	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
651	>	for (int i = 0; i < nef; i++) {
652	>	snap_->atomData.electricField[i] += efield_tmp[i];
653	>	efield_tmp[i] = 0.0;
654	>	}
655	>
656	>	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
657	>	for (int i = 0; i < nef; i++)
658	>	snap_->atomData.electricField[i] += efield_tmp[i];
659	>	}
660	>
661	>	if (storageLayout_ & DataStorage::dslSitePotential) {
662	>
663	>	int nsp = snap_->atomData.sitePotential.size();
664	>	vector<RealType> sp_tmp(nsp, 0.0);
665	>
666	>	AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
667	>	for (int i = 0; i < nsp; i++) {
668	>	snap_->atomData.sitePotential[i] += sp_tmp[i];
669	>	sp_tmp[i] = 0.0;
670	>	}
671	>
672	>	AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
673	>	for (int i = 0; i < nsp; i++)
674	>	snap_->atomData.sitePotential[i] += sp_tmp[i];
675	>	}
676	>
677	>	nLocal_ = snap_->getNumberOfAtoms();
678	>
679	>	vector<potVec> pot_temp(nLocal_,
680	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
681	>	vector<potVec> expot_temp(nLocal_,
682	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
683	>
684	>	// scatter/gather pot_row into the members of my column
685	>
686	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
687	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
688	>
689	>	for (std::size_t ii = 0;  ii < pot_temp.size(); ii++ )
690	>	pairwisePot += pot_temp[ii];
691	>
692	>	for (std::size_t ii = 0;  ii < expot_temp.size(); ii++ )
693	>	excludedPot += expot_temp[ii];
694
695	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
696	<	AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
697	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
698	<	pot_local[i] += pot_temp[i][ii];
695	>	if (storageLayout_ & DataStorage::dslParticlePot) {
696	>	// This is the pairwise contribution to the particle pot.  The
697	>	// embedding contribution is added in each of the low level
698	>	// non-bonded routines.  In single processor, this is done in
699	>	// unpackInteractionData, not in collectData.
700	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
701	>	for (int i = 0; i < nLocal_; i++) {
702	>	// factor of two is because the total potential terms are divided
703	>	// by 2 in parallel due to row/ column scatter
704	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
705	>	}
706		}
707		}
708	+
709	+	fill(pot_temp.begin(), pot_temp.end(),
710	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
711	+	fill(expot_temp.begin(), expot_temp.end(),
712	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
713	+
714	+	AtomPlanPotColumn->scatter(pot_col, pot_temp);
715	+	AtomPlanPotColumn->scatter(expot_col, expot_temp);
716	+
717	+	for (std::size_t ii = 0;  ii < pot_temp.size(); ii++ )
718	+	pairwisePot += pot_temp[ii];
719	+
720	+	for (std::size_t ii = 0;  ii < expot_temp.size(); ii++ )
721	+	excludedPot += expot_temp[ii];
722	+
723	+	if (storageLayout_ & DataStorage::dslParticlePot) {
724	+	// This is the pairwise contribution to the particle pot.  The
725	+	// embedding contribution is added in each of the low level
726	+	// non-bonded routines.  In single processor, this is done in
727	+	// unpackInteractionData, not in collectData.
728	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
729	+	for (int i = 0; i < nLocal_; i++) {
730	+	// factor of two is because the total potential terms are divided
731	+	// by 2 in parallel due to row/ column scatter
732	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
733	+	}
734	+	}
735	+	}
736	+
737	+	if (storageLayout_ & DataStorage::dslParticlePot) {
738	+	int npp = snap_->atomData.particlePot.size();
739	+	vector<RealType> ppot_temp(npp, 0.0);
740	+
741	+	// This is the direct or embedding contribution to the particle
742	+	// pot.
743	+
744	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
745	+	for (int i = 0; i < npp; i++) {
746	+	snap_->atomData.particlePot[i] += ppot_temp[i];
747	+	}
748	+
749	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
750	+
751	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
752	+	for (int i = 0; i < npp; i++) {
753	+	snap_->atomData.particlePot[i] += ppot_temp[i];
754	+	}
755	+	}
756	+
757	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
758	+	RealType ploc1 = pairwisePot[ii];
759	+	RealType ploc2 = 0.0;
760	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
761	+	pairwisePot[ii] = ploc2;
762	+	}
763	+
764	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
765	+	RealType ploc1 = excludedPot[ii];
766	+	RealType ploc2 = 0.0;
767	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
768	+	excludedPot[ii] = ploc2;
769	+	}
770	+
771	+	// Here be dragons.
772	+	MPI_Comm col = colComm.getComm();
773	+
774	+	MPI_Allreduce(MPI_IN_PLACE,
775	+	&snap_->frameData.conductiveHeatFlux[0], 3,
776	+	MPI_REALTYPE, MPI_SUM, col);
777	+
778	+
779		#endif
780	+
781		}
782	+
783	+	/**
784	+	* Collects information obtained during the post-pair (and embedding
785	+	* functional) loops onto local data structures.
786	+	*/
787	+	void ForceMatrixDecomposition::collectSelfData() {
788	+
789	+	#ifdef IS_MPI
790	+	snap_ = sman_->getCurrentSnapshot();
791	+	storageLayout_ = sman_->getStorageLayout();
792	+
793	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
794	+	RealType ploc1 = embeddingPot[ii];
795	+	RealType ploc2 = 0.0;
796	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
797	+	embeddingPot[ii] = ploc2;
798	+	}
799	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
800	+	RealType ploc1 = excludedSelfPot[ii];
801	+	RealType ploc2 = 0.0;
802	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
803	+	excludedSelfPot[ii] = ploc2;
804	+	}
805	+	#endif
806	+
807	+	}
808	+
809	+	int& ForceMatrixDecomposition::getNAtomsInRow() {
810	+	#ifdef IS_MPI
811	+	return nAtomsInRow_;
812	+	#else
813	+	return nLocal_;
814	+	#endif
815	+	}
816	+
817	+	/**
818	+	* returns the list of atoms belonging to this group.
819	+	*/
820	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
821	+	#ifdef IS_MPI
822	+	return groupListRow_[cg1];
823	+	#else
824	+	return groupList_[cg1];
825	+	#endif
826	+	}
827	+
828	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
829	+	#ifdef IS_MPI
830	+	return groupListCol_[cg2];
831	+	#else
832	+	return groupList_[cg2];
833	+	#endif
834	+	}
835	+
836	+	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1,
837	+	int cg2){
838	+
839	+	Vector3d d;
840	+	#ifdef IS_MPI
841	+	d = cgColData.position[cg2] - cgRowData.position[cg1];
842	+	#else
843	+	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
844	+	#endif
845	+
846	+	if (usePeriodicBoundaryConditions_) {
847	+	snap_->wrapVector(d);
848	+	}
849	+	return d;
850	+	}
851	+
852	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
853	+	#ifdef IS_MPI
854	+	return cgColData.velocity[cg2];
855	+	#else
856	+	return snap_->cgData.velocity[cg2];
857	+	#endif
858	+	}
859	+
860	+	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
861	+	#ifdef IS_MPI
862	+	return atomColData.velocity[atom2];
863	+	#else
864	+	return snap_->atomData.velocity[atom2];
865	+	#endif
866	+	}
867	+
868	+
869	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1,
870	+	int cg1) {
871	+	Vector3d d;
872	+
873	+	#ifdef IS_MPI
874	+	d = cgRowData.position[cg1] - atomRowData.position[atom1];
875	+	#else
876	+	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
877	+	#endif
878	+	if (usePeriodicBoundaryConditions_) {
879	+	snap_->wrapVector(d);
880	+	}
881	+	return d;
882	+	}
883	+
884	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2,
885	+	int cg2) {
886	+	Vector3d d;
887	+
888	+	#ifdef IS_MPI
889	+	d = cgColData.position[cg2] - atomColData.position[atom2];
890	+	#else
891	+	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
892	+	#endif
893	+	if (usePeriodicBoundaryConditions_) {
894	+	snap_->wrapVector(d);
895	+	}
896	+	return d;
897	+	}
898	+
899	+	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
900	+	#ifdef IS_MPI
901	+	return massFactorsRow[atom1];
902	+	#else
903	+	return massFactors[atom1];
904	+	#endif
905	+	}
906	+
907	+	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
908	+	#ifdef IS_MPI
909	+	return massFactorsCol[atom2];
910	+	#else
911	+	return massFactors[atom2];
912	+	#endif
913	+
914	+	}
915	+
916	+	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1,
917	+	int atom2){
918	+	Vector3d d;
919	+
920	+	#ifdef IS_MPI
921	+	d = atomColData.position[atom2] - atomRowData.position[atom1];
922	+	#else
923	+	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
924	+	#endif
925	+	if (usePeriodicBoundaryConditions_) {
926	+	snap_->wrapVector(d);
927	+	}
928	+	return d;
929	+	}
930	+
931	+	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
932	+	return excludesForAtom[atom1];
933	+	}
934	+
935	+	/**
936	+	* We need to exclude some overcounted interactions that result from
937	+	* the parallel decomposition.
938	+	*/
939	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2,
940	+	int cg1, int cg2) {
941	+	int unique_id_1, unique_id_2;
942	+
943	+	#ifdef IS_MPI
944	+	// in MPI, we have to look up the unique IDs for each atom
945	+	unique_id_1 = AtomRowToGlobal[atom1];
946	+	unique_id_2 = AtomColToGlobal[atom2];
947	+	// group1 = cgRowToGlobal[cg1];
948	+	// group2 = cgColToGlobal[cg2];
949	+	#else
950	+	unique_id_1 = AtomLocalToGlobal[atom1];
951	+	unique_id_2 = AtomLocalToGlobal[atom2];
952	+	int group1 = cgLocalToGlobal[cg1];
953	+	int group2 = cgLocalToGlobal[cg2];
954	+	#endif
955	+
956	+	if (unique_id_1 == unique_id_2) return true;
957	+
958	+	#ifdef IS_MPI
959	+	// this prevents us from doing the pair on multiple processors
960	+	if (unique_id_1 < unique_id_2) {
961	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
962	+	} else {
963	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
964	+	}
965	+	#endif
966	+
967	+	#ifndef IS_MPI
968	+	if (group1 == group2) {
969	+	if (unique_id_1 < unique_id_2) return true;
970	+	}
971	+	#endif
972	+
973	+	return false;
974	+	}
975	+
976	+	/**
977	+	* We need to handle the interactions for atoms who are involved in
978	+	* the same rigid body as well as some short range interactions
979	+	* (bonds, bends, torsions) differently from other interactions.
980	+	* We'll still visit the pairwise routines, but with a flag that
981	+	* tells those routines to exclude the pair from direct long range
982	+	* interactions.  Some indirect interactions (notably reaction
983	+	* field) must still be handled for these pairs.
984	+	*/
985	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
986	+
987	+	// excludesForAtom was constructed to use row/column indices in the MPI
988	+	// version, and to use local IDs in the non-MPI version:
989	+
990	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
991	+	i != excludesForAtom[atom1].end(); ++i) {
992	+	if ( (*i) == atom2 ) return true;
993	+	}
994	+
995	+	return false;
996	+	}
997	+
998	+
999	+	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1000	+	#ifdef IS_MPI
1001	+	atomRowData.force[atom1] += fg;
1002	+	#else
1003	+	snap_->atomData.force[atom1] += fg;
1004	+	#endif
1005	+	}
1006	+
1007	+	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
1008	+	#ifdef IS_MPI
1009	+	atomColData.force[atom2] += fg;
1010	+	#else
1011	+	snap_->atomData.force[atom2] += fg;
1012	+	#endif
1013	+	}
1014	+
1015	+	// filling interaction blocks with pointers
1016	+	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1017	+	int atom1, int atom2,
1018	+	bool newAtom1) {
1019	+
1020	+	idat.excluded = excludeAtomPair(atom1, atom2);
1021	+
1022	+	if (newAtom1) {
1023	+
1024	+	#ifdef IS_MPI
1025	+	idat.atid1 = identsRow[atom1];
1026	+	idat.atid2 = identsCol[atom2];
1027	+
1028	+	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1029	+	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1030	+	} else {
1031	+	idat.sameRegion = false;
1032	+	}
1033	+
1034	+	if (storageLayout_ & DataStorage::dslAmat) {
1035	+	idat.A1 = &(atomRowData.aMat[atom1]);
1036	+	idat.A2 = &(atomColData.aMat[atom2]);
1037	+	}
1038	+
1039	+	if (storageLayout_ & DataStorage::dslTorque) {
1040	+	idat.t1 = &(atomRowData.torque[atom1]);
1041	+	idat.t2 = &(atomColData.torque[atom2]);
1042	+	}
1043	+
1044	+	if (storageLayout_ & DataStorage::dslDipole) {
1045	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1046	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1047	+	}
1048	+
1049	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1050	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1051	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1052	+	}
1053	+
1054	+	if (storageLayout_ & DataStorage::dslDensity) {
1055	+	idat.rho1 = &(atomRowData.density[atom1]);
1056	+	idat.rho2 = &(atomColData.density[atom2]);
1057	+	}
1058	+
1059	+	if (storageLayout_ & DataStorage::dslFunctional) {
1060	+	idat.frho1 = &(atomRowData.functional[atom1]);
1061	+	idat.frho2 = &(atomColData.functional[atom2]);
1062	+	}
1063	+
1064	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1065	+	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1066	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1067	+	}
1068	+
1069	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1070	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1071	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1072	+	}
1073	+
1074	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1075	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1076	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1077	+	}
1078	+
1079	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1080	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1081	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1082	+	}
1083	+
1084	+	#else
1085	+
1086	+	idat.atid1 = idents[atom1];
1087	+	idat.atid2 = idents[atom2];
1088	+
1089	+	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1090	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1091	+	} else {
1092	+	idat.sameRegion = false;
1093	+	}
1094	+
1095	+	if (storageLayout_ & DataStorage::dslAmat) {
1096	+	idat.A1 = &(snap_->atomData.aMat[atom1]);
1097	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1098	+	}
1099	+
1100	+	if (storageLayout_ & DataStorage::dslTorque) {
1101	+	idat.t1 = &(snap_->atomData.torque[atom1]);
1102	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1103	+	}
1104	+
1105	+	if (storageLayout_ & DataStorage::dslDipole) {
1106	+	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1107	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1108	+	}
1109	+
1110	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1111	+	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1112	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1113	+	}
1114	+
1115	+	if (storageLayout_ & DataStorage::dslDensity) {
1116	+	idat.rho1 = &(snap_->atomData.density[atom1]);
1117	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1118	+	}
1119	+
1120	+	if (storageLayout_ & DataStorage::dslFunctional) {
1121	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1122	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1123	+	}
1124	+
1125	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1126	+	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1127	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1128	+	}
1129	+
1130	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1131	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1132	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1133	+	}
1134	+
1135	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1136	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1137	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1138	+	}
1139	+
1140	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1141	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1142	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1143	+	}
1144	+	#endif
1145	+
1146	+	} else {
1147	+	// atom1 is not new, so don't bother updating properties of that atom:
1148	+	#ifdef IS_MPI
1149	+	idat.atid2 = identsCol[atom2];
1150	+
1151	+	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1152	+	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1153	+	} else {
1154	+	idat.sameRegion = false;
1155	+	}
1156	+
1157	+	if (storageLayout_ & DataStorage::dslAmat) {
1158	+	idat.A2 = &(atomColData.aMat[atom2]);
1159	+	}
1160	+
1161	+	if (storageLayout_ & DataStorage::dslTorque) {
1162	+	idat.t2 = &(atomColData.torque[atom2]);
1163	+	}
1164	+
1165	+	if (storageLayout_ & DataStorage::dslDipole) {
1166	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1167	+	}
1168	+
1169	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1170	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1171	+	}
1172	+
1173	+	if (storageLayout_ & DataStorage::dslDensity) {
1174	+	idat.rho2 = &(atomColData.density[atom2]);
1175	+	}
1176	+
1177	+	if (storageLayout_ & DataStorage::dslFunctional) {
1178	+	idat.frho2 = &(atomColData.functional[atom2]);
1179	+	}
1180	+
1181	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1182	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1183	+	}
1184	+
1185	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1186	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1187	+	}
1188	+
1189	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1190	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1191	+	}
1192	+
1193	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1194	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1195	+	}
1196	+
1197	+	#else
1198	+	idat.atid2 = idents[atom2];
1199	+
1200	+	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1201	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1202	+	} else {
1203	+	idat.sameRegion = false;
1204	+	}
1205	+
1206	+	if (storageLayout_ & DataStorage::dslAmat) {
1207	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1208	+	}
1209	+
1210	+	if (storageLayout_ & DataStorage::dslTorque) {
1211	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1212	+	}
1213	+
1214	+	if (storageLayout_ & DataStorage::dslDipole) {
1215	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1216	+	}
1217	+
1218	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1219	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1220	+	}
1221	+
1222	+	if (storageLayout_ & DataStorage::dslDensity) {
1223	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1224	+	}
1225	+
1226	+	if (storageLayout_ & DataStorage::dslFunctional) {
1227	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1228	+	}
1229	+
1230	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1231	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1232	+	}
1233	+
1234	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1235	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1236	+	}
1237	+
1238	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1239	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1240	+	}
1241	+
1242	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1243	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1244	+	}
1245	+
1246	+	#endif
1247	+	}
1248	+	}
1249
1250	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat,
1251	+	int atom1, int atom2) {
1252	+	#ifdef IS_MPI
1253	+	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1254	+	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1255	+	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1256	+	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1257	+
1258	+	atomRowData.force[atom1] += *(idat.f1);
1259	+	atomColData.force[atom2] -= *(idat.f1);
1260	+
1261	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1262	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1263	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1264	+	}
1265	+
1266	+	if (storageLayout_ & DataStorage::dslElectricField) {
1267	+	atomRowData.electricField[atom1] += *(idat.eField1);
1268	+	atomColData.electricField[atom2] += *(idat.eField2);
1269	+	}
1270	+
1271	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1272	+	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1273	+	atomColData.sitePotential[atom2] += *(idat.sPot2);
1274	+	}
1275	+
1276	+	#else
1277	+	pairwisePot += *(idat.pot);
1278	+	excludedPot += *(idat.excludedPot);
1279	+
1280	+	snap_->atomData.force[atom1] += *(idat.f1);
1281	+	snap_->atomData.force[atom2] -= *(idat.f1);
1282	+
1283	+	if (idat.doParticlePot) {
1284	+	// This is the pairwise contribution to the particle pot.  The
1285	+	// embedding contribution is added in each of the low level
1286	+	// non-bonded routines.  In parallel, this calculation is done
1287	+	// in collectData, not in unpackInteractionData.
1288	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1289	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1290	+	}
1291	+
1292	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1293	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1294	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1295	+	}
1296	+
1297	+	if (storageLayout_ & DataStorage::dslElectricField) {
1298	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1299	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1300	+	}
1301	+
1302	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1303	+	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1304	+	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1305	+	}
1306	+
1307	+	#endif
1308	+
1309	+	}
1310	+
1311	+	/*
1312	+	* buildNeighborList
1313	+	*
1314	+	* Constructs the Verlet neighbor list for a force-matrix
1315	+	* decomposition.  In this case, each processor is responsible for
1316	+	* row-site interactions with column-sites.
1317	+	*
1318	+	* neighborList is returned as a packed array of neighboring
1319	+	* column-ordered CutoffGroups.  The starting position in
1320	+	* neighborList for each row-ordered CutoffGroup is given by the
1321	+	* returned vector point.
1322	+	*/
1323	+	void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
1324	+	vector<int>& point) {
1325	+	neighborList.clear();
1326	+	point.clear();
1327	+	int len = 0;
1328	+
1329	+	bool doAllPairs = false;
1330	+
1331	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1332	+	Mat3x3d box;
1333	+	Mat3x3d invBox;
1334	+
1335	+	Vector3d rs, scaled, dr;
1336	+	Vector3i whichCell;
1337	+	int cellIndex;
1338	+
1339	+	#ifdef IS_MPI
1340	+	cellListRow_.clear();
1341	+	cellListCol_.clear();
1342	+	point.resize(nGroupsInRow_+1);
1343	+	#else
1344	+	cellList_.clear();
1345	+	point.resize(nGroups_+1);
1346	+	#endif
1347	+
1348	+	if (!usePeriodicBoundaryConditions_) {
1349	+	box = snap_->getBoundingBox();
1350	+	invBox = snap_->getInvBoundingBox();
1351	+	} else {
1352	+	box = snap_->getHmat();
1353	+	invBox = snap_->getInvHmat();
1354	+	}
1355	+
1356	+	Vector3d A = box.getColumn(0);
1357	+	Vector3d B = box.getColumn(1);
1358	+	Vector3d C = box.getColumn(2);
1359	+
1360	+	// Required for triclinic cells
1361	+	Vector3d AxB = cross(A, B);
1362	+	Vector3d BxC = cross(B, C);
1363	+	Vector3d CxA = cross(C, A);
1364	+
1365	+	// unit vectors perpendicular to the faces of the triclinic cell:
1366	+	AxB.normalize();
1367	+	BxC.normalize();
1368	+	CxA.normalize();
1369	+
1370	+	// A set of perpendicular lengths in triclinic cells:
1371	+	RealType Wa = abs(dot(A, BxC));
1372	+	RealType Wb = abs(dot(B, CxA));
1373	+	RealType Wc = abs(dot(C, AxB));
1374	+
1375	+	nCells_.x() = int( Wa / rList_ );
1376	+	nCells_.y() = int( Wb / rList_ );
1377	+	nCells_.z() = int( Wc / rList_ );
1378	+
1379	+	// handle small boxes where the cell offsets can end up repeating cells
1380	+	if (nCells_.x() < 3) doAllPairs = true;
1381	+	if (nCells_.y() < 3) doAllPairs = true;
1382	+	if (nCells_.z() < 3) doAllPairs = true;
1383	+
1384	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1385	+
1386	+	#ifdef IS_MPI
1387	+	cellListRow_.resize(nCtot);
1388	+	cellListCol_.resize(nCtot);
1389	+	#else
1390	+	cellList_.resize(nCtot);
1391	+	#endif
1392	+
1393	+	if (!doAllPairs) {
1394	+
1395	+	#ifdef IS_MPI
1396	+
1397	+	for (int i = 0; i < nGroupsInRow_; i++) {
1398	+	rs = cgRowData.position[i];
1399	+
1400	+	// scaled positions relative to the box vectors
1401	+	scaled = invBox * rs;
1402	+
1403	+	// wrap the vector back into the unit box by subtracting integer box
1404	+	// numbers
1405	+	for (int j = 0; j < 3; j++) {
1406	+	scaled[j] -= roundMe(scaled[j]);
1407	+	scaled[j] += 0.5;
1408	+	// Handle the special case when an object is exactly on the
1409	+	// boundary (a scaled coordinate of 1.0 is the same as
1410	+	// scaled coordinate of 0.0)
1411	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1412	+	}
1413	+
1414	+	// find xyz-indices of cell that cutoffGroup is in.
1415	+	whichCell.x() = nCells_.x() * scaled.x();
1416	+	whichCell.y() = nCells_.y() * scaled.y();
1417	+	whichCell.z() = nCells_.z() * scaled.z();
1418	+
1419	+	// find single index of this cell:
1420	+	cellIndex = Vlinear(whichCell, nCells_);
1421	+
1422	+	// add this cutoff group to the list of groups in this cell;
1423	+	cellListRow_[cellIndex].push_back(i);
1424	+	}
1425	+	for (int i = 0; i < nGroupsInCol_; i++) {
1426	+	rs = cgColData.position[i];
1427	+
1428	+	// scaled positions relative to the box vectors
1429	+	scaled = invBox * rs;
1430	+
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	+	scaled[j] += 0.5;
1436	+	// Handle the special case when an object is exactly on the
1437	+	// boundary (a scaled coordinate of 1.0 is the same as
1438	+	// scaled coordinate of 0.0)
1439	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1440	+	}
1441	+
1442	+	// find xyz-indices of cell that cutoffGroup is in.
1443	+	whichCell.x() = nCells_.x() * scaled.x();
1444	+	whichCell.y() = nCells_.y() * scaled.y();
1445	+	whichCell.z() = nCells_.z() * scaled.z();
1446	+
1447	+	// find single index of this cell:
1448	+	cellIndex = Vlinear(whichCell, nCells_);
1449	+
1450	+	// add this cutoff group to the list of groups in this cell;
1451	+	cellListCol_[cellIndex].push_back(i);
1452	+	}
1453	+
1454	+	#else
1455	+	for (int i = 0; i < nGroups_; i++) {
1456	+	rs = snap_->cgData.position[i];
1457	+
1458	+	// scaled positions relative to the box vectors
1459	+	scaled = invBox * rs;
1460	+
1461	+	// wrap the vector back into the unit box by subtracting integer box
1462	+	// numbers
1463	+	for (int j = 0; j < 3; j++) {
1464	+	scaled[j] -= roundMe(scaled[j]);
1465	+	scaled[j] += 0.5;
1466	+	// Handle the special case when an object is exactly on the
1467	+	// boundary (a scaled coordinate of 1.0 is the same as
1468	+	// scaled coordinate of 0.0)
1469	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1470	+	}
1471	+
1472	+	// find xyz-indices of cell that cutoffGroup is in.
1473	+	whichCell.x() = int(nCells_.x() * scaled.x());
1474	+	whichCell.y() = int(nCells_.y() * scaled.y());
1475	+	whichCell.z() = int(nCells_.z() * scaled.z());
1476	+
1477	+	// find single index of this cell:
1478	+	cellIndex = Vlinear(whichCell, nCells_);
1479	+
1480	+	// add this cutoff group to the list of groups in this cell;
1481	+	cellList_[cellIndex].push_back(i);
1482	+	}
1483	+
1484	+	#endif
1485	+
1486	+	#ifdef IS_MPI
1487	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1488	+	rs = cgRowData.position[j1];
1489	+	#else
1490	+
1491	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1492	+	rs = snap_->cgData.position[j1];
1493	+	#endif
1494	+	point[j1] = len;
1495	+
1496	+	// scaled positions relative to the box vectors
1497	+	scaled = invBox * rs;
1498	+
1499	+	// wrap the vector back into the unit box by subtracting integer box
1500	+	// numbers
1501	+	for (int j = 0; j < 3; j++) {
1502	+	scaled[j] -= roundMe(scaled[j]);
1503	+	scaled[j] += 0.5;
1504	+	// Handle the special case when an object is exactly on the
1505	+	// boundary (a scaled coordinate of 1.0 is the same as
1506	+	// scaled coordinate of 0.0)
1507	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1508	+	}
1509	+
1510	+	// find xyz-indices of cell that cutoffGroup is in.
1511	+	whichCell.x() = nCells_.x() * scaled.x();
1512	+	whichCell.y() = nCells_.y() * scaled.y();
1513	+	whichCell.z() = nCells_.z() * scaled.z();
1514	+
1515	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1516	+	os != cellOffsets_.end(); ++os) {
1517	+
1518	+	Vector3i m2v = whichCell + (*os);
1519	+
1520	+	if (m2v.x() >= nCells_.x()) {
1521	+	m2v.x() = 0;
1522	+	} else if (m2v.x() < 0) {
1523	+	m2v.x() = nCells_.x() - 1;
1524	+	}
1525	+
1526	+	if (m2v.y() >= nCells_.y()) {
1527	+	m2v.y() = 0;
1528	+	} else if (m2v.y() < 0) {
1529	+	m2v.y() = nCells_.y() - 1;
1530	+	}
1531	+
1532	+	if (m2v.z() >= nCells_.z()) {
1533	+	m2v.z() = 0;
1534	+	} else if (m2v.z() < 0) {
1535	+	m2v.z() = nCells_.z() - 1;
1536	+	}
1537	+	int m2 = Vlinear (m2v, nCells_);
1538	+	#ifdef IS_MPI
1539	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1540	+	j2 != cellListCol_[m2].end(); ++j2) {
1541	+
1542	+	// In parallel, we need to visit *all* pairs of row
1543	+	// & column indicies and will divide labor in the
1544	+	// force evaluation later.
1545	+	dr = cgColData.position[(*j2)] - rs;
1546	+	if (usePeriodicBoundaryConditions_) {
1547	+	snap_->wrapVector(dr);
1548	+	}
1549	+	if (dr.lengthSquare() < rListSq_) {
1550	+	neighborList.push_back( (*j2) );
1551	+	++len;
1552	+	}
1553	+	}
1554	+	#else
1555	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1556	+	j2 != cellList_[m2].end(); ++j2) {
1557	+
1558	+	// Always do this if we're in different cells or if
1559	+	// we're in the same cell and the global index of
1560	+	// the j2 cutoff group is greater than or equal to
1561	+	// the j1 cutoff group.  Note that Rappaport's code
1562	+	// has a "less than" conditional here, but that
1563	+	// deals with atom-by-atom computation.  OpenMD
1564	+	// allows atoms within a single cutoff group to
1565	+	// interact with each other.
1566	+
1567	+	if ( (*j2) >= j1 ) {
1568	+
1569	+	dr = snap_->cgData.position[(*j2)] - rs;
1570	+	if (usePeriodicBoundaryConditions_) {
1571	+	snap_->wrapVector(dr);
1572	+	}
1573	+	if ( dr.lengthSquare() < rListSq_) {
1574	+	neighborList.push_back( (*j2) );
1575	+	++len;
1576	+	}
1577	+	}
1578	+	}
1579	+	#endif
1580	+	}
1581	+	}
1582	+	} else {
1583	+	// branch to do all cutoff group pairs
1584	+	#ifdef IS_MPI
1585	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1586	+	point[j1] = len;
1587	+	rs = cgRowData.position[j1];
1588	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1589	+	dr = cgColData.position[j2] - rs;
1590	+	if (usePeriodicBoundaryConditions_) {
1591	+	snap_->wrapVector(dr);
1592	+	}
1593	+	if (dr.lengthSquare() < rListSq_) {
1594	+	neighborList.push_back( j2 );
1595	+	++len;
1596	+	}
1597	+	}
1598	+	}
1599	+	#else
1600	+	// include all groups here.
1601	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1602	+	point[j1] = len;
1603	+	rs = snap_->cgData.position[j1];
1604	+	// include self group interactions j2 == j1
1605	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1606	+	dr = snap_->cgData.position[j2] - rs;
1607	+	if (usePeriodicBoundaryConditions_) {
1608	+	snap_->wrapVector(dr);
1609	+	}
1610	+	if (dr.lengthSquare() < rListSq_) {
1611	+	neighborList.push_back( j2 );
1612	+	++len;
1613	+	}
1614	+	}
1615	+	}
1616	+	#endif
1617	+	}
1618	+
1619	+	#ifdef IS_MPI
1620	+	point[nGroupsInRow_] = len;
1621	+	#else
1622	+	point[nGroups_] = len;
1623	+	#endif
1624	+
1625	+	// save the local cutoff group positions for the check that is
1626	+	// done on each loop:
1627	+	saved_CG_positions_.clear();
1628	+	saved_CG_positions_.reserve(nGroups_);
1629	+	for (int i = 0; i < nGroups_; i++)
1630	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1631	+	}
1632		} //end namespace OpenMD

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