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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 2061 by gezelter, Tue Mar 3 16:24:44 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	>	snap_ = sman_->getCurrentSnapshot();
517	>	storageLayout_ = sman_->getStorageLayout();
518		#ifdef IS_MPI
149	–	Snapshot* snap = sman_->getCurrentSnapshot();
519
520	<	if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
520	>	if (storageLayout_ & DataStorage::dslDensity) {
521	>
522	>	AtomPlanRealRow->scatter(atomRowData.density,
523	>	snap_->atomData.density);
524	>
525	>	int n = snap_->atomData.density.size();
526	>	vector<RealType> rho_tmp(n, 0.0);
527	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
528	>	for (int i = 0; i < n; i++)
529	>	snap_->atomData.density[i] += rho_tmp[i];
530	>	}
531
532	<	AtomCommRealI->scatter(snap->atomIData.density,
533	<	snap->atomData.density);
534	<
535	<	int n = snap->atomData.density.size();
536	<	std::vector<RealType> rho_tmp(n, 0.0);
537	<	AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
532	>	// this isn't necessary if we don't have polarizable atoms, but
533	>	// we'll leave it here for now.
534	>	if (storageLayout_ & DataStorage::dslElectricField) {
535	>
536	>	AtomPlanVectorRow->scatter(atomRowData.electricField,
537	>	snap_->atomData.electricField);
538	>
539	>	int n = snap_->atomData.electricField.size();
540	>	vector<Vector3d> field_tmp(n, V3Zero);
541	>	AtomPlanVectorColumn->scatter(atomColData.electricField,
542	>	field_tmp);
543		for (int i = 0; i < n; i++)
544	<	snap->atomData.density[i] += rho_tmp[i];
544	>	snap_->atomData.electricField[i] += field_tmp[i];
545		}
546		#endif
547		}
548	<
549	<	void ForceDecomposition::distributeIntermediateData() {
548	>
549	>	/*
550	>	* redistributes information obtained during the pre-pair loop out to
551	>	* row and column-indexed data structures
552	>	*/
553	>	void ForceMatrixDecomposition::distributeIntermediateData() {
554	>	snap_ = sman_->getCurrentSnapshot();
555	>	storageLayout_ = sman_->getStorageLayout();
556		#ifdef IS_MPI
557	<	Snapshot* snap = sman_->getCurrentSnapshot();
558	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
559	<	AtomCommRealI->gather(snap->atomData.functional,
560	<	snap->atomIData.functional);
561	<	AtomCommRealJ->gather(snap->atomData.functional,
172	<	snap->atomJData.functional);
557	>	if (storageLayout_ & DataStorage::dslFunctional) {
558	>	AtomPlanRealRow->gather(snap_->atomData.functional,
559	>	atomRowData.functional);
560	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
561	>	atomColData.functional);
562		}
563
564	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
565	<	AtomCommRealI->gather(snap->atomData.functionalDerivative,
566	<	snap->atomIData.functionalDerivative);
567	<	AtomCommRealJ->gather(snap->atomData.functionalDerivative,
568	<	snap->atomJData.functionalDerivative);
564	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
565	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
566	>	atomRowData.functionalDerivative);
567	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
568	>	atomColData.functionalDerivative);
569		}
570		#endif
571		}
572
573
574	<	void ForceDecomposition::collectData() {
575	<	#ifdef IS_MPI
576	<	Snapshot* snap = sman_->getCurrentSnapshot();
577	<
578	<	int n = snap->atomData.force.size();
574	>	void ForceMatrixDecomposition::collectData() {
575	>	snap_ = sman_->getCurrentSnapshot();
576	>	storageLayout_ = sman_->getStorageLayout();
577	>	#ifdef IS_MPI
578	>	int n = snap_->atomData.force.size();
579		vector<Vector3d> frc_tmp(n, V3Zero);
580
581	<	AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
581	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
582		for (int i = 0; i < n; i++) {
583	<	snap->atomData.force[i] += frc_tmp[i];
583	>	snap_->atomData.force[i] += frc_tmp[i];
584		frc_tmp[i] = 0.0;
585		}
586
587	<	AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
588	<	for (int i = 0; i < n; i++)
589	<	snap->atomData.force[i] += frc_tmp[i];
590	<
591	<
592	<	if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
587	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
588	>	for (int i = 0; i < n; i++) {
589	>	snap_->atomData.force[i] += frc_tmp[i];
590	>	}
591	>
592	>	if (storageLayout_ & DataStorage::dslTorque) {
593
594	<	int nt = snap->atomData.force.size();
594	>	int nt = snap_->atomData.torque.size();
595		vector<Vector3d> trq_tmp(nt, V3Zero);
596
597	<	AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
598	<	for (int i = 0; i < n; i++) {
599	<	snap->atomData.torque[i] += trq_tmp[i];
597	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
598	>	for (int i = 0; i < nt; i++) {
599	>	snap_->atomData.torque[i] += trq_tmp[i];
600		trq_tmp[i] = 0.0;
601		}
602
603	<	AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
604	<	for (int i = 0; i < n; i++)
605	<	snap->atomData.torque[i] += trq_tmp[i];
603	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
604	>	for (int i = 0; i < nt; i++)
605	>	snap_->atomData.torque[i] += trq_tmp[i];
606		}
607	+
608	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
609	+
610	+	int ns = snap_->atomData.skippedCharge.size();
611	+	vector<RealType> skch_tmp(ns, 0.0);
612	+
613	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
614	+	for (int i = 0; i < ns; i++) {
615	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
616	+	skch_tmp[i] = 0.0;
617	+	}
618	+
619	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
620	+	for (int i = 0; i < ns; i++)
621	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
622	+
623	+	}
624
625	<	int nLocal = snap->getNumberOfAtoms();
625	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
626
627	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
628	<	vector<RealType> (nLocal, 0.0));
627	>	int nq = snap_->atomData.flucQFrc.size();
628	>	vector<RealType> fqfrc_tmp(nq, 0.0);
629	>
630	>	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
631	>	for (int i = 0; i < nq; i++) {
632	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
633	>	fqfrc_tmp[i] = 0.0;
634	>	}
635	>
636	>	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
637	>	for (int i = 0; i < nq; i++)
638	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
639	>
640	>	}
641	>
642	>	if (storageLayout_ & DataStorage::dslElectricField) {
643	>
644	>	int nef = snap_->atomData.electricField.size();
645	>	vector<Vector3d> efield_tmp(nef, V3Zero);
646	>
647	>	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
648	>	for (int i = 0; i < nef; i++) {
649	>	snap_->atomData.electricField[i] += efield_tmp[i];
650	>	efield_tmp[i] = 0.0;
651	>	}
652	>
653	>	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
654	>	for (int i = 0; i < nef; i++)
655	>	snap_->atomData.electricField[i] += efield_tmp[i];
656	>	}
657	>
658	>	if (storageLayout_ & DataStorage::dslSitePotential) {
659	>
660	>	int nsp = snap_->atomData.sitePotential.size();
661	>	vector<RealType> sp_tmp(nsp, 0.0);
662	>
663	>	AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
664	>	for (int i = 0; i < nsp; i++) {
665	>	snap_->atomData.sitePotential[i] += sp_tmp[i];
666	>	sp_tmp[i] = 0.0;
667	>	}
668	>
669	>	AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
670	>	for (int i = 0; i < nsp; i++)
671	>	snap_->atomData.sitePotential[i] += sp_tmp[i];
672	>	}
673	>
674	>	nLocal_ = snap_->getNumberOfAtoms();
675	>
676	>	vector<potVec> pot_temp(nLocal_,
677	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
678	>	vector<potVec> expot_temp(nLocal_,
679	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
680	>
681	>	// scatter/gather pot_row into the members of my column
682	>
683	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
684	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
685	>
686	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
687	>	pairwisePot += pot_temp[ii];
688	>
689	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
690	>	excludedPot += expot_temp[ii];
691	>
692	>	if (storageLayout_ & DataStorage::dslParticlePot) {
693	>	// This is the pairwise contribution to the particle pot.  The
694	>	// embedding contribution is added in each of the low level
695	>	// non-bonded routines.  In single processor, this is done in
696	>	// unpackInteractionData, not in collectData.
697	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
698	>	for (int i = 0; i < nLocal_; i++) {
699	>	// factor of two is because the total potential terms are divided
700	>	// by 2 in parallel due to row/ column scatter
701	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
702	>	}
703	>	}
704	>	}
705	>
706	>	fill(pot_temp.begin(), pot_temp.end(),
707	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
708	>	fill(expot_temp.begin(), expot_temp.end(),
709	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
710	>
711	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
712	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
713
714	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
715	<	AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
716	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
717	<	pot_local[i] += pot_temp[i][ii];
714	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
715	>	pairwisePot += pot_temp[ii];
716	>
717	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
718	>	excludedPot += expot_temp[ii];
719	>
720	>	if (storageLayout_ & DataStorage::dslParticlePot) {
721	>	// This is the pairwise contribution to the particle pot.  The
722	>	// embedding contribution is added in each of the low level
723	>	// non-bonded routines.  In single processor, this is done in
724	>	// unpackInteractionData, not in collectData.
725	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
726	>	for (int i = 0; i < nLocal_; i++) {
727	>	// factor of two is because the total potential terms are divided
728	>	// by 2 in parallel due to row/ column scatter
729	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
730	>	}
731	>	}
732	>	}
733	>
734	>	if (storageLayout_ & DataStorage::dslParticlePot) {
735	>	int npp = snap_->atomData.particlePot.size();
736	>	vector<RealType> ppot_temp(npp, 0.0);
737	>
738	>	// This is the direct or embedding contribution to the particle
739	>	// pot.
740	>
741	>	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
742	>	for (int i = 0; i < npp; i++) {
743	>	snap_->atomData.particlePot[i] += ppot_temp[i];
744	>	}
745	>
746	>	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
747	>
748	>	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
749	>	for (int i = 0; i < npp; i++) {
750	>	snap_->atomData.particlePot[i] += ppot_temp[i];
751	>	}
752	>	}
753	>
754	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
755	>	RealType ploc1 = pairwisePot[ii];
756	>	RealType ploc2 = 0.0;
757	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
758	>	pairwisePot[ii] = ploc2;
759	>	}
760	>
761	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
762	>	RealType ploc1 = excludedPot[ii];
763	>	RealType ploc2 = 0.0;
764	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
765	>	excludedPot[ii] = ploc2;
766	>	}
767	>
768	>	// Here be dragons.
769	>	MPI_Comm col = colComm.getComm();
770	>
771	>	MPI_Allreduce(MPI_IN_PLACE,
772	>	&snap_->frameData.conductiveHeatFlux[0], 3,
773	>	MPI_REALTYPE, MPI_SUM, col);
774	>
775	>
776	>	#endif
777	>
778	>	}
779	>
780	>	/**
781	>	* Collects information obtained during the post-pair (and embedding
782	>	* functional) loops onto local data structures.
783	>	*/
784	>	void ForceMatrixDecomposition::collectSelfData() {
785	>	snap_ = sman_->getCurrentSnapshot();
786	>	storageLayout_ = sman_->getStorageLayout();
787	>
788	>	#ifdef IS_MPI
789	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
790	>	RealType ploc1 = embeddingPot[ii];
791	>	RealType ploc2 = 0.0;
792	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
793	>	embeddingPot[ii] = ploc2;
794	>	}
795	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
796	>	RealType ploc1 = excludedSelfPot[ii];
797	>	RealType ploc2 = 0.0;
798	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
799	>	excludedSelfPot[ii] = ploc2;
800	>	}
801	>	#endif
802	>
803	>	}
804	>
805	>
806	>
807	>	int& ForceMatrixDecomposition::getNAtomsInRow() {
808	>	#ifdef IS_MPI
809	>	return nAtomsInRow_;
810	>	#else
811	>	return nLocal_;
812	>	#endif
813	>	}
814	>
815	>	/**
816	>	* returns the list of atoms belonging to this group.
817	>	*/
818	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
819	>	#ifdef IS_MPI
820	>	return groupListRow_[cg1];
821	>	#else
822	>	return groupList_[cg1];
823	>	#endif
824	>	}
825	>
826	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
827	>	#ifdef IS_MPI
828	>	return groupListCol_[cg2];
829	>	#else
830	>	return groupList_[cg2];
831	>	#endif
832	>	}
833	>
834	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
835	>	Vector3d d;
836	>
837	>	#ifdef IS_MPI
838	>	d = cgColData.position[cg2] - cgRowData.position[cg1];
839	>	#else
840	>	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
841	>	#endif
842	>
843	>	if (usePeriodicBoundaryConditions_) {
844	>	snap_->wrapVector(d);
845	>	}
846	>	return d;
847	>	}
848	>
849	>	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
850	>	#ifdef IS_MPI
851	>	return cgColData.velocity[cg2];
852	>	#else
853	>	return snap_->cgData.velocity[cg2];
854	>	#endif
855	>	}
856	>
857	>	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
858	>	#ifdef IS_MPI
859	>	return atomColData.velocity[atom2];
860	>	#else
861	>	return snap_->atomData.velocity[atom2];
862	>	#endif
863	>	}
864	>
865	>
866	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
867	>
868	>	Vector3d d;
869	>
870	>	#ifdef IS_MPI
871	>	d = cgRowData.position[cg1] - atomRowData.position[atom1];
872	>	#else
873	>	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
874	>	#endif
875	>	if (usePeriodicBoundaryConditions_) {
876	>	snap_->wrapVector(d);
877	>	}
878	>	return d;
879	>	}
880	>
881	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
882	>	Vector3d d;
883	>
884	>	#ifdef IS_MPI
885	>	d = cgColData.position[cg2] - atomColData.position[atom2];
886	>	#else
887	>	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
888	>	#endif
889	>	if (usePeriodicBoundaryConditions_) {
890	>	snap_->wrapVector(d);
891	>	}
892	>	return d;
893	>	}
894	>
895	>	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
896	>	#ifdef IS_MPI
897	>	return massFactorsRow[atom1];
898	>	#else
899	>	return massFactors[atom1];
900	>	#endif
901	>	}
902	>
903	>	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
904	>	#ifdef IS_MPI
905	>	return massFactorsCol[atom2];
906	>	#else
907	>	return massFactors[atom2];
908	>	#endif
909	>
910	>	}
911	>
912	>	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
913	>	Vector3d d;
914	>
915	>	#ifdef IS_MPI
916	>	d = atomColData.position[atom2] - atomRowData.position[atom1];
917	>	#else
918	>	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
919	>	#endif
920	>	if (usePeriodicBoundaryConditions_) {
921	>	snap_->wrapVector(d);
922	>	}
923	>	return d;
924	>	}
925	>
926	>	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
927	>	return excludesForAtom[atom1];
928	>	}
929	>
930	>	/**
931	>	* We need to exclude some overcounted interactions that result from
932	>	* the parallel decomposition.
933	>	*/
934	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
935	>	int unique_id_1, unique_id_2;
936	>
937	>	#ifdef IS_MPI
938	>	// in MPI, we have to look up the unique IDs for each atom
939	>	unique_id_1 = AtomRowToGlobal[atom1];
940	>	unique_id_2 = AtomColToGlobal[atom2];
941	>	// group1 = cgRowToGlobal[cg1];
942	>	// group2 = cgColToGlobal[cg2];
943	>	#else
944	>	unique_id_1 = AtomLocalToGlobal[atom1];
945	>	unique_id_2 = AtomLocalToGlobal[atom2];
946	>	int group1 = cgLocalToGlobal[cg1];
947	>	int group2 = cgLocalToGlobal[cg2];
948	>	#endif
949	>
950	>	if (unique_id_1 == unique_id_2) return true;
951	>
952	>	#ifdef IS_MPI
953	>	// this prevents us from doing the pair on multiple processors
954	>	if (unique_id_1 < unique_id_2) {
955	>	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
956	>	} else {
957	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
958	>	}
959	>	#endif
960	>
961	>	#ifndef IS_MPI
962	>	if (group1 == group2) {
963	>	if (unique_id_1 < unique_id_2) return true;
964	>	}
965	>	#endif
966	>
967	>	return false;
968	>	}
969	>
970	>	/**
971	>	* We need to handle the interactions for atoms who are involved in
972	>	* the same rigid body as well as some short range interactions
973	>	* (bonds, bends, torsions) differently from other interactions.
974	>	* We'll still visit the pairwise routines, but with a flag that
975	>	* tells those routines to exclude the pair from direct long range
976	>	* interactions.  Some indirect interactions (notably reaction
977	>	* field) must still be handled for these pairs.
978	>	*/
979	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
980	>
981	>	// excludesForAtom was constructed to use row/column indices in the MPI
982	>	// version, and to use local IDs in the non-MPI version:
983	>
984	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
985	>	i != excludesForAtom[atom1].end(); ++i) {
986	>	if ( (*i) == atom2 ) return true;
987	>	}
988	>
989	>	return false;
990	>	}
991	>
992	>
993	>	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
994	>	#ifdef IS_MPI
995	>	atomRowData.force[atom1] += fg;
996	>	#else
997	>	snap_->atomData.force[atom1] += fg;
998	>	#endif
999	>	}
1000	>
1001	>	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
1002	>	#ifdef IS_MPI
1003	>	atomColData.force[atom2] += fg;
1004	>	#else
1005	>	snap_->atomData.force[atom2] += fg;
1006	>	#endif
1007	>	}
1008	>
1009	>	// filling interaction blocks with pointers
1010	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1011	>	int atom1, int atom2,
1012	>	bool newAtom1) {
1013	>
1014	>	idat.excluded = excludeAtomPair(atom1, atom2);
1015	>
1016	>	if (newAtom1) {
1017	>
1018	>	#ifdef IS_MPI
1019	>	idat.atid1 = identsRow[atom1];
1020	>	idat.atid2 = identsCol[atom2];
1021	>
1022	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1023	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1024	>	} else {
1025	>	idat.sameRegion = false;
1026		}
1027	+
1028	+	if (storageLayout_ & DataStorage::dslAmat) {
1029	+	idat.A1 = &(atomRowData.aMat[atom1]);
1030	+	idat.A2 = &(atomColData.aMat[atom2]);
1031	+	}
1032	+
1033	+	if (storageLayout_ & DataStorage::dslTorque) {
1034	+	idat.t1 = &(atomRowData.torque[atom1]);
1035	+	idat.t2 = &(atomColData.torque[atom2]);
1036	+	}
1037	+
1038	+	if (storageLayout_ & DataStorage::dslDipole) {
1039	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1040	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1041	+	}
1042	+
1043	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1044	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1045	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1046	+	}
1047	+
1048	+	if (storageLayout_ & DataStorage::dslDensity) {
1049	+	idat.rho1 = &(atomRowData.density[atom1]);
1050	+	idat.rho2 = &(atomColData.density[atom2]);
1051	+	}
1052	+
1053	+	if (storageLayout_ & DataStorage::dslFunctional) {
1054	+	idat.frho1 = &(atomRowData.functional[atom1]);
1055	+	idat.frho2 = &(atomColData.functional[atom2]);
1056	+	}
1057	+
1058	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1059	+	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1060	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1061	+	}
1062	+
1063	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1064	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1065	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1066	+	}
1067	+
1068	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1069	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1070	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1071	+	}
1072	+
1073	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1074	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1075	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1076	+	}
1077	+
1078	+	#else
1079	+
1080	+	idat.atid1 = idents[atom1];
1081	+	idat.atid2 = idents[atom2];
1082	+
1083	+	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1084	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1085	+	} else {
1086	+	idat.sameRegion = false;
1087	+	}
1088	+
1089	+	if (storageLayout_ & DataStorage::dslAmat) {
1090	+	idat.A1 = &(snap_->atomData.aMat[atom1]);
1091	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1092	+	}
1093	+
1094	+	if (storageLayout_ & DataStorage::dslTorque) {
1095	+	idat.t1 = &(snap_->atomData.torque[atom1]);
1096	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1097	+	}
1098	+
1099	+	if (storageLayout_ & DataStorage::dslDipole) {
1100	+	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1101	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1102	+	}
1103	+
1104	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1105	+	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1106	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1107	+	}
1108	+
1109	+	if (storageLayout_ & DataStorage::dslDensity) {
1110	+	idat.rho1 = &(snap_->atomData.density[atom1]);
1111	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1112	+	}
1113	+
1114	+	if (storageLayout_ & DataStorage::dslFunctional) {
1115	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1116	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1117	+	}
1118	+
1119	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1120	+	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1121	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1122	+	}
1123	+
1124	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1125	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1126	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1127	+	}
1128	+
1129	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1130	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1131	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1132	+	}
1133	+
1134	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1135	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1136	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1137	+	}
1138	+	#endif
1139	+
1140	+	} else {
1141	+	// atom1 is not new, so don't bother updating properties of that atom:
1142	+	#ifdef IS_MPI
1143	+	idat.atid2 = identsCol[atom2];
1144	+
1145	+	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1146	+	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1147	+	} else {
1148	+	idat.sameRegion = false;
1149		}
1150	+
1151	+	if (storageLayout_ & DataStorage::dslAmat) {
1152	+	idat.A2 = &(atomColData.aMat[atom2]);
1153	+	}
1154	+
1155	+	if (storageLayout_ & DataStorage::dslTorque) {
1156	+	idat.t2 = &(atomColData.torque[atom2]);
1157	+	}
1158	+
1159	+	if (storageLayout_ & DataStorage::dslDipole) {
1160	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1161	+	}
1162	+
1163	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1164	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1165	+	}
1166	+
1167	+	if (storageLayout_ & DataStorage::dslDensity) {
1168	+	idat.rho2 = &(atomColData.density[atom2]);
1169	+	}
1170	+
1171	+	if (storageLayout_ & DataStorage::dslFunctional) {
1172	+	idat.frho2 = &(atomColData.functional[atom2]);
1173	+	}
1174	+
1175	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1176	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1177	+	}
1178	+
1179	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1180	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1181	+	}
1182	+
1183	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1184	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1185	+	}
1186	+
1187	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1188	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1189	+	}
1190	+
1191	+	#else
1192	+	idat.atid2 = idents[atom2];
1193	+
1194	+	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1195	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1196	+	} else {
1197	+	idat.sameRegion = false;
1198	+	}
1199	+
1200	+	if (storageLayout_ & DataStorage::dslAmat) {
1201	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1202	+	}
1203	+
1204	+	if (storageLayout_ & DataStorage::dslTorque) {
1205	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1206	+	}
1207	+
1208	+	if (storageLayout_ & DataStorage::dslDipole) {
1209	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1210	+	}
1211	+
1212	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1213	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1214	+	}
1215	+
1216	+	if (storageLayout_ & DataStorage::dslDensity) {
1217	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1218	+	}
1219	+
1220	+	if (storageLayout_ & DataStorage::dslFunctional) {
1221	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1222	+	}
1223	+
1224	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1225	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1226	+	}
1227	+
1228	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1229	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1230	+	}
1231	+
1232	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1233	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1234	+	}
1235	+
1236	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1237	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1238	+	}
1239	+
1240		#endif
1241	+	}
1242		}
1243
1244	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat,
1245	+	int atom1, int atom2) {
1246	+	#ifdef IS_MPI
1247	+	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1248	+	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1249	+	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1250	+	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1251	+
1252	+	atomRowData.force[atom1] += *(idat.f1);
1253	+	atomColData.force[atom2] -= *(idat.f1);
1254	+
1255	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1256	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1257	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1258	+	}
1259	+
1260	+	if (storageLayout_ & DataStorage::dslElectricField) {
1261	+	atomRowData.electricField[atom1] += *(idat.eField1);
1262	+	atomColData.electricField[atom2] += *(idat.eField2);
1263	+	}
1264	+
1265	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1266	+	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1267	+	atomColData.sitePotential[atom2] += *(idat.sPot2);
1268	+	}
1269	+
1270	+	#else
1271	+	pairwisePot += *(idat.pot);
1272	+	excludedPot += *(idat.excludedPot);
1273	+
1274	+	snap_->atomData.force[atom1] += *(idat.f1);
1275	+	snap_->atomData.force[atom2] -= *(idat.f1);
1276	+
1277	+	if (idat.doParticlePot) {
1278	+	// This is the pairwise contribution to the particle pot.  The
1279	+	// embedding contribution is added in each of the low level
1280	+	// non-bonded routines.  In parallel, this calculation is done
1281	+	// in collectData, not in unpackInteractionData.
1282	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1283	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1284	+	}
1285	+
1286	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1287	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1288	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1289	+	}
1290	+
1291	+	if (storageLayout_ & DataStorage::dslElectricField) {
1292	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1293	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1294	+	}
1295	+
1296	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1297	+	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1298	+	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1299	+	}
1300	+
1301	+	#endif
1302	+
1303	+	}
1304	+
1305	+	/*
1306	+	* buildNeighborList
1307	+	*
1308	+	* Constructs the Verlet neighbor list for a force-matrix
1309	+	* decomposition.  In this case, each processor is responsible for
1310	+	* row-site interactions with column-sites.
1311	+	*
1312	+	* neighborList is returned as a packed array of neighboring
1313	+	* column-ordered CutoffGroups.  The starting position in
1314	+	* neighborList for each row-ordered CutoffGroup is given by the
1315	+	* returned vector point.
1316	+	*/
1317	+	void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
1318	+	vector<int>& point) {
1319	+	neighborList.clear();
1320	+	point.clear();
1321	+	int len = 0;
1322	+
1323	+	bool doAllPairs = false;
1324	+
1325	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1326	+	Mat3x3d box;
1327	+	Mat3x3d invBox;
1328	+
1329	+	Vector3d rs, scaled, dr;
1330	+	Vector3i whichCell;
1331	+	int cellIndex;
1332	+
1333	+	#ifdef IS_MPI
1334	+	cellListRow_.clear();
1335	+	cellListCol_.clear();
1336	+	point.resize(nGroupsInRow_+1);
1337	+	#else
1338	+	cellList_.clear();
1339	+	point.resize(nGroups_+1);
1340	+	#endif
1341	+
1342	+	if (!usePeriodicBoundaryConditions_) {
1343	+	box = snap_->getBoundingBox();
1344	+	invBox = snap_->getInvBoundingBox();
1345	+	} else {
1346	+	box = snap_->getHmat();
1347	+	invBox = snap_->getInvHmat();
1348	+	}
1349	+
1350	+	Vector3d A = box.getColumn(0);
1351	+	Vector3d B = box.getColumn(1);
1352	+	Vector3d C = box.getColumn(2);
1353	+
1354	+	// Required for triclinic cells
1355	+	Vector3d AxB = cross(A, B);
1356	+	Vector3d BxC = cross(B, C);
1357	+	Vector3d CxA = cross(C, A);
1358	+
1359	+	// unit vectors perpendicular to the faces of the triclinic cell:
1360	+	AxB.normalize();
1361	+	BxC.normalize();
1362	+	CxA.normalize();
1363	+
1364	+	// A set of perpendicular lengths in triclinic cells:
1365	+	RealType Wa = abs(dot(A, BxC));
1366	+	RealType Wb = abs(dot(B, CxA));
1367	+	RealType Wc = abs(dot(C, AxB));
1368	+
1369	+	nCells_.x() = int( Wa / rList_ );
1370	+	nCells_.y() = int( Wb / rList_ );
1371	+	nCells_.z() = int( Wc / rList_ );
1372	+
1373	+	// handle small boxes where the cell offsets can end up repeating cells
1374	+	if (nCells_.x() < 3) doAllPairs = true;
1375	+	if (nCells_.y() < 3) doAllPairs = true;
1376	+	if (nCells_.z() < 3) doAllPairs = true;
1377	+
1378	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1379	+
1380	+	#ifdef IS_MPI
1381	+	cellListRow_.resize(nCtot);
1382	+	cellListCol_.resize(nCtot);
1383	+	#else
1384	+	cellList_.resize(nCtot);
1385	+	#endif
1386	+
1387	+	if (!doAllPairs) {
1388	+
1389	+	#ifdef IS_MPI
1390	+
1391	+	for (int i = 0; i < nGroupsInRow_; i++) {
1392	+	rs = cgRowData.position[i];
1393	+
1394	+	// scaled positions relative to the box vectors
1395	+	scaled = invBox * rs;
1396	+
1397	+	// wrap the vector back into the unit box by subtracting integer box
1398	+	// numbers
1399	+	for (int j = 0; j < 3; j++) {
1400	+	scaled[j] -= roundMe(scaled[j]);
1401	+	scaled[j] += 0.5;
1402	+	// Handle the special case when an object is exactly on the
1403	+	// boundary (a scaled coordinate of 1.0 is the same as
1404	+	// scaled coordinate of 0.0)
1405	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1406	+	}
1407	+
1408	+	// find xyz-indices of cell that cutoffGroup is in.
1409	+	whichCell.x() = nCells_.x() * scaled.x();
1410	+	whichCell.y() = nCells_.y() * scaled.y();
1411	+	whichCell.z() = nCells_.z() * scaled.z();
1412	+
1413	+	// find single index of this cell:
1414	+	cellIndex = Vlinear(whichCell, nCells_);
1415	+
1416	+	// add this cutoff group to the list of groups in this cell;
1417	+	cellListRow_[cellIndex].push_back(i);
1418	+	}
1419	+	for (int i = 0; i < nGroupsInCol_; i++) {
1420	+	rs = cgColData.position[i];
1421	+
1422	+	// scaled positions relative to the box vectors
1423	+	scaled = invBox * rs;
1424	+
1425	+	// wrap the vector back into the unit box by subtracting integer box
1426	+	// numbers
1427	+	for (int j = 0; j < 3; j++) {
1428	+	scaled[j] -= roundMe(scaled[j]);
1429	+	scaled[j] += 0.5;
1430	+	// Handle the special case when an object is exactly on the
1431	+	// boundary (a scaled coordinate of 1.0 is the same as
1432	+	// scaled coordinate of 0.0)
1433	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1434	+	}
1435	+
1436	+	// find xyz-indices of cell that cutoffGroup is in.
1437	+	whichCell.x() = nCells_.x() * scaled.x();
1438	+	whichCell.y() = nCells_.y() * scaled.y();
1439	+	whichCell.z() = nCells_.z() * scaled.z();
1440	+
1441	+	// find single index of this cell:
1442	+	cellIndex = Vlinear(whichCell, nCells_);
1443	+
1444	+	// add this cutoff group to the list of groups in this cell;
1445	+	cellListCol_[cellIndex].push_back(i);
1446	+	}
1447	+
1448	+	#else
1449	+	for (int i = 0; i < nGroups_; i++) {
1450	+	rs = snap_->cgData.position[i];
1451	+
1452	+	// scaled positions relative to the box vectors
1453	+	scaled = invBox * rs;
1454	+
1455	+	// wrap the vector back into the unit box by subtracting integer box
1456	+	// numbers
1457	+	for (int j = 0; j < 3; j++) {
1458	+	scaled[j] -= roundMe(scaled[j]);
1459	+	scaled[j] += 0.5;
1460	+	// Handle the special case when an object is exactly on the
1461	+	// boundary (a scaled coordinate of 1.0 is the same as
1462	+	// scaled coordinate of 0.0)
1463	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1464	+	}
1465	+
1466	+	// find xyz-indices of cell that cutoffGroup is in.
1467	+	whichCell.x() = int(nCells_.x() * scaled.x());
1468	+	whichCell.y() = int(nCells_.y() * scaled.y());
1469	+	whichCell.z() = int(nCells_.z() * scaled.z());
1470	+
1471	+	// find single index of this cell:
1472	+	cellIndex = Vlinear(whichCell, nCells_);
1473	+
1474	+	// add this cutoff group to the list of groups in this cell;
1475	+	cellList_[cellIndex].push_back(i);
1476	+	}
1477	+
1478	+	#endif
1479	+
1480	+	#ifdef IS_MPI
1481	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1482	+	rs = cgRowData.position[j1];
1483	+	#else
1484	+
1485	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1486	+	rs = snap_->cgData.position[j1];
1487	+	#endif
1488	+	point[j1] = len;
1489	+
1490	+	// scaled positions relative to the box vectors
1491	+	scaled = invBox * rs;
1492	+
1493	+	// wrap the vector back into the unit box by subtracting integer box
1494	+	// numbers
1495	+	for (int j = 0; j < 3; j++) {
1496	+	scaled[j] -= roundMe(scaled[j]);
1497	+	scaled[j] += 0.5;
1498	+	// Handle the special case when an object is exactly on the
1499	+	// boundary (a scaled coordinate of 1.0 is the same as
1500	+	// scaled coordinate of 0.0)
1501	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1502	+	}
1503	+
1504	+	// find xyz-indices of cell that cutoffGroup is in.
1505	+	whichCell.x() = nCells_.x() * scaled.x();
1506	+	whichCell.y() = nCells_.y() * scaled.y();
1507	+	whichCell.z() = nCells_.z() * scaled.z();
1508	+
1509	+	// find single index of this cell:
1510	+	int m1 = Vlinear(whichCell, nCells_);
1511	+
1512	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1513	+	os != cellOffsets_.end(); ++os) {
1514	+
1515	+	Vector3i m2v = whichCell + (*os);
1516	+
1517	+	if (m2v.x() >= nCells_.x()) {
1518	+	m2v.x() = 0;
1519	+	} else if (m2v.x() < 0) {
1520	+	m2v.x() = nCells_.x() - 1;
1521	+	}
1522	+
1523	+	if (m2v.y() >= nCells_.y()) {
1524	+	m2v.y() = 0;
1525	+	} else if (m2v.y() < 0) {
1526	+	m2v.y() = nCells_.y() - 1;
1527	+	}
1528	+
1529	+	if (m2v.z() >= nCells_.z()) {
1530	+	m2v.z() = 0;
1531	+	} else if (m2v.z() < 0) {
1532	+	m2v.z() = nCells_.z() - 1;
1533	+	}
1534	+	int m2 = Vlinear (m2v, nCells_);
1535	+	#ifdef IS_MPI
1536	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1537	+	j2 != cellListCol_[m2].end(); ++j2) {
1538	+
1539	+	// In parallel, we need to visit *all* pairs of row
1540	+	// & column indicies and will divide labor in the
1541	+	// force evaluation later.
1542	+	dr = cgColData.position[(*j2)] - rs;
1543	+	if (usePeriodicBoundaryConditions_) {
1544	+	snap_->wrapVector(dr);
1545	+	}
1546	+	if (dr.lengthSquare() < rListSq_) {
1547	+	neighborList.push_back( (*j2) );
1548	+	++len;
1549	+	}
1550	+	}
1551	+	#else
1552	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1553	+	j2 != cellList_[m2].end(); ++j2) {
1554	+
1555	+	// Always do this if we're in different cells or if
1556	+	// we're in the same cell and the global index of
1557	+	// the j2 cutoff group is greater than or equal to
1558	+	// the j1 cutoff group.  Note that Rappaport's code
1559	+	// has a "less than" conditional here, but that
1560	+	// deals with atom-by-atom computation.  OpenMD
1561	+	// allows atoms within a single cutoff group to
1562	+	// interact with each other.
1563	+
1564	+	if ( (*j2) >= j1 ) {
1565	+
1566	+	dr = snap_->cgData.position[(*j2)] - rs;
1567	+	if (usePeriodicBoundaryConditions_) {
1568	+	snap_->wrapVector(dr);
1569	+	}
1570	+	if ( dr.lengthSquare() < rListSq_) {
1571	+	neighborList.push_back( (*j2) );
1572	+	++len;
1573	+	}
1574	+	}
1575	+	}
1576	+	#endif
1577	+	}
1578	+	}
1579	+	} else {
1580	+	// branch to do all cutoff group pairs
1581	+	#ifdef IS_MPI
1582	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1583	+	point[j1] = len;
1584	+	rs = cgRowData.position[j1];
1585	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1586	+	dr = cgColData.position[j2] - rs;
1587	+	if (usePeriodicBoundaryConditions_) {
1588	+	snap_->wrapVector(dr);
1589	+	}
1590	+	if (dr.lengthSquare() < rListSq_) {
1591	+	neighborList.push_back( j2 );
1592	+	++len;
1593	+	}
1594	+	}
1595	+	}
1596	+	#else
1597	+	// include all groups here.
1598	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1599	+	point[j1] = len;
1600	+	rs = snap_->cgData.position[j1];
1601	+	// include self group interactions j2 == j1
1602	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1603	+	dr = snap_->cgData.position[j2] - rs;
1604	+	if (usePeriodicBoundaryConditions_) {
1605	+	snap_->wrapVector(dr);
1606	+	}
1607	+	if (dr.lengthSquare() < rListSq_) {
1608	+	neighborList.push_back( j2 );
1609	+	++len;
1610	+	}
1611	+	}
1612	+	}
1613	+	#endif
1614	+	}
1615	+
1616	+	#ifdef IS_MPI
1617	+	point[nGroupsInRow_] = len;
1618	+	#else
1619	+	point[nGroups_] = len;
1620	+	#endif
1621	+
1622	+	// save the local cutoff group positions for the check that is
1623	+	// done on each loop:
1624	+	saved_CG_positions_.clear();
1625	+	saved_CG_positions_.reserve(nGroups_);
1626	+	for (int i = 0; i < nGroups_; i++)
1627	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1628	+	}
1629		} //end namespace OpenMD

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