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

Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1551 by gezelter, Thu Apr 28 18:38:21 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 2057 by gezelter, Tue Mar 3 15:22:26 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/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		*/
53	–
89		void ForceMatrixDecomposition::distributeInitialData() {
90		snap_ = sman_->getCurrentSnapshot();
91		storageLayout_ = sman_->getStorageLayout();
92	<	#ifdef IS_MPI
93	<	int nLocal = snap_->getNumberOfAtoms();
94	<	int nGroups = snap_->getNumberOfCutoffGroups();
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	>	massFactors = info_->getMassFactors();
104	>
105	>	PairList* excludes = info_->getExcludedInteractions();
106	>	PairList* oneTwo = info_->getOneTwoInteractions();
107	>	PairList* oneThree = info_->getOneThreeInteractions();
108	>	PairList* oneFour = info_->getOneFourInteractions();
109
110	<	AtomCommIntRow = new Communicator<Row,int>(nLocal);
111	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
112	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
113	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
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	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal);
122	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
123	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
124	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
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	<	cgCommIntRow = new Communicator<Row,int>(nGroups);
128	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
129	<	cgCommIntColumn = new Communicator<Column,int>(nGroups);
130	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
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	<	int nAtomsInRow = AtomCommIntRow->getSize();
134	<	int nAtomsInCol = AtomCommIntColumn->getSize();
135	<	int nGroupsInRow = cgCommIntRow->getSize();
136	<	int nGroupsInCol = cgCommIntColumn->getSize();
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);
144	>	atomRowData.resize(nAtomsInRow_);
145		atomRowData.setStorageLayout(storageLayout_);
146	<	atomColData.resize(nAtomsInCol);
146	>	atomColData.resize(nAtomsInCol_);
147		atomColData.setStorageLayout(storageLayout_);
148	<	cgRowData.resize(nGroupsInRow);
148	>	cgRowData.resize(nGroupsInRow_);
149		cgRowData.setStorageLayout(DataStorage::dslPosition);
150	<	cgColData.resize(nGroupsInCol);
151	<	cgColData.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<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
162	<	vector<RealType> (nAtomsInRow, 0.0));
93	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
94	<	vector<RealType> (nAtomsInCol, 0.0));
161	>	AtomPlanIntRow->gather(idents, identsRow);
162	>	AtomPlanIntColumn->gather(idents, identsCol);
163
164	<
165	<	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
164	>	regionsRow.resize(nAtomsInRow_);
165	>	regionsCol.resize(nAtomsInCol_);
166
167	<	// gather the information for atomtype IDs (atids):
168	<	vector<int> identsLocal = info_->getIdentArray();
101	<	identsRow.reserve(nAtomsInRow);
102	<	identsCol.reserve(nAtomsInCol);
167	>	AtomPlanIntRow->gather(regions, regionsRow);
168	>	AtomPlanIntColumn->gather(regions, regionsCol);
169
170	<	AtomCommIntRow->gather(identsLocal, identsRow);
171	<	AtomCommIntColumn->gather(identsLocal, identsCol);
172	<
107	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
108	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
109	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
110	<
111	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
112	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
113	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
170	>	// allocate memory for the parallel objects
171	>	atypesRow.resize(nAtomsInRow_);
172	>	atypesCol.resize(nAtomsInCol_);
173
174	<	// still need:
175	<	// topoDist
176	<	// exclude
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	>	pot_row.resize(nAtomsInRow_);
180	>	pot_col.resize(nAtomsInCol_);
181	>
182	>	expot_row.resize(nAtomsInRow_);
183	>	expot_col.resize(nAtomsInCol_);
184	>
185	>	AtomRowToGlobal.resize(nAtomsInRow_);
186	>	AtomColToGlobal.resize(nAtomsInCol_);
187	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
188	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
189	>
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
322	+	#ifdef IS_MPI
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		snap_ = sman_->getCurrentSnapshot();
440		storageLayout_ = sman_->getStorageLayout();
441	+
442	+	bool needsCG = true;
443	+	if(info_->getNCutoffGroups() != info_->getNAtoms())
444	+	needsCG = false;
445	+
446		#ifdef IS_MPI
447
448		// gather up the atomic positions
449	<	AtomCommVectorRow->gather(snap_->atomData.position,
449	>	AtomPlanVectorRow->gather(snap_->atomData.position,
450		atomRowData.position);
451	<	AtomCommVectorColumn->gather(snap_->atomData.position,
451	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
452		atomColData.position);
453
454		// gather up the cutoff group positions
455	<	cgCommVectorRow->gather(snap_->cgData.position,
456	<	cgRowData.position);
457	<	cgCommVectorColumn->gather(snap_->cgData.position,
458	<	cgColData.position);
455	>
456	>	if (needsCG) {
457	>	cgPlanVectorRow->gather(snap_->cgData.position,
458	>	cgRowData.position);
459	>
460	>	cgPlanVectorColumn->gather(snap_->cgData.position,
461	>	cgColData.position);
462	>	}
463	>
464	>
465	>	if (needVelocities_) {
466	>	// gather up the atomic velocities
467	>	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
468	>	atomColData.velocity);
469	>
470	>	if (needsCG) {
471	>	cgPlanVectorColumn->gather(snap_->cgData.velocity,
472	>	cgColData.velocity);
473	>	}
474	>	}
475	>
476
477		// if needed, gather the atomic rotation matrices
478		if (storageLayout_ & DataStorage::dslAmat) {
479	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
479	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
480		atomRowData.aMat);
481	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
481	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
482		atomColData.aMat);
483		}
484	<
485	<	// if needed, gather the atomic eletrostatic frames
486	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
487	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
488	<	atomRowData.electroFrame);
489	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
490	<	atomColData.electroFrame);
484	>
485	>	// if needed, gather the atomic eletrostatic information
486	>	if (storageLayout_ & DataStorage::dslDipole) {
487	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
488	>	atomRowData.dipole);
489	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
490	>	atomColData.dipole);
491		}
492	+
493	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
494	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
495	+	atomRowData.quadrupole);
496	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
497	+	atomColData.quadrupole);
498	+	}
499	+
500	+	// if needed, gather the atomic fluctuating charge values
501	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
502	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
503	+	atomRowData.flucQPos);
504	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
505	+	atomColData.flucQPos);
506	+	}
507	+
508		#endif
509		}
510
511	+	/* collects information obtained during the pre-pair loop onto local
512	+	* data structures.
513	+	*/
514		void ForceMatrixDecomposition::collectIntermediateData() {
515		snap_ = sman_->getCurrentSnapshot();
516		storageLayout_ = sman_->getStorageLayout();
#	Line 162 | Line 518 | namespace OpenMD {
518
519		if (storageLayout_ & DataStorage::dslDensity) {
520
521	<	AtomCommRealRow->scatter(atomRowData.density,
521	>	AtomPlanRealRow->scatter(atomRowData.density,
522		snap_->atomData.density);
523
524		int n = snap_->atomData.density.size();
525	<	std::vector<RealType> rho_tmp(n, 0.0);
526	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
525	>	vector<RealType> rho_tmp(n, 0.0);
526	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
527		for (int i = 0; i < n; i++)
528		snap_->atomData.density[i] += rho_tmp[i];
529		}
530	+
531	+	// this isn't necessary if we don't have polarizable atoms, but
532	+	// we'll leave it here for now.
533	+	if (storageLayout_ & DataStorage::dslElectricField) {
534	+
535	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
536	+	snap_->atomData.electricField);
537	+
538	+	int n = snap_->atomData.electricField.size();
539	+	vector<Vector3d> field_tmp(n, V3Zero);
540	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
541	+	field_tmp);
542	+	for (int i = 0; i < n; i++)
543	+	snap_->atomData.electricField[i] += field_tmp[i];
544	+	}
545		#endif
546		}
547	<
547	>
548	>	/*
549	>	* redistributes information obtained during the pre-pair loop out to
550	>	* row and column-indexed data structures
551	>	*/
552		void ForceMatrixDecomposition::distributeIntermediateData() {
553		snap_ = sman_->getCurrentSnapshot();
554		storageLayout_ = sman_->getStorageLayout();
555		#ifdef IS_MPI
556		if (storageLayout_ & DataStorage::dslFunctional) {
557	<	AtomCommRealRow->gather(snap_->atomData.functional,
557	>	AtomPlanRealRow->gather(snap_->atomData.functional,
558		atomRowData.functional);
559	<	AtomCommRealColumn->gather(snap_->atomData.functional,
559	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
560		atomColData.functional);
561		}
562
563		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
564	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
564	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
565		atomRowData.functionalDerivative);
566	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
566	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
567		atomColData.functionalDerivative);
568		}
569		#endif
#	Line 202 | Line 577 | namespace OpenMD {
577		int n = snap_->atomData.force.size();
578		vector<Vector3d> frc_tmp(n, V3Zero);
579
580	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
580	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
581		for (int i = 0; i < n; i++) {
582		snap_->atomData.force[i] += frc_tmp[i];
583		frc_tmp[i] = 0.0;
584		}
585
586	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
587	<	for (int i = 0; i < n; i++)
586	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
587	>	for (int i = 0; i < n; i++) {
588		snap_->atomData.force[i] += frc_tmp[i];
589	<
590	<
589	>	}
590	>
591		if (storageLayout_ & DataStorage::dslTorque) {
592
593	<	int nt = snap_->atomData.force.size();
593	>	int nt = snap_->atomData.torque.size();
594		vector<Vector3d> trq_tmp(nt, V3Zero);
595
596	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
597	<	for (int i = 0; i < n; i++) {
596	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
597	>	for (int i = 0; i < nt; i++) {
598		snap_->atomData.torque[i] += trq_tmp[i];
599		trq_tmp[i] = 0.0;
600		}
601
602	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
603	<	for (int i = 0; i < n; i++)
602	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
603	>	for (int i = 0; i < nt; i++)
604		snap_->atomData.torque[i] += trq_tmp[i];
605		}
606	+
607	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
608	+
609	+	int ns = snap_->atomData.skippedCharge.size();
610	+	vector<RealType> skch_tmp(ns, 0.0);
611	+
612	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
613	+	for (int i = 0; i < ns; i++) {
614	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
615	+	skch_tmp[i] = 0.0;
616	+	}
617	+
618	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
619	+	for (int i = 0; i < ns; i++)
620	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
621	+
622	+	}
623
624	<	int nLocal = snap_->getNumberOfAtoms();
624	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
625
626	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
627	<	vector<RealType> (nLocal, 0.0));
626	>	int nq = snap_->atomData.flucQFrc.size();
627	>	vector<RealType> fqfrc_tmp(nq, 0.0);
628	>
629	>	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
630	>	for (int i = 0; i < nq; i++) {
631	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
632	>	fqfrc_tmp[i] = 0.0;
633	>	}
634	>
635	>	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
636	>	for (int i = 0; i < nq; i++)
637	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
638	>
639	>	}
640	>
641	>	if (storageLayout_ & DataStorage::dslElectricField) {
642	>
643	>	int nef = snap_->atomData.electricField.size();
644	>	vector<Vector3d> efield_tmp(nef, V3Zero);
645	>
646	>	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
647	>	for (int i = 0; i < nef; i++) {
648	>	snap_->atomData.electricField[i] += efield_tmp[i];
649	>	efield_tmp[i] = 0.0;
650	>	}
651	>
652	>	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
653	>	for (int i = 0; i < nef; i++)
654	>	snap_->atomData.electricField[i] += efield_tmp[i];
655	>	}
656	>
657	>	if (storageLayout_ & DataStorage::dslSitePotential) {
658	>
659	>	int nsp = snap_->atomData.sitePotential.size();
660	>	vector<RealType> sp_tmp(nsp, 0.0);
661	>
662	>	AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
663	>	for (int i = 0; i < nsp; i++) {
664	>	snap_->atomData.sitePotential[i] += sp_tmp[i];
665	>	sp_tmp[i] = 0.0;
666	>	}
667	>
668	>	AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
669	>	for (int i = 0; i < nsp; i++)
670	>	snap_->atomData.sitePotential[i] += sp_tmp[i];
671	>	}
672	>
673	>	nLocal_ = snap_->getNumberOfAtoms();
674	>
675	>	vector<potVec> pot_temp(nLocal_,
676	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
677	>	vector<potVec> expot_temp(nLocal_,
678	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
679	>
680	>	// scatter/gather pot_row into the members of my column
681	>
682	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
683	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
684	>
685	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
686	>	pairwisePot += pot_temp[ii];
687	>
688	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
689	>	excludedPot += expot_temp[ii];
690	>
691	>	if (storageLayout_ & DataStorage::dslParticlePot) {
692	>	// This is the pairwise contribution to the particle pot.  The
693	>	// embedding contribution is added in each of the low level
694	>	// non-bonded routines.  In single processor, this is done in
695	>	// unpackInteractionData, not in collectData.
696	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
697	>	for (int i = 0; i < nLocal_; i++) {
698	>	// factor of two is because the total potential terms are divided
699	>	// by 2 in parallel due to row/ column scatter
700	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
701	>	}
702	>	}
703	>	}
704	>
705	>	fill(pot_temp.begin(), pot_temp.end(),
706	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
707	>	fill(expot_temp.begin(), expot_temp.end(),
708	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
709	>
710	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
711	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
712
713	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
714	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
715	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
716	<	pot_local[i] += pot_temp[i][ii];
713	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
714	>	pairwisePot += pot_temp[ii];
715	>
716	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
717	>	excludedPot += expot_temp[ii];
718	>
719	>	if (storageLayout_ & DataStorage::dslParticlePot) {
720	>	// This is the pairwise contribution to the particle pot.  The
721	>	// embedding contribution is added in each of the low level
722	>	// non-bonded routines.  In single processor, this is done in
723	>	// unpackInteractionData, not in collectData.
724	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
725	>	for (int i = 0; i < nLocal_; i++) {
726	>	// factor of two is because the total potential terms are divided
727	>	// by 2 in parallel due to row/ column scatter
728	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
729	>	}
730		}
731		}
732	+
733	+	if (storageLayout_ & DataStorage::dslParticlePot) {
734	+	int npp = snap_->atomData.particlePot.size();
735	+	vector<RealType> ppot_temp(npp, 0.0);
736	+
737	+	// This is the direct or embedding contribution to the particle
738	+	// pot.
739	+
740	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
741	+	for (int i = 0; i < npp; i++) {
742	+	snap_->atomData.particlePot[i] += ppot_temp[i];
743	+	}
744	+
745	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
746	+
747	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
748	+	for (int i = 0; i < npp; i++) {
749	+	snap_->atomData.particlePot[i] += ppot_temp[i];
750	+	}
751	+	}
752	+
753	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
754	+	RealType ploc1 = pairwisePot[ii];
755	+	RealType ploc2 = 0.0;
756	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
757	+	pairwisePot[ii] = ploc2;
758	+	}
759	+
760	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
761	+	RealType ploc1 = excludedPot[ii];
762	+	RealType ploc2 = 0.0;
763	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
764	+	excludedPot[ii] = ploc2;
765	+	}
766	+
767	+	// Here be dragons.
768	+	MPI_Comm col = colComm.getComm();
769	+
770	+	MPI_Allreduce(MPI_IN_PLACE,
771	+	&snap_->frameData.conductiveHeatFlux[0], 3,
772	+	MPI_REALTYPE, MPI_SUM, col);
773	+
774	+
775		#endif
776	+
777		}
778
779	+	/**
780	+	* Collects information obtained during the post-pair (and embedding
781	+	* functional) loops onto local data structures.
782	+	*/
783	+	void ForceMatrixDecomposition::collectSelfData() {
784	+	snap_ = sman_->getCurrentSnapshot();
785	+	storageLayout_ = sman_->getStorageLayout();
786	+
787	+	#ifdef IS_MPI
788	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
789	+	RealType ploc1 = embeddingPot[ii];
790	+	RealType ploc2 = 0.0;
791	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
792	+	embeddingPot[ii] = ploc2;
793	+	}
794	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
795	+	RealType ploc1 = excludedSelfPot[ii];
796	+	RealType ploc2 = 0.0;
797	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
798	+	excludedSelfPot[ii] = ploc2;
799	+	}
800	+	#endif
801	+
802	+	}
803	+
804	+
805	+
806	+	int& ForceMatrixDecomposition::getNAtomsInRow() {
807	+	#ifdef IS_MPI
808	+	return nAtomsInRow_;
809	+	#else
810	+	return nLocal_;
811	+	#endif
812	+	}
813	+
814	+	/**
815	+	* returns the list of atoms belonging to this group.
816	+	*/
817	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
818	+	#ifdef IS_MPI
819	+	return groupListRow_[cg1];
820	+	#else
821	+	return groupList_[cg1];
822	+	#endif
823	+	}
824	+
825	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
826	+	#ifdef IS_MPI
827	+	return groupListCol_[cg2];
828	+	#else
829	+	return groupList_[cg2];
830	+	#endif
831	+	}
832
833		Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
834		Vector3d d;
#	Line 253 | Line 839 | namespace OpenMD {
839		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
840		#endif
841
842	<	snap_->wrapVector(d);
842	>	if (usePeriodicBoundaryConditions_) {
843	>	snap_->wrapVector(d);
844	>	}
845		return d;
846		}
847
848	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
849	+	#ifdef IS_MPI
850	+	return cgColData.velocity[cg2];
851	+	#else
852	+	return snap_->cgData.velocity[cg2];
853	+	#endif
854	+	}
855
856	+	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
857	+	#ifdef IS_MPI
858	+	return atomColData.velocity[atom2];
859	+	#else
860	+	return snap_->atomData.velocity[atom2];
861	+	#endif
862	+	}
863	+
864	+
865		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
866
867		Vector3d d;
#	Line 267 | Line 871 | namespace OpenMD {
871		#else
872		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
873		#endif
874	<
875	<	snap_->wrapVector(d);
874	>	if (usePeriodicBoundaryConditions_) {
875	>	snap_->wrapVector(d);
876	>	}
877		return d;
878		}
879
#	Line 280 | Line 885 | namespace OpenMD {
885		#else
886		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
887		#endif
888	<
889	<	snap_->wrapVector(d);
888	>	if (usePeriodicBoundaryConditions_) {
889	>	snap_->wrapVector(d);
890	>	}
891		return d;
892		}
893	+
894	+	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
895	+	#ifdef IS_MPI
896	+	return massFactorsRow[atom1];
897	+	#else
898	+	return massFactors[atom1];
899	+	#endif
900	+	}
901	+
902	+	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
903	+	#ifdef IS_MPI
904	+	return massFactorsCol[atom2];
905	+	#else
906	+	return massFactors[atom2];
907	+	#endif
908	+
909	+	}
910
911		Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
912		Vector3d d;
#	Line 293 | Line 916 | namespace OpenMD {
916		#else
917		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
918		#endif
919	<
920	<	snap_->wrapVector(d);
919	>	if (usePeriodicBoundaryConditions_) {
920	>	snap_->wrapVector(d);
921	>	}
922		return d;
923		}
924
925	+	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
926	+	return excludesForAtom[atom1];
927	+	}
928	+
929	+	/**
930	+	* We need to exclude some overcounted interactions that result from
931	+	* the parallel decomposition.
932	+	*/
933	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
934	+	int unique_id_1, unique_id_2;
935	+
936	+	#ifdef IS_MPI
937	+	// in MPI, we have to look up the unique IDs for each atom
938	+	unique_id_1 = AtomRowToGlobal[atom1];
939	+	unique_id_2 = AtomColToGlobal[atom2];
940	+	// group1 = cgRowToGlobal[cg1];
941	+	// group2 = cgColToGlobal[cg2];
942	+	#else
943	+	unique_id_1 = AtomLocalToGlobal[atom1];
944	+	unique_id_2 = AtomLocalToGlobal[atom2];
945	+	int group1 = cgLocalToGlobal[cg1];
946	+	int group2 = cgLocalToGlobal[cg2];
947	+	#endif
948	+
949	+	if (unique_id_1 == unique_id_2) return true;
950	+
951	+	#ifdef IS_MPI
952	+	// this prevents us from doing the pair on multiple processors
953	+	if (unique_id_1 < unique_id_2) {
954	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
955	+	} else {
956	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
957	+	}
958	+	#endif
959	+
960	+	#ifndef IS_MPI
961	+	if (group1 == group2) {
962	+	if (unique_id_1 < unique_id_2) return true;
963	+	}
964	+	#endif
965	+
966	+	return false;
967	+	}
968	+
969	+	/**
970	+	* We need to handle the interactions for atoms who are involved in
971	+	* the same rigid body as well as some short range interactions
972	+	* (bonds, bends, torsions) differently from other interactions.
973	+	* We'll still visit the pairwise routines, but with a flag that
974	+	* tells those routines to exclude the pair from direct long range
975	+	* interactions.  Some indirect interactions (notably reaction
976	+	* field) must still be handled for these pairs.
977	+	*/
978	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
979	+
980	+	// excludesForAtom was constructed to use row/column indices in the MPI
981	+	// version, and to use local IDs in the non-MPI version:
982	+
983	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
984	+	i != excludesForAtom[atom1].end(); ++i) {
985	+	if ( (*i) == atom2 ) return true;
986	+	}
987	+
988	+	return false;
989	+	}
990	+
991	+
992		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
993		#ifdef IS_MPI
994		atomRowData.force[atom1] += fg;
#	Line 312 | Line 1003 | namespace OpenMD {
1003		#else
1004		snap_->atomData.force[atom2] += fg;
1005		#endif
315	–
1006		}
1007
1008		// filling interaction blocks with pointers
1009	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1009	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1010	>	int atom1, int atom2,
1011	>	bool newAtom1) {
1012
1013	<	InteractionData idat;
1013	>	idat.excluded = excludeAtomPair(atom1, atom2);
1014	>
1015	>	if (newAtom1) {
1016	>
1017	>	#ifdef IS_MPI
1018	>	idat.atid1 = identsRow[atom1];
1019	>	idat.atid2 = identsCol[atom2];
1020	>
1021	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1022	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1023	>	} else {
1024	>	idat.sameRegion = false;
1025	>	}
1026	>
1027	>	if (storageLayout_ & DataStorage::dslAmat) {
1028	>	idat.A1 = &(atomRowData.aMat[atom1]);
1029	>	idat.A2 = &(atomColData.aMat[atom2]);
1030	>	}
1031	>
1032	>	if (storageLayout_ & DataStorage::dslTorque) {
1033	>	idat.t1 = &(atomRowData.torque[atom1]);
1034	>	idat.t2 = &(atomColData.torque[atom2]);
1035	>	}
1036	>
1037	>	if (storageLayout_ & DataStorage::dslDipole) {
1038	>	idat.dipole1 = &(atomRowData.dipole[atom1]);
1039	>	idat.dipole2 = &(atomColData.dipole[atom2]);
1040	>	}
1041	>
1042	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1043	>	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1044	>	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1045	>	}
1046	>
1047	>	if (storageLayout_ & DataStorage::dslDensity) {
1048	>	idat.rho1 = &(atomRowData.density[atom1]);
1049	>	idat.rho2 = &(atomColData.density[atom2]);
1050	>	}
1051	>
1052	>	if (storageLayout_ & DataStorage::dslFunctional) {
1053	>	idat.frho1 = &(atomRowData.functional[atom1]);
1054	>	idat.frho2 = &(atomColData.functional[atom2]);
1055	>	}
1056	>
1057	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1058	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1059	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1060	>	}
1061	>
1062	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1063	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1064	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1065	>	}
1066	>
1067	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1068	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1069	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1070	>	}
1071	>
1072	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1073	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1074	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1075	>	}
1076	>
1077	>	#else
1078	>
1079	>	idat.atid1 = idents[atom1];
1080	>	idat.atid2 = idents[atom2];
1081	>
1082	>	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1083	>	idat.sameRegion = (regions[atom1] == regions[atom2]);
1084	>	} else {
1085	>	idat.sameRegion = false;
1086	>	}
1087	>
1088	>	if (storageLayout_ & DataStorage::dslAmat) {
1089	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1090	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1091	>	}
1092	>
1093	>	if (storageLayout_ & DataStorage::dslTorque) {
1094	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1095	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1096	>	}
1097	>
1098	>	if (storageLayout_ & DataStorage::dslDipole) {
1099	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1100	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1101	>	}
1102	>
1103	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1104	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1105	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1106	>	}
1107	>
1108	>	if (storageLayout_ & DataStorage::dslDensity) {
1109	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1110	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1111	>	}
1112	>
1113	>	if (storageLayout_ & DataStorage::dslFunctional) {
1114	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1115	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1116	>	}
1117	>
1118	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1119	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1120	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1121	>	}
1122	>
1123	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1124	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1125	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1126	>	}
1127	>
1128	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1129	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1130	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1131	>	}
1132	>
1133	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1134	>	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1135	>	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1136	>	}
1137	>	#endif
1138	>
1139	>	} else {
1140	>	// atom1 is not new, so don't bother updating properties of that atom:
1141		#ifdef IS_MPI
1142	+	idat.atid2 = identsCol[atom2];
1143	+
1144	+	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1145	+	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1146	+	} else {
1147	+	idat.sameRegion = false;
1148	+	}
1149	+
1150		if (storageLayout_ & DataStorage::dslAmat) {
1151	<	idat.A1 = atomRowData.aMat[atom1];
325	<	idat.A2 = atomColData.aMat[atom2];
1151	>	idat.A2 = &(atomColData.aMat[atom2]);
1152		}
1153	+
1154	+	if (storageLayout_ & DataStorage::dslTorque) {
1155	+	idat.t2 = &(atomColData.torque[atom2]);
1156	+	}
1157
1158	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1159	<	idat.eFrame1 = atomRowData.electroFrame[atom1];
330	<	idat.eFrame2 = atomColData.electroFrame[atom2];
1158	>	if (storageLayout_ & DataStorage::dslDipole) {
1159	>	idat.dipole2 = &(atomColData.dipole[atom2]);
1160		}
1161
1162	<	if (storageLayout_ & DataStorage::dslTorque) {
1163	<	idat.t1 = atomRowData.torque[atom1];
335	<	idat.t2 = atomColData.torque[atom2];
1162	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1163	>	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1164		}
1165
1166		if (storageLayout_ & DataStorage::dslDensity) {
1167	<	idat.rho1 = atomRowData.density[atom1];
340	<	idat.rho2 = atomColData.density[atom2];
1167	>	idat.rho2 = &(atomColData.density[atom2]);
1168		}
1169
1170	+	if (storageLayout_ & DataStorage::dslFunctional) {
1171	+	idat.frho2 = &(atomColData.functional[atom2]);
1172	+	}
1173	+
1174		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1175	<	idat.dfrho1 = atomRowData.functionalDerivative[atom1];
345	<	idat.dfrho2 = atomColData.functionalDerivative[atom2];
1175	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1176		}
1177	+
1178	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1179	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1180	+	}
1181	+
1182	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1183	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1184	+	}
1185	+
1186	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1187	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1188	+	}
1189	+
1190	+	#else
1191	+	idat.atid2 = idents[atom2];
1192	+
1193	+	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1194	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1195	+	} else {
1196	+	idat.sameRegion = false;
1197	+	}
1198	+
1199	+	if (storageLayout_ & DataStorage::dslAmat) {
1200	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1201	+	}
1202	+
1203	+	if (storageLayout_ & DataStorage::dslTorque) {
1204	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1205	+	}
1206	+
1207	+	if (storageLayout_ & DataStorage::dslDipole) {
1208	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1209	+	}
1210	+
1211	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1212	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1213	+	}
1214	+
1215	+	if (storageLayout_ & DataStorage::dslDensity) {
1216	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1217	+	}
1218	+
1219	+	if (storageLayout_ & DataStorage::dslFunctional) {
1220	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1221	+	}
1222	+
1223	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1224	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1225	+	}
1226	+
1227	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1228	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1229	+	}
1230	+
1231	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1232	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1233	+	}
1234	+
1235	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1236	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1237	+	}
1238	+
1239		#endif
1240	<
1240	>	}
1241		}
1242	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1243	<	}
1244	<	SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
1242	>
1243	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat,
1244	>	int atom1, int atom2) {
1245	>	#ifdef IS_MPI
1246	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1247	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1248	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1249	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1250	>
1251	>	atomRowData.force[atom1] += *(idat.f1);
1252	>	atomColData.force[atom2] -= *(idat.f1);
1253	>
1254	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1255	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1256	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1257	>	}
1258	>
1259	>	if (storageLayout_ & DataStorage::dslElectricField) {
1260	>	atomRowData.electricField[atom1] += *(idat.eField1);
1261	>	atomColData.electricField[atom2] += *(idat.eField2);
1262	>	}
1263	>
1264	>	if (storageLayout_ & DataStorage::dslSitePotential) {
1265	>	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1266	>	atomColData.sitePotential[atom2] += *(idat.sPot2);
1267	>	}
1268	>
1269	>	#else
1270	>	pairwisePot += *(idat.pot);
1271	>	excludedPot += *(idat.excludedPot);
1272	>
1273	>	snap_->atomData.force[atom1] += *(idat.f1);
1274	>	snap_->atomData.force[atom2] -= *(idat.f1);
1275	>
1276	>	if (idat.doParticlePot) {
1277	>	// This is the pairwise contribution to the particle pot.  The
1278	>	// embedding contribution is added in each of the low level
1279	>	// non-bonded routines.  In parallel, this calculation is done
1280	>	// in collectData, not in unpackInteractionData.
1281	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1282	>	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1283	>	}
1284	>
1285	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1286	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1287	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1288	>	}
1289	>
1290	>	if (storageLayout_ & DataStorage::dslElectricField) {
1291	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1292	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1293	>	}
1294	>
1295	>	if (storageLayout_ & DataStorage::dslSitePotential) {
1296	>	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1297	>	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1298	>	}
1299	>
1300	>	#endif
1301	>
1302		}
1303
1304	+	/*
1305	+	* buildNeighborList
1306	+	*
1307	+	* Constructs the Verlet neighbor list for a force-matrix
1308	+	* decomposition.  In this case, each processor is responsible for
1309	+	* row-site interactions with column-sites.
1310	+	*
1311	+	* neighborList is returned as a packed array of neighboring
1312	+	* column-ordered CutoffGroups.  The starting position in
1313	+	* neighborList for each row-ordered CutoffGroup is given by the
1314	+	* returned vector point.
1315	+	*/
1316	+	void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
1317	+	vector<int>& point) {
1318	+	neighborList.clear();
1319	+	point.clear();
1320	+	int len = 0;
1321	+
1322	+	bool doAllPairs = false;
1323	+
1324	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1325	+	Mat3x3d box;
1326	+	Mat3x3d invBox;
1327	+
1328	+	Vector3d rs, scaled, dr;
1329	+	Vector3i whichCell;
1330	+	int cellIndex;
1331	+
1332	+	#ifdef IS_MPI
1333	+	cellListRow_.clear();
1334	+	cellListCol_.clear();
1335	+	point.resize(nGroupsInRow_+1);
1336	+	#else
1337	+	cellList_.clear();
1338	+	point.resize(nGroups_+1);
1339	+	#endif
1340	+
1341	+	if (!usePeriodicBoundaryConditions_) {
1342	+	box = snap_->getBoundingBox();
1343	+	invBox = snap_->getInvBoundingBox();
1344	+	} else {
1345	+	box = snap_->getHmat();
1346	+	invBox = snap_->getInvHmat();
1347	+	}
1348	+
1349	+	Vector3d A = box.getColumn(0);
1350	+	Vector3d B = box.getColumn(1);
1351	+	Vector3d C = box.getColumn(2);
1352	+
1353	+	// Required for triclinic cells
1354	+	Vector3d AxB = cross(A, B);
1355	+	Vector3d BxC = cross(B, C);
1356	+	Vector3d CxA = cross(C, A);
1357	+
1358	+	// unit vectors perpendicular to the faces of the triclinic cell:
1359	+	AxB.normalize();
1360	+	BxC.normalize();
1361	+	CxA.normalize();
1362	+
1363	+	// A set of perpendicular lengths in triclinic cells:
1364	+	RealType Wa = abs(dot(A, BxC));
1365	+	RealType Wb = abs(dot(B, CxA));
1366	+	RealType Wc = abs(dot(C, AxB));
1367	+
1368	+	nCells_.x() = int( Wa / rList_ );
1369	+	nCells_.y() = int( Wb / rList_ );
1370	+	nCells_.z() = int( Wc / rList_ );
1371	+
1372	+	// handle small boxes where the cell offsets can end up repeating cells
1373	+	if (nCells_.x() < 3) doAllPairs = true;
1374	+	if (nCells_.y() < 3) doAllPairs = true;
1375	+	if (nCells_.z() < 3) doAllPairs = true;
1376	+
1377	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1378	+
1379	+	#ifdef IS_MPI
1380	+	cellListRow_.resize(nCtot);
1381	+	cellListCol_.resize(nCtot);
1382	+	#else
1383	+	cellList_.resize(nCtot);
1384	+	#endif
1385	+
1386	+	if (!doAllPairs) {
1387	+
1388	+	#ifdef IS_MPI
1389	+
1390	+	for (int i = 0; i < nGroupsInRow_; i++) {
1391	+	rs = cgRowData.position[i];
1392	+
1393	+	// scaled positions relative to the box vectors
1394	+	scaled = invBox * rs;
1395	+
1396	+	// wrap the vector back into the unit box by subtracting integer box
1397	+	// numbers
1398	+	for (int j = 0; j < 3; j++) {
1399	+	scaled[j] -= roundMe(scaled[j]);
1400	+	scaled[j] += 0.5;
1401	+	// Handle the special case when an object is exactly on the
1402	+	// boundary (a scaled coordinate of 1.0 is the same as
1403	+	// scaled coordinate of 0.0)
1404	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1405	+	}
1406	+
1407	+	// find xyz-indices of cell that cutoffGroup is in.
1408	+	whichCell.x() = nCells_.x() * scaled.x();
1409	+	whichCell.y() = nCells_.y() * scaled.y();
1410	+	whichCell.z() = nCells_.z() * scaled.z();
1411	+
1412	+	// find single index of this cell:
1413	+	cellIndex = Vlinear(whichCell, nCells_);
1414	+
1415	+	// add this cutoff group to the list of groups in this cell;
1416	+	cellListRow_[cellIndex].push_back(i);
1417	+	}
1418	+	for (int i = 0; i < nGroupsInCol_; i++) {
1419	+	rs = cgColData.position[i];
1420	+
1421	+	// scaled positions relative to the box vectors
1422	+	scaled = invBox * rs;
1423	+
1424	+	// wrap the vector back into the unit box by subtracting integer box
1425	+	// numbers
1426	+	for (int j = 0; j < 3; j++) {
1427	+	scaled[j] -= roundMe(scaled[j]);
1428	+	scaled[j] += 0.5;
1429	+	// Handle the special case when an object is exactly on the
1430	+	// boundary (a scaled coordinate of 1.0 is the same as
1431	+	// scaled coordinate of 0.0)
1432	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1433	+	}
1434	+
1435	+	// find xyz-indices of cell that cutoffGroup is in.
1436	+	whichCell.x() = nCells_.x() * scaled.x();
1437	+	whichCell.y() = nCells_.y() * scaled.y();
1438	+	whichCell.z() = nCells_.z() * scaled.z();
1439	+
1440	+	// find single index of this cell:
1441	+	cellIndex = Vlinear(whichCell, nCells_);
1442	+
1443	+	// add this cutoff group to the list of groups in this cell;
1444	+	cellListCol_[cellIndex].push_back(i);
1445	+	}
1446	+
1447	+	#else
1448	+	for (int i = 0; i < nGroups_; i++) {
1449	+	rs = snap_->cgData.position[i];
1450	+
1451	+	// scaled positions relative to the box vectors
1452	+	scaled = invBox * rs;
1453	+
1454	+	// wrap the vector back into the unit box by subtracting integer box
1455	+	// numbers
1456	+	for (int j = 0; j < 3; j++) {
1457	+	scaled[j] -= roundMe(scaled[j]);
1458	+	scaled[j] += 0.5;
1459	+	// Handle the special case when an object is exactly on the
1460	+	// boundary (a scaled coordinate of 1.0 is the same as
1461	+	// scaled coordinate of 0.0)
1462	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1463	+	}
1464	+
1465	+	// find xyz-indices of cell that cutoffGroup is in.
1466	+	whichCell.x() = int(nCells_.x() * scaled.x());
1467	+	whichCell.y() = int(nCells_.y() * scaled.y());
1468	+	whichCell.z() = int(nCells_.z() * scaled.z());
1469	+
1470	+	// find single index of this cell:
1471	+	cellIndex = Vlinear(whichCell, nCells_);
1472	+
1473	+	// add this cutoff group to the list of groups in this cell;
1474	+	cellList_[cellIndex].push_back(i);
1475	+	}
1476	+
1477	+	#endif
1478	+
1479	+	#ifdef IS_MPI
1480	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1481	+	rs = cgRowData.position[j1];
1482	+	#else
1483	+
1484	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1485	+	rs = snap_->cgData.position[j1];
1486	+	#endif
1487	+	point[j1] = len;
1488	+
1489	+	// scaled positions relative to the box vectors
1490	+	scaled = invBox * rs;
1491	+
1492	+	// wrap the vector back into the unit box by subtracting integer box
1493	+	// numbers
1494	+	for (int j = 0; j < 3; j++) {
1495	+	scaled[j] -= roundMe(scaled[j]);
1496	+	scaled[j] += 0.5;
1497	+	// Handle the special case when an object is exactly on the
1498	+	// boundary (a scaled coordinate of 1.0 is the same as
1499	+	// scaled coordinate of 0.0)
1500	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1501	+	}
1502	+
1503	+	// find xyz-indices of cell that cutoffGroup is in.
1504	+	whichCell.x() = nCells_.x() * scaled.x();
1505	+	whichCell.y() = nCells_.y() * scaled.y();
1506	+	whichCell.z() = nCells_.z() * scaled.z();
1507	+
1508	+	// find single index of this cell:
1509	+	int m1 = Vlinear(whichCell, nCells_);
1510	+
1511	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1512	+	os != cellOffsets_.end(); ++os) {
1513	+
1514	+	Vector3i m2v = whichCell + (*os);
1515	+
1516	+	if (m2v.x() >= nCells_.x()) {
1517	+	m2v.x() = 0;
1518	+	} else if (m2v.x() < 0) {
1519	+	m2v.x() = nCells_.x() - 1;
1520	+	}
1521	+
1522	+	if (m2v.y() >= nCells_.y()) {
1523	+	m2v.y() = 0;
1524	+	} else if (m2v.y() < 0) {
1525	+	m2v.y() = nCells_.y() - 1;
1526	+	}
1527	+
1528	+	if (m2v.z() >= nCells_.z()) {
1529	+	m2v.z() = 0;
1530	+	} else if (m2v.z() < 0) {
1531	+	m2v.z() = nCells_.z() - 1;
1532	+	}
1533	+	int m2 = Vlinear (m2v, nCells_);
1534	+	#ifdef IS_MPI
1535	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1536	+	j2 != cellListCol_[m2].end(); ++j2) {
1537	+
1538	+	// In parallel, we need to visit *all* pairs of row
1539	+	// & column indicies and will divide labor in the
1540	+	// force evaluation later.
1541	+	dr = cgColData.position[(*j2)] - rs;
1542	+	if (usePeriodicBoundaryConditions_) {
1543	+	snap_->wrapVector(dr);
1544	+	}
1545	+	if (dr.lengthSquare() < rListSq_) {
1546	+	neighborList.push_back( (*j2) );
1547	+	++len;
1548	+	}
1549	+	}
1550	+	#else
1551	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1552	+	j2 != cellList_[m2].end(); ++j2) {
1553	+
1554	+	// Always do this if we're in different cells or if
1555	+	// we're in the same cell and the global index of
1556	+	// the j2 cutoff group is greater than or equal to
1557	+	// the j1 cutoff group.  Note that Rappaport's code
1558	+	// has a "less than" conditional here, but that
1559	+	// deals with atom-by-atom computation.  OpenMD
1560	+	// allows atoms within a single cutoff group to
1561	+	// interact with each other.
1562	+
1563	+	if ( (*j2) >= j1 ) {
1564	+
1565	+	dr = snap_->cgData.position[(*j2)] - rs;
1566	+	if (usePeriodicBoundaryConditions_) {
1567	+	snap_->wrapVector(dr);
1568	+	}
1569	+	if ( dr.lengthSquare() < rListSq_) {
1570	+	neighborList.push_back( (*j2) );
1571	+	++len;
1572	+	}
1573	+	}
1574	+	}
1575	+	#endif
1576	+	}
1577	+	}
1578	+	} else {
1579	+	// branch to do all cutoff group pairs
1580	+	#ifdef IS_MPI
1581	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1582	+	point[j1] = len;
1583	+	rs = cgRowData.position[j1];
1584	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1585	+	dr = cgColData.position[j2] - rs;
1586	+	if (usePeriodicBoundaryConditions_) {
1587	+	snap_->wrapVector(dr);
1588	+	}
1589	+	if (dr.lengthSquare() < rListSq_) {
1590	+	neighborList.push_back( j2 );
1591	+	++len;
1592	+	}
1593	+	}
1594	+	}
1595	+	#else
1596	+	// include all groups here.
1597	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1598	+	point[j1] = len;
1599	+	rs = snap_->cgData.position[j1];
1600	+	// include self group interactions j2 == j1
1601	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1602	+	dr = snap_->cgData.position[j2] - rs;
1603	+	if (usePeriodicBoundaryConditions_) {
1604	+	snap_->wrapVector(dr);
1605	+	}
1606	+	if (dr.lengthSquare() < rListSq_) {
1607	+	neighborList.push_back( j2 );
1608	+	++len;
1609	+	}
1610	+	}
1611	+	}
1612	+	#endif
1613	+	}
1614	+
1615	+	#ifdef IS_MPI
1616	+	point[nGroupsInRow_] = len;
1617	+	#else
1618	+	point[nGroups_] = len;
1619	+	#endif
1620
1621	+	// save the local cutoff group positions for the check that is
1622	+	// done on each loop:
1623	+	saved_CG_positions_.clear();
1624	+	saved_CG_positions_.reserve(nGroups_);
1625	+	for (int i = 0; i < nGroups_; i++)
1626	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1627	+	}
1628		} //end namespace OpenMD

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