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

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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1539 by gezelter, Fri Jan 14 22:31:31 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1761 by gezelter, Fri Jun 22 20:01:37 2012 UTC

#	Line 36 | Line 36
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).
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/Communicator.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	<	void ForceDecomposition::distributeInitialData() {
51	>	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	>
53	>	// In a parallel computation, row and colum scans must visit all
54	>	// surrounding cells (not just the 14 upper triangular blocks that
55	>	// are used when the processor can see all pairs)
56		#ifdef IS_MPI
57	+	cellOffsets_.clear();
58	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
66	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	+	#endif
86	+	}
87
50	–	int nAtoms;
51	–	int nGroups;
88
89	<	AtomCommRealI = new Comm<I,RealType>(nAtoms);
90	<	AtomCommVectorI = new Comm<I,Vector3d>(nAtoms);
91	<	AtomCommMatrixI = new Comm<I,Mat3x3d>(nAtoms);
89	>	/**
90	>	* distributeInitialData is essentially a copy of the older fortran
91	>	* SimulationSetup
92	>	*/
93	>	void ForceMatrixDecomposition::distributeInitialData() {
94	>	snap_ = sman_->getCurrentSnapshot();
95	>	storageLayout_ = sman_->getStorageLayout();
96	>	ff_ = info_->getForceField();
97	>	nLocal_ = snap_->getNumberOfAtoms();
98	>
99	>	nGroups_ = info_->getNLocalCutoffGroups();
100	>	// gather the information for atomtype IDs (atids):
101	>	idents = info_->getIdentArray();
102	>	AtomLocalToGlobal = info_->getGlobalAtomIndices();
103	>	cgLocalToGlobal = info_->getGlobalGroupIndices();
104	>	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
105
106	<	AtomCommRealJ = new Comm<J,RealType>(nAtoms);
58	<	AtomCommVectorJ = new Comm<J,Vector3d>(nAtoms);
59	<	AtomCommMatrixJ = new Comm<J,Mat3x3d>(nAtoms);
106	>	massFactors = info_->getMassFactors();
107
108	<	cgCommVectorI = new Comm<I,Vector3d>(nGroups);
109	<	cgCommVectorJ = new Comm<J,Vector3d>(nGroups);
110	<	// more to come
108	>	PairList* excludes = info_->getExcludedInteractions();
109	>	PairList* oneTwo = info_->getOneTwoInteractions();
110	>	PairList* oneThree = info_->getOneThreeInteractions();
111	>	PairList* oneFour = info_->getOneFourInteractions();
112	>
113	>	if (needVelocities_)
114	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
115	>	DataStorage::dslVelocity);
116	>	else
117	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118	>
119	>	#ifdef IS_MPI
120	>
121	>	MPI::Intracomm row = rowComm.getComm();
122	>	MPI::Intracomm col = colComm.getComm();
123	>
124	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
125	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
126	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
127	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
128	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
129	>
130	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
131	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
132	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
133	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
134	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
135	>
136	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
137	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
138	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
139	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
140	>
141	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
142	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
143	>	nGroupsInRow_ = cgPlanIntRow->getSize();
144	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
145	>
146	>	// Modify the data storage objects with the correct layouts and sizes:
147	>	atomRowData.resize(nAtomsInRow_);
148	>	atomRowData.setStorageLayout(storageLayout_);
149	>	atomColData.resize(nAtomsInCol_);
150	>	atomColData.setStorageLayout(storageLayout_);
151	>	cgRowData.resize(nGroupsInRow_);
152	>	cgRowData.setStorageLayout(DataStorage::dslPosition);
153	>	cgColData.resize(nGroupsInCol_);
154	>	if (needVelocities_)
155	>	// we only need column velocities if we need them.
156	>	cgColData.setStorageLayout(DataStorage::dslPosition |
157	>	DataStorage::dslVelocity);
158	>	else
159	>	cgColData.setStorageLayout(DataStorage::dslPosition);
160	>
161	>	identsRow.resize(nAtomsInRow_);
162	>	identsCol.resize(nAtomsInCol_);
163	>
164	>	AtomPlanIntRow->gather(idents, identsRow);
165	>	AtomPlanIntColumn->gather(idents, identsCol);
166	>
167	>	// allocate memory for the parallel objects
168	>	atypesRow.resize(nAtomsInRow_);
169	>	atypesCol.resize(nAtomsInCol_);
170	>
171	>	for (int i = 0; i < nAtomsInRow_; i++)
172	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
173	>	for (int i = 0; i < nAtomsInCol_; i++)
174	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
175	>
176	>	pot_row.resize(nAtomsInRow_);
177	>	pot_col.resize(nAtomsInCol_);
178	>
179	>	expot_row.resize(nAtomsInRow_);
180	>	expot_col.resize(nAtomsInCol_);
181	>
182	>	AtomRowToGlobal.resize(nAtomsInRow_);
183	>	AtomColToGlobal.resize(nAtomsInCol_);
184	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
185	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
186	>
187	>	cgRowToGlobal.resize(nGroupsInRow_);
188	>	cgColToGlobal.resize(nGroupsInCol_);
189	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
190	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
191	>
192	>	massFactorsRow.resize(nAtomsInRow_);
193	>	massFactorsCol.resize(nAtomsInCol_);
194	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
195	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
196	>
197	>	groupListRow_.clear();
198	>	groupListRow_.resize(nGroupsInRow_);
199	>	for (int i = 0; i < nGroupsInRow_; i++) {
200	>	int gid = cgRowToGlobal[i];
201	>	for (int j = 0; j < nAtomsInRow_; j++) {
202	>	int aid = AtomRowToGlobal[j];
203	>	if (globalGroupMembership[aid] == gid)
204	>	groupListRow_[i].push_back(j);
205	>	}
206	>	}
207	>
208	>	groupListCol_.clear();
209	>	groupListCol_.resize(nGroupsInCol_);
210	>	for (int i = 0; i < nGroupsInCol_; i++) {
211	>	int gid = cgColToGlobal[i];
212	>	for (int j = 0; j < nAtomsInCol_; j++) {
213	>	int aid = AtomColToGlobal[j];
214	>	if (globalGroupMembership[aid] == gid)
215	>	groupListCol_[i].push_back(j);
216	>	}
217	>	}
218	>
219	>	excludesForAtom.clear();
220	>	excludesForAtom.resize(nAtomsInRow_);
221	>	toposForAtom.clear();
222	>	toposForAtom.resize(nAtomsInRow_);
223	>	topoDist.clear();
224	>	topoDist.resize(nAtomsInRow_);
225	>	for (int i = 0; i < nAtomsInRow_; i++) {
226	>	int iglob = AtomRowToGlobal[i];
227	>
228	>	for (int j = 0; j < nAtomsInCol_; j++) {
229	>	int jglob = AtomColToGlobal[j];
230	>
231	>	if (excludes->hasPair(iglob, jglob))
232	>	excludesForAtom[i].push_back(j);
233	>
234	>	if (oneTwo->hasPair(iglob, jglob)) {
235	>	toposForAtom[i].push_back(j);
236	>	topoDist[i].push_back(1);
237	>	} else {
238	>	if (oneThree->hasPair(iglob, jglob)) {
239	>	toposForAtom[i].push_back(j);
240	>	topoDist[i].push_back(2);
241	>	} else {
242	>	if (oneFour->hasPair(iglob, jglob)) {
243	>	toposForAtom[i].push_back(j);
244	>	topoDist[i].push_back(3);
245	>	}
246	>	}
247	>	}
248	>	}
249	>	}
250	>
251	>	#else
252	>	excludesForAtom.clear();
253	>	excludesForAtom.resize(nLocal_);
254	>	toposForAtom.clear();
255	>	toposForAtom.resize(nLocal_);
256	>	topoDist.clear();
257	>	topoDist.resize(nLocal_);
258	>
259	>	for (int i = 0; i < nLocal_; i++) {
260	>	int iglob = AtomLocalToGlobal[i];
261	>
262	>	for (int j = 0; j < nLocal_; j++) {
263	>	int jglob = AtomLocalToGlobal[j];
264	>
265	>	if (excludes->hasPair(iglob, jglob))
266	>	excludesForAtom[i].push_back(j);
267	>
268	>	if (oneTwo->hasPair(iglob, jglob)) {
269	>	toposForAtom[i].push_back(j);
270	>	topoDist[i].push_back(1);
271	>	} else {
272	>	if (oneThree->hasPair(iglob, jglob)) {
273	>	toposForAtom[i].push_back(j);
274	>	topoDist[i].push_back(2);
275	>	} else {
276	>	if (oneFour->hasPair(iglob, jglob)) {
277	>	toposForAtom[i].push_back(j);
278	>	topoDist[i].push_back(3);
279	>	}
280	>	}
281	>	}
282	>	}
283	>	}
284		#endif
285	+
286	+	// allocate memory for the parallel objects
287	+	atypesLocal.resize(nLocal_);
288	+
289	+	for (int i = 0; i < nLocal_; i++)
290	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
291	+
292	+	groupList_.clear();
293	+	groupList_.resize(nGroups_);
294	+	for (int i = 0; i < nGroups_; i++) {
295	+	int gid = cgLocalToGlobal[i];
296	+	for (int j = 0; j < nLocal_; j++) {
297	+	int aid = AtomLocalToGlobal[j];
298	+	if (globalGroupMembership[aid] == gid) {
299	+	groupList_[i].push_back(j);
300	+	}
301	+	}
302	+	}
303	+
304	+
305	+	createGtypeCutoffMap();
306	+
307		}
308	+
309	+	void ForceMatrixDecomposition::createGtypeCutoffMap() {
310
311	+	RealType tol = 1e-6;
312	+	largestRcut_ = 0.0;
313	+	RealType rc;
314	+	int atid;
315	+	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
316	+
317	+	map<int, RealType> atypeCutoff;
318	+
319	+	for (set<AtomType*>::iterator at = atypes.begin();
320	+	at != atypes.end(); ++at){
321	+	atid = (*at)->getIdent();
322	+	if (userChoseCutoff_)
323	+	atypeCutoff[atid] = userCutoff_;
324	+	else
325	+	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
326	+	}
327	+
328	+	vector<RealType> gTypeCutoffs;
329	+	// first we do a single loop over the cutoff groups to find the
330	+	// largest cutoff for any atypes present in this group.
331	+	#ifdef IS_MPI
332	+	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
333	+	groupRowToGtype.resize(nGroupsInRow_);
334	+	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
335	+	vector<int> atomListRow = getAtomsInGroupRow(cg1);
336	+	for (vector<int>::iterator ia = atomListRow.begin();
337	+	ia != atomListRow.end(); ++ia) {
338	+	int atom1 = (*ia);
339	+	atid = identsRow[atom1];
340	+	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
341	+	groupCutoffRow[cg1] = atypeCutoff[atid];
342	+	}
343	+	}
344
345	+	bool gTypeFound = false;
346	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
347	+	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
348	+	groupRowToGtype[cg1] = gt;
349	+	gTypeFound = true;
350	+	}
351	+	}
352	+	if (!gTypeFound) {
353	+	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
354	+	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
355	+	}
356	+
357	+	}
358	+	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
359	+	groupColToGtype.resize(nGroupsInCol_);
360	+	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
361	+	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
362	+	for (vector<int>::iterator jb = atomListCol.begin();
363	+	jb != atomListCol.end(); ++jb) {
364	+	int atom2 = (*jb);
365	+	atid = identsCol[atom2];
366	+	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
367	+	groupCutoffCol[cg2] = atypeCutoff[atid];
368	+	}
369	+	}
370	+	bool gTypeFound = false;
371	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
372	+	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
373	+	groupColToGtype[cg2] = gt;
374	+	gTypeFound = true;
375	+	}
376	+	}
377	+	if (!gTypeFound) {
378	+	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
379	+	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
380	+	}
381	+	}
382	+	#else
383
384	<	void ForceDecomposition::distributeData()  {
384	>	vector<RealType> groupCutoff(nGroups_, 0.0);
385	>	groupToGtype.resize(nGroups_);
386	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
387	>	groupCutoff[cg1] = 0.0;
388	>	vector<int> atomList = getAtomsInGroupRow(cg1);
389	>	for (vector<int>::iterator ia = atomList.begin();
390	>	ia != atomList.end(); ++ia) {
391	>	int atom1 = (*ia);
392	>	atid = idents[atom1];
393	>	if (atypeCutoff[atid] > groupCutoff[cg1])
394	>	groupCutoff[cg1] = atypeCutoff[atid];
395	>	}
396	>
397	>	bool gTypeFound = false;
398	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
399	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
400	>	groupToGtype[cg1] = gt;
401	>	gTypeFound = true;
402	>	}
403	>	}
404	>	if (!gTypeFound) {
405	>	gTypeCutoffs.push_back( groupCutoff[cg1] );
406	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
407	>	}
408	>	}
409	>	#endif
410	>
411	>	// Now we find the maximum group cutoff value present in the simulation
412	>
413	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
414	>	gTypeCutoffs.end());
415	>
416		#ifdef IS_MPI
417	<	Snapshot* snap = sman_->getCurrentSnapshot();
417	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
418	>	MPI::MAX);
419	>	#endif
420	>
421	>	RealType tradRcut = groupMax;
422
423	+	for (int i = 0; i < gTypeCutoffs.size();  i++) {
424	+	for (int j = 0; j < gTypeCutoffs.size();  j++) {
425	+	RealType thisRcut;
426	+	switch(cutoffPolicy_) {
427	+	case TRADITIONAL:
428	+	thisRcut = tradRcut;
429	+	break;
430	+	case MIX:
431	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
432	+	break;
433	+	case MAX:
434	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
435	+	break;
436	+	default:
437	+	sprintf(painCave.errMsg,
438	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
439	+	"hit an unknown cutoff policy!\n");
440	+	painCave.severity = OPENMD_ERROR;
441	+	painCave.isFatal = 1;
442	+	simError();
443	+	break;
444	+	}
445	+
446	+	pair<int,int> key = make_pair(i,j);
447	+	gTypeCutoffMap[key].first = thisRcut;
448	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
449	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
450	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
451	+	// sanity check
452	+
453	+	if (userChoseCutoff_) {
454	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
455	+	sprintf(painCave.errMsg,
456	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
457	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
458	+	painCave.severity = OPENMD_ERROR;
459	+	painCave.isFatal = 1;
460	+	simError();
461	+	}
462	+	}
463	+	}
464	+	}
465	+	}
466	+
467	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
468	+	int i, j;
469	+	#ifdef IS_MPI
470	+	i = groupRowToGtype[cg1];
471	+	j = groupColToGtype[cg2];
472	+	#else
473	+	i = groupToGtype[cg1];
474	+	j = groupToGtype[cg2];
475	+	#endif
476	+	return gTypeCutoffMap[make_pair(i,j)];
477	+	}
478	+
479	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
480	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
481	+	if (toposForAtom[atom1][j] == atom2)
482	+	return topoDist[atom1][j];
483	+	}
484	+	return 0;
485	+	}
486	+
487	+	void ForceMatrixDecomposition::zeroWorkArrays() {
488	+	pairwisePot = 0.0;
489	+	embeddingPot = 0.0;
490	+	excludedPot = 0.0;
491	+	excludedSelfPot = 0.0;
492	+
493	+	#ifdef IS_MPI
494	+	if (storageLayout_ & DataStorage::dslForce) {
495	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
496	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
497	+	}
498	+
499	+	if (storageLayout_ & DataStorage::dslTorque) {
500	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
501	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
502	+	}
503	+
504	+	fill(pot_row.begin(), pot_row.end(),
505	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
506	+
507	+	fill(pot_col.begin(), pot_col.end(),
508	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
509	+
510	+	fill(expot_row.begin(), expot_row.end(),
511	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
512	+
513	+	fill(expot_col.begin(), expot_col.end(),
514	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
515	+
516	+	if (storageLayout_ & DataStorage::dslParticlePot) {
517	+	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
518	+	0.0);
519	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
520	+	0.0);
521	+	}
522	+
523	+	if (storageLayout_ & DataStorage::dslDensity) {
524	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
525	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
526	+	}
527	+
528	+	if (storageLayout_ & DataStorage::dslFunctional) {
529	+	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
530	+	0.0);
531	+	fill(atomColData.functional.begin(), atomColData.functional.end(),
532	+	0.0);
533	+	}
534	+
535	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
536	+	fill(atomRowData.functionalDerivative.begin(),
537	+	atomRowData.functionalDerivative.end(), 0.0);
538	+	fill(atomColData.functionalDerivative.begin(),
539	+	atomColData.functionalDerivative.end(), 0.0);
540	+	}
541	+
542	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
543	+	fill(atomRowData.skippedCharge.begin(),
544	+	atomRowData.skippedCharge.end(), 0.0);
545	+	fill(atomColData.skippedCharge.begin(),
546	+	atomColData.skippedCharge.end(), 0.0);
547	+	}
548	+
549	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
550	+	fill(atomRowData.flucQFrc.begin(),
551	+	atomRowData.flucQFrc.end(), 0.0);
552	+	fill(atomColData.flucQFrc.begin(),
553	+	atomColData.flucQFrc.end(), 0.0);
554	+	}
555	+
556	+	if (storageLayout_ & DataStorage::dslElectricField) {
557	+	fill(atomRowData.electricField.begin(),
558	+	atomRowData.electricField.end(), V3Zero);
559	+	fill(atomColData.electricField.begin(),
560	+	atomColData.electricField.end(), V3Zero);
561	+	}
562	+
563	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
564	+	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
565	+	0.0);
566	+	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
567	+	0.0);
568	+	}
569	+
570	+	#endif
571	+	// even in parallel, we need to zero out the local arrays:
572	+
573	+	if (storageLayout_ & DataStorage::dslParticlePot) {
574	+	fill(snap_->atomData.particlePot.begin(),
575	+	snap_->atomData.particlePot.end(), 0.0);
576	+	}
577	+
578	+	if (storageLayout_ & DataStorage::dslDensity) {
579	+	fill(snap_->atomData.density.begin(),
580	+	snap_->atomData.density.end(), 0.0);
581	+	}
582	+
583	+	if (storageLayout_ & DataStorage::dslFunctional) {
584	+	fill(snap_->atomData.functional.begin(),
585	+	snap_->atomData.functional.end(), 0.0);
586	+	}
587	+
588	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
589	+	fill(snap_->atomData.functionalDerivative.begin(),
590	+	snap_->atomData.functionalDerivative.end(), 0.0);
591	+	}
592	+
593	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
594	+	fill(snap_->atomData.skippedCharge.begin(),
595	+	snap_->atomData.skippedCharge.end(), 0.0);
596	+	}
597	+
598	+	if (storageLayout_ & DataStorage::dslElectricField) {
599	+	fill(snap_->atomData.electricField.begin(),
600	+	snap_->atomData.electricField.end(), V3Zero);
601	+	}
602	+	}
603	+
604	+
605	+	void ForceMatrixDecomposition::distributeData()  {
606	+	snap_ = sman_->getCurrentSnapshot();
607	+	storageLayout_ = sman_->getStorageLayout();
608	+	#ifdef IS_MPI
609	+
610		// gather up the atomic positions
611	<	AtomCommVectorI->gather(snap->atomData.position,
612	<	snap->atomIData.position);
613	<	AtomCommVectorJ->gather(snap->atomData.position,
614	<	snap->atomJData.position);
611	>	AtomPlanVectorRow->gather(snap_->atomData.position,
612	>	atomRowData.position);
613	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
614	>	atomColData.position);
615
616		// gather up the cutoff group positions
617	<	cgCommVectorI->gather(snap->cgData.position,
618	<	snap->cgIData.position);
619	<	cgCommVectorJ->gather(snap->cgData.position,
620	<	snap->cgJData.position);
617	>
618	>	cgPlanVectorRow->gather(snap_->cgData.position,
619	>	cgRowData.position);
620	>
621	>	cgPlanVectorColumn->gather(snap_->cgData.position,
622	>	cgColData.position);
623	>
624	>
625	>
626	>	if (needVelocities_) {
627	>	// gather up the atomic velocities
628	>	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
629	>	atomColData.velocity);
630	>
631	>	cgPlanVectorColumn->gather(snap_->cgData.velocity,
632	>	cgColData.velocity);
633	>	}
634	>
635
636		// if needed, gather the atomic rotation matrices
637	<	if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
638	<	AtomCommMatrixI->gather(snap->atomData.aMat,
639	<	snap->atomIData.aMat);
640	<	AtomCommMatrixJ->gather(snap->atomData.aMat,
641	<	snap->atomJData.aMat);
637	>	if (storageLayout_ & DataStorage::dslAmat) {
638	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
639	>	atomRowData.aMat);
640	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
641	>	atomColData.aMat);
642		}
643
644		// if needed, gather the atomic eletrostatic frames
645	<	if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
646	<	AtomCommMatrixI->gather(snap->atomData.electroFrame,
647	<	snap->atomIData.electroFrame);
648	<	AtomCommMatrixJ->gather(snap->atomData.electroFrame,
649	<	snap->atomJData.electroFrame);
645	>	if (storageLayout_ & DataStorage::dslElectroFrame) {
646	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
647	>	atomRowData.electroFrame);
648	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
649	>	atomColData.electroFrame);
650		}
651	+
652	+	// if needed, gather the atomic fluctuating charge values
653	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
654	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
655	+	atomRowData.flucQPos);
656	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
657	+	atomColData.flucQPos);
658	+	}
659	+
660		#endif
661		}
662
663	<	void ForceDecomposition::collectIntermediateData() {
663	>	/* collects information obtained during the pre-pair loop onto local
664	>	* data structures.
665	>	*/
666	>	void ForceMatrixDecomposition::collectIntermediateData() {
667	>	snap_ = sman_->getCurrentSnapshot();
668	>	storageLayout_ = sman_->getStorageLayout();
669		#ifdef IS_MPI
105	–	Snapshot* snap = sman_->getCurrentSnapshot();
106	–	// gather up the atomic positions
670
671	<	if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
672	<	AtomCommRealI->scatter(snap->atomIData.density,
673	<	snap->atomData.density);
674	<	std::vector<RealType> rho_tmp;
675	<	int n = snap->getNumberOfAtoms();
676	<	rho_tmp.reserve( n );
677	<	AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
671	>	if (storageLayout_ & DataStorage::dslDensity) {
672	>
673	>	AtomPlanRealRow->scatter(atomRowData.density,
674	>	snap_->atomData.density);
675	>
676	>	int n = snap_->atomData.density.size();
677	>	vector<RealType> rho_tmp(n, 0.0);
678	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
679		for (int i = 0; i < n; i++)
680	<	snap->atomData.density[i] += rho_tmp[i];
680	>	snap_->atomData.density[i] += rho_tmp[i];
681		}
682	+
683	+	if (storageLayout_ & DataStorage::dslElectricField) {
684	+
685	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
686	+	snap_->atomData.electricField);
687	+
688	+	int n = snap_->atomData.electricField.size();
689	+	vector<Vector3d> field_tmp(n, V3Zero);
690	+	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
691	+	for (int i = 0; i < n; i++)
692	+	snap_->atomData.electricField[i] += field_tmp[i];
693	+	}
694		#endif
695		}
696	<
697	<	void ForceDecomposition::distributeIntermediateData() {
696	>
697	>	/*
698	>	* redistributes information obtained during the pre-pair loop out to
699	>	* row and column-indexed data structures
700	>	*/
701	>	void ForceMatrixDecomposition::distributeIntermediateData() {
702	>	snap_ = sman_->getCurrentSnapshot();
703	>	storageLayout_ = sman_->getStorageLayout();
704		#ifdef IS_MPI
705	<	Snapshot* snap = sman_->getCurrentSnapshot();
706	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
707	<	AtomCommRealI->gather(snap->atomData.functional,
708	<	snap->atomIData.functional);
709	<	AtomCommRealJ->gather(snap->atomData.functional,
128	<	snap->atomJData.functional);
705	>	if (storageLayout_ & DataStorage::dslFunctional) {
706	>	AtomPlanRealRow->gather(snap_->atomData.functional,
707	>	atomRowData.functional);
708	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
709	>	atomColData.functional);
710		}
711
712	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
713	<	AtomCommRealI->gather(snap->atomData.functionalDerivative,
714	<	snap->atomIData.functionalDerivative);
715	<	AtomCommRealJ->gather(snap->atomData.functionalDerivative,
716	<	snap->atomJData.functionalDerivative);
712	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
713	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
714	>	atomRowData.functionalDerivative);
715	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
716	>	atomColData.functionalDerivative);
717		}
718		#endif
719		}
720
721
722	<	void ForceDecomposition::collectData() {
722	>	void ForceMatrixDecomposition::collectData() {
723	>	snap_ = sman_->getCurrentSnapshot();
724	>	storageLayout_ = sman_->getStorageLayout();
725	>	#ifdef IS_MPI
726	>	int n = snap_->atomData.force.size();
727	>	vector<Vector3d> frc_tmp(n, V3Zero);
728	>
729	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
730	>	for (int i = 0; i < n; i++) {
731	>	snap_->atomData.force[i] += frc_tmp[i];
732	>	frc_tmp[i] = 0.0;
733	>	}
734	>
735	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
736	>	for (int i = 0; i < n; i++) {
737	>	snap_->atomData.force[i] += frc_tmp[i];
738	>	}
739	>
740	>	if (storageLayout_ & DataStorage::dslTorque) {
741	>
742	>	int nt = snap_->atomData.torque.size();
743	>	vector<Vector3d> trq_tmp(nt, V3Zero);
744	>
745	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
746	>	for (int i = 0; i < nt; i++) {
747	>	snap_->atomData.torque[i] += trq_tmp[i];
748	>	trq_tmp[i] = 0.0;
749	>	}
750	>
751	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
752	>	for (int i = 0; i < nt; i++)
753	>	snap_->atomData.torque[i] += trq_tmp[i];
754	>	}
755	>
756	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
757	>
758	>	int ns = snap_->atomData.skippedCharge.size();
759	>	vector<RealType> skch_tmp(ns, 0.0);
760	>
761	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
762	>	for (int i = 0; i < ns; i++) {
763	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
764	>	skch_tmp[i] = 0.0;
765	>	}
766	>
767	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
768	>	for (int i = 0; i < ns; i++)
769	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
770	>
771	>	}
772	>
773	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
774	>
775	>	int nq = snap_->atomData.flucQFrc.size();
776	>	vector<RealType> fqfrc_tmp(nq, 0.0);
777	>
778	>	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
779	>	for (int i = 0; i < nq; i++) {
780	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
781	>	fqfrc_tmp[i] = 0.0;
782	>	}
783	>
784	>	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
785	>	for (int i = 0; i < nq; i++)
786	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
787	>
788	>	}
789	>
790	>	nLocal_ = snap_->getNumberOfAtoms();
791	>
792	>	vector<potVec> pot_temp(nLocal_,
793	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
794	>	vector<potVec> expot_temp(nLocal_,
795	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
796	>
797	>	// scatter/gather pot_row into the members of my column
798	>
799	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
800	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
801	>
802	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
803	>	pairwisePot += pot_temp[ii];
804	>
805	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
806	>	excludedPot += expot_temp[ii];
807	>
808	>	if (storageLayout_ & DataStorage::dslParticlePot) {
809	>	// This is the pairwise contribution to the particle pot.  The
810	>	// embedding contribution is added in each of the low level
811	>	// non-bonded routines.  In single processor, this is done in
812	>	// unpackInteractionData, not in collectData.
813	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
814	>	for (int i = 0; i < nLocal_; i++) {
815	>	// factor of two is because the total potential terms are divided
816	>	// by 2 in parallel due to row/ column scatter
817	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
818	>	}
819	>	}
820	>	}
821	>
822	>	fill(pot_temp.begin(), pot_temp.end(),
823	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
824	>	fill(expot_temp.begin(), expot_temp.end(),
825	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
826	>
827	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
828	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
829	>
830	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
831	>	pairwisePot += pot_temp[ii];
832	>
833	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
834	>	excludedPot += expot_temp[ii];
835	>
836	>	if (storageLayout_ & DataStorage::dslParticlePot) {
837	>	// This is the pairwise contribution to the particle pot.  The
838	>	// embedding contribution is added in each of the low level
839	>	// non-bonded routines.  In single processor, this is done in
840	>	// unpackInteractionData, not in collectData.
841	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
842	>	for (int i = 0; i < nLocal_; i++) {
843	>	// factor of two is because the total potential terms are divided
844	>	// by 2 in parallel due to row/ column scatter
845	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
846	>	}
847	>	}
848	>	}
849	>
850	>	if (storageLayout_ & DataStorage::dslParticlePot) {
851	>	int npp = snap_->atomData.particlePot.size();
852	>	vector<RealType> ppot_temp(npp, 0.0);
853	>
854	>	// This is the direct or embedding contribution to the particle
855	>	// pot.
856	>
857	>	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
858	>	for (int i = 0; i < npp; i++) {
859	>	snap_->atomData.particlePot[i] += ppot_temp[i];
860	>	}
861	>
862	>	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
863	>
864	>	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
865	>	for (int i = 0; i < npp; i++) {
866	>	snap_->atomData.particlePot[i] += ppot_temp[i];
867	>	}
868	>	}
869	>
870	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
871	>	RealType ploc1 = pairwisePot[ii];
872	>	RealType ploc2 = 0.0;
873	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
874	>	pairwisePot[ii] = ploc2;
875	>	}
876	>
877	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
878	>	RealType ploc1 = excludedPot[ii];
879	>	RealType ploc2 = 0.0;
880	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
881	>	excludedPot[ii] = ploc2;
882	>	}
883	>
884	>	// Here be dragons.
885	>	MPI::Intracomm col = colComm.getComm();
886	>
887	>	col.Allreduce(MPI::IN_PLACE,
888	>	&snap_->frameData.conductiveHeatFlux[0], 3,
889	>	MPI::REALTYPE, MPI::SUM);
890	>
891	>
892	>	#endif
893	>
894	>	}
895	>
896	>	/**
897	>	* Collects information obtained during the post-pair (and embedding
898	>	* functional) loops onto local data structures.
899	>	*/
900	>	void ForceMatrixDecomposition::collectSelfData() {
901	>	snap_ = sman_->getCurrentSnapshot();
902	>	storageLayout_ = sman_->getStorageLayout();
903	>
904		#ifdef IS_MPI
905	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
906	+	RealType ploc1 = embeddingPot[ii];
907	+	RealType ploc2 = 0.0;
908	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
909	+	embeddingPot[ii] = ploc2;
910	+	}
911	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
912	+	RealType ploc1 = excludedSelfPot[ii];
913	+	RealType ploc2 = 0.0;
914	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
915	+	excludedSelfPot[ii] = ploc2;
916	+	}
917	+	#endif
918	+
919	+	}
920	+
921	+
922	+
923	+	int ForceMatrixDecomposition::getNAtomsInRow() {
924	+	#ifdef IS_MPI
925	+	return nAtomsInRow_;
926	+	#else
927	+	return nLocal_;
928	+	#endif
929	+	}
930	+
931	+	/**
932	+	* returns the list of atoms belonging to this group.
933	+	*/
934	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
935	+	#ifdef IS_MPI
936	+	return groupListRow_[cg1];
937	+	#else
938	+	return groupList_[cg1];
939	+	#endif
940	+	}
941	+
942	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
943	+	#ifdef IS_MPI
944	+	return groupListCol_[cg2];
945	+	#else
946	+	return groupList_[cg2];
947	+	#endif
948	+	}
949	+
950	+	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
951	+	Vector3d d;
952	+
953	+	#ifdef IS_MPI
954	+	d = cgColData.position[cg2] - cgRowData.position[cg1];
955	+	#else
956	+	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
957	+	#endif
958	+
959	+	snap_->wrapVector(d);
960	+	return d;
961	+	}
962	+
963	+	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
964	+	#ifdef IS_MPI
965	+	return cgColData.velocity[cg2];
966	+	#else
967	+	return snap_->cgData.velocity[cg2];
968	+	#endif
969	+	}
970	+
971	+	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
972	+	#ifdef IS_MPI
973	+	return atomColData.velocity[atom2];
974	+	#else
975	+	return snap_->atomData.velocity[atom2];
976	+	#endif
977	+	}
978	+
979	+
980	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
981	+
982	+	Vector3d d;
983	+
984	+	#ifdef IS_MPI
985	+	d = cgRowData.position[cg1] - atomRowData.position[atom1];
986	+	#else
987	+	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
988	+	#endif
989	+
990	+	snap_->wrapVector(d);
991	+	return d;
992	+	}
993	+
994	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
995	+	Vector3d d;
996	+
997	+	#ifdef IS_MPI
998	+	d = cgColData.position[cg2] - atomColData.position[atom2];
999	+	#else
1000	+	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1001	+	#endif
1002	+
1003	+	snap_->wrapVector(d);
1004	+	return d;
1005	+	}
1006	+
1007	+	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1008	+	#ifdef IS_MPI
1009	+	return massFactorsRow[atom1];
1010	+	#else
1011	+	return massFactors[atom1];
1012	+	#endif
1013	+	}
1014	+
1015	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1016	+	#ifdef IS_MPI
1017	+	return massFactorsCol[atom2];
1018	+	#else
1019	+	return massFactors[atom2];
1020	+	#endif
1021	+
1022	+	}
1023	+
1024	+	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
1025	+	Vector3d d;
1026	+
1027	+	#ifdef IS_MPI
1028	+	d = atomColData.position[atom2] - atomRowData.position[atom1];
1029	+	#else
1030	+	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1031	+	#endif
1032	+
1033	+	snap_->wrapVector(d);
1034	+	return d;
1035	+	}
1036	+
1037	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1038	+	return excludesForAtom[atom1];
1039	+	}
1040	+
1041	+	/**
1042	+	* We need to exclude some overcounted interactions that result from
1043	+	* the parallel decomposition.
1044	+	*/
1045	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1046	+	int unique_id_1, unique_id_2, group1, group2;
1047	+
1048	+	#ifdef IS_MPI
1049	+	// in MPI, we have to look up the unique IDs for each atom
1050	+	unique_id_1 = AtomRowToGlobal[atom1];
1051	+	unique_id_2 = AtomColToGlobal[atom2];
1052	+	group1 = cgRowToGlobal[cg1];
1053	+	group2 = cgColToGlobal[cg2];
1054	+	#else
1055	+	unique_id_1 = AtomLocalToGlobal[atom1];
1056	+	unique_id_2 = AtomLocalToGlobal[atom2];
1057	+	group1 = cgLocalToGlobal[cg1];
1058	+	group2 = cgLocalToGlobal[cg2];
1059	+	#endif
1060	+
1061	+	if (unique_id_1 == unique_id_2) return true;
1062	+
1063	+	#ifdef IS_MPI
1064	+	// this prevents us from doing the pair on multiple processors
1065	+	if (unique_id_1 < unique_id_2) {
1066	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1067	+	} else {
1068	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1069	+	}
1070	+	#endif
1071	+
1072	+	#ifndef IS_MPI
1073	+	if (group1 == group2) {
1074	+	if (unique_id_1 < unique_id_2) return true;
1075	+	}
1076	+	#endif
1077	+
1078	+	return false;
1079	+	}
1080	+
1081	+	/**
1082	+	* We need to handle the interactions for atoms who are involved in
1083	+	* the same rigid body as well as some short range interactions
1084	+	* (bonds, bends, torsions) differently from other interactions.
1085	+	* We'll still visit the pairwise routines, but with a flag that
1086	+	* tells those routines to exclude the pair from direct long range
1087	+	* interactions.  Some indirect interactions (notably reaction
1088	+	* field) must still be handled for these pairs.
1089	+	*/
1090	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1091	+
1092	+	// excludesForAtom was constructed to use row/column indices in the MPI
1093	+	// version, and to use local IDs in the non-MPI version:
1094	+
1095	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1096	+	i != excludesForAtom[atom1].end(); ++i) {
1097	+	if ( (*i) == atom2 ) return true;
1098	+	}
1099	+
1100	+	return false;
1101	+	}
1102	+
1103	+
1104	+	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1105	+	#ifdef IS_MPI
1106	+	atomRowData.force[atom1] += fg;
1107	+	#else
1108	+	snap_->atomData.force[atom1] += fg;
1109	+	#endif
1110	+	}
1111	+
1112	+	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
1113	+	#ifdef IS_MPI
1114	+	atomColData.force[atom2] += fg;
1115	+	#else
1116	+	snap_->atomData.force[atom2] += fg;
1117	+	#endif
1118	+	}
1119	+
1120	+	// filling interaction blocks with pointers
1121	+	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1122	+	int atom1, int atom2) {
1123	+
1124	+	idat.excluded = excludeAtomPair(atom1, atom2);
1125	+
1126	+	#ifdef IS_MPI
1127	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1128	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1129	+	//                         ff_->getAtomType(identsCol[atom2]) );
1130	+
1131	+	if (storageLayout_ & DataStorage::dslAmat) {
1132	+	idat.A1 = &(atomRowData.aMat[atom1]);
1133	+	idat.A2 = &(atomColData.aMat[atom2]);
1134	+	}
1135	+
1136	+	if (storageLayout_ & DataStorage::dslElectroFrame) {
1137	+	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1138	+	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1139	+	}
1140	+
1141	+	if (storageLayout_ & DataStorage::dslTorque) {
1142	+	idat.t1 = &(atomRowData.torque[atom1]);
1143	+	idat.t2 = &(atomColData.torque[atom2]);
1144	+	}
1145	+
1146	+	if (storageLayout_ & DataStorage::dslDensity) {
1147	+	idat.rho1 = &(atomRowData.density[atom1]);
1148	+	idat.rho2 = &(atomColData.density[atom2]);
1149	+	}
1150	+
1151	+	if (storageLayout_ & DataStorage::dslFunctional) {
1152	+	idat.frho1 = &(atomRowData.functional[atom1]);
1153	+	idat.frho2 = &(atomColData.functional[atom2]);
1154	+	}
1155	+
1156	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1157	+	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1158	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1159	+	}
1160	+
1161	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1162	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1163	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1164	+	}
1165	+
1166	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1167	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1168	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1169	+	}
1170	+
1171	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1172	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1173	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1174	+	}
1175	+
1176	+	#else
1177	+
1178	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1179	+
1180	+	if (storageLayout_ & DataStorage::dslAmat) {
1181	+	idat.A1 = &(snap_->atomData.aMat[atom1]);
1182	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1183	+	}
1184	+
1185	+	if (storageLayout_ & DataStorage::dslElectroFrame) {
1186	+	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1187	+	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1188	+	}
1189	+
1190	+	if (storageLayout_ & DataStorage::dslTorque) {
1191	+	idat.t1 = &(snap_->atomData.torque[atom1]);
1192	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1193	+	}
1194	+
1195	+	if (storageLayout_ & DataStorage::dslDensity) {
1196	+	idat.rho1 = &(snap_->atomData.density[atom1]);
1197	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1198	+	}
1199	+
1200	+	if (storageLayout_ & DataStorage::dslFunctional) {
1201	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1202	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1203	+	}
1204	+
1205	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1206	+	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1207	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1208	+	}
1209	+
1210	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1211	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1212	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1213	+	}
1214	+
1215	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1216	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1217	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1218	+	}
1219	+
1220	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1221	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1222	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1223	+	}
1224	+
1225		#endif
1226		}
1227	+
1228
1229	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1230	+	#ifdef IS_MPI
1231	+	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1232	+	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1233	+	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1234	+	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1235	+
1236	+	atomRowData.force[atom1] += *(idat.f1);
1237	+	atomColData.force[atom2] -= *(idat.f1);
1238	+
1239	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1240	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1241	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1242	+	}
1243	+
1244	+	if (storageLayout_ & DataStorage::dslElectricField) {
1245	+	atomRowData.electricField[atom1] += *(idat.eField1);
1246	+	atomColData.electricField[atom2] += *(idat.eField2);
1247	+	}
1248	+
1249	+	#else
1250	+	pairwisePot += *(idat.pot);
1251	+	excludedPot += *(idat.excludedPot);
1252	+
1253	+	snap_->atomData.force[atom1] += *(idat.f1);
1254	+	snap_->atomData.force[atom2] -= *(idat.f1);
1255	+
1256	+	if (idat.doParticlePot) {
1257	+	// This is the pairwise contribution to the particle pot.  The
1258	+	// embedding contribution is added in each of the low level
1259	+	// non-bonded routines.  In parallel, this calculation is done
1260	+	// in collectData, not in unpackInteractionData.
1261	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1262	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1263	+	}
1264	+
1265	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1266	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1267	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1268	+	}
1269	+
1270	+	if (storageLayout_ & DataStorage::dslElectricField) {
1271	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1272	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1273	+	}
1274	+
1275	+	#endif
1276	+
1277	+	}
1278	+
1279	+	/*
1280	+	* buildNeighborList
1281	+	*
1282	+	* first element of pair is row-indexed CutoffGroup
1283	+	* second element of pair is column-indexed CutoffGroup
1284	+	*/
1285	+	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1286	+
1287	+	vector<pair<int, int> > neighborList;
1288	+	groupCutoffs cuts;
1289	+	bool doAllPairs = false;
1290	+
1291	+	#ifdef IS_MPI
1292	+	cellListRow_.clear();
1293	+	cellListCol_.clear();
1294	+	#else
1295	+	cellList_.clear();
1296	+	#endif
1297	+
1298	+	RealType rList_ = (largestRcut_ + skinThickness_);
1299	+	RealType rl2 = rList_ * rList_;
1300	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1301	+	Mat3x3d Hmat = snap_->getHmat();
1302	+	Vector3d Hx = Hmat.getColumn(0);
1303	+	Vector3d Hy = Hmat.getColumn(1);
1304	+	Vector3d Hz = Hmat.getColumn(2);
1305	+
1306	+	nCells_.x() = (int) ( Hx.length() )/ rList_;
1307	+	nCells_.y() = (int) ( Hy.length() )/ rList_;
1308	+	nCells_.z() = (int) ( Hz.length() )/ rList_;
1309	+
1310	+	// handle small boxes where the cell offsets can end up repeating cells
1311	+
1312	+	if (nCells_.x() < 3) doAllPairs = true;
1313	+	if (nCells_.y() < 3) doAllPairs = true;
1314	+	if (nCells_.z() < 3) doAllPairs = true;
1315	+
1316	+	Mat3x3d invHmat = snap_->getInvHmat();
1317	+	Vector3d rs, scaled, dr;
1318	+	Vector3i whichCell;
1319	+	int cellIndex;
1320	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1321	+
1322	+	#ifdef IS_MPI
1323	+	cellListRow_.resize(nCtot);
1324	+	cellListCol_.resize(nCtot);
1325	+	#else
1326	+	cellList_.resize(nCtot);
1327	+	#endif
1328	+
1329	+	if (!doAllPairs) {
1330	+	#ifdef IS_MPI
1331	+
1332	+	for (int i = 0; i < nGroupsInRow_; i++) {
1333	+	rs = cgRowData.position[i];
1334	+
1335	+	// scaled positions relative to the box vectors
1336	+	scaled = invHmat * rs;
1337	+
1338	+	// wrap the vector back into the unit box by subtracting integer box
1339	+	// numbers
1340	+	for (int j = 0; j < 3; j++) {
1341	+	scaled[j] -= roundMe(scaled[j]);
1342	+	scaled[j] += 0.5;
1343	+	}
1344	+
1345	+	// find xyz-indices of cell that cutoffGroup is in.
1346	+	whichCell.x() = nCells_.x() * scaled.x();
1347	+	whichCell.y() = nCells_.y() * scaled.y();
1348	+	whichCell.z() = nCells_.z() * scaled.z();
1349	+
1350	+	// find single index of this cell:
1351	+	cellIndex = Vlinear(whichCell, nCells_);
1352	+
1353	+	// add this cutoff group to the list of groups in this cell;
1354	+	cellListRow_[cellIndex].push_back(i);
1355	+	}
1356	+	for (int i = 0; i < nGroupsInCol_; i++) {
1357	+	rs = cgColData.position[i];
1358	+
1359	+	// scaled positions relative to the box vectors
1360	+	scaled = invHmat * rs;
1361	+
1362	+	// wrap the vector back into the unit box by subtracting integer box
1363	+	// numbers
1364	+	for (int j = 0; j < 3; j++) {
1365	+	scaled[j] -= roundMe(scaled[j]);
1366	+	scaled[j] += 0.5;
1367	+	}
1368	+
1369	+	// find xyz-indices of cell that cutoffGroup is in.
1370	+	whichCell.x() = nCells_.x() * scaled.x();
1371	+	whichCell.y() = nCells_.y() * scaled.y();
1372	+	whichCell.z() = nCells_.z() * scaled.z();
1373	+
1374	+	// find single index of this cell:
1375	+	cellIndex = Vlinear(whichCell, nCells_);
1376	+
1377	+	// add this cutoff group to the list of groups in this cell;
1378	+	cellListCol_[cellIndex].push_back(i);
1379	+	}
1380	+
1381	+	#else
1382	+	for (int i = 0; i < nGroups_; i++) {
1383	+	rs = snap_->cgData.position[i];
1384	+
1385	+	// scaled positions relative to the box vectors
1386	+	scaled = invHmat * rs;
1387	+
1388	+	// wrap the vector back into the unit box by subtracting integer box
1389	+	// numbers
1390	+	for (int j = 0; j < 3; j++) {
1391	+	scaled[j] -= roundMe(scaled[j]);
1392	+	scaled[j] += 0.5;
1393	+	}
1394	+
1395	+	// find xyz-indices of cell that cutoffGroup is in.
1396	+	whichCell.x() = nCells_.x() * scaled.x();
1397	+	whichCell.y() = nCells_.y() * scaled.y();
1398	+	whichCell.z() = nCells_.z() * scaled.z();
1399	+
1400	+	// find single index of this cell:
1401	+	cellIndex = Vlinear(whichCell, nCells_);
1402	+
1403	+	// add this cutoff group to the list of groups in this cell;
1404	+	cellList_[cellIndex].push_back(i);
1405	+	}
1406	+
1407	+	#endif
1408	+
1409	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1410	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1411	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1412	+	Vector3i m1v(m1x, m1y, m1z);
1413	+	int m1 = Vlinear(m1v, nCells_);
1414	+
1415	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1416	+	os != cellOffsets_.end(); ++os) {
1417	+
1418	+	Vector3i m2v = m1v + (*os);
1419	+
1420	+
1421	+	if (m2v.x() >= nCells_.x()) {
1422	+	m2v.x() = 0;
1423	+	} else if (m2v.x() < 0) {
1424	+	m2v.x() = nCells_.x() - 1;
1425	+	}
1426	+
1427	+	if (m2v.y() >= nCells_.y()) {
1428	+	m2v.y() = 0;
1429	+	} else if (m2v.y() < 0) {
1430	+	m2v.y() = nCells_.y() - 1;
1431	+	}
1432	+
1433	+	if (m2v.z() >= nCells_.z()) {
1434	+	m2v.z() = 0;
1435	+	} else if (m2v.z() < 0) {
1436	+	m2v.z() = nCells_.z() - 1;
1437	+	}
1438	+
1439	+	int m2 = Vlinear (m2v, nCells_);
1440	+
1441	+	#ifdef IS_MPI
1442	+	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1443	+	j1 != cellListRow_[m1].end(); ++j1) {
1444	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1445	+	j2 != cellListCol_[m2].end(); ++j2) {
1446	+
1447	+	// In parallel, we need to visit *all* pairs of row
1448	+	// & column indicies and will divide labor in the
1449	+	// force evaluation later.
1450	+	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1451	+	snap_->wrapVector(dr);
1452	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1453	+	if (dr.lengthSquare() < cuts.third) {
1454	+	neighborList.push_back(make_pair((*j1), (*j2)));
1455	+	}
1456	+	}
1457	+	}
1458	+	#else
1459	+	for (vector<int>::iterator j1 = cellList_[m1].begin();
1460	+	j1 != cellList_[m1].end(); ++j1) {
1461	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1462	+	j2 != cellList_[m2].end(); ++j2) {
1463	+
1464	+	// Always do this if we're in different cells or if
1465	+	// we're in the same cell and the global index of
1466	+	// the j2 cutoff group is greater than or equal to
1467	+	// the j1 cutoff group.  Note that Rappaport's code
1468	+	// has a "less than" conditional here, but that
1469	+	// deals with atom-by-atom computation.  OpenMD
1470	+	// allows atoms within a single cutoff group to
1471	+	// interact with each other.
1472	+
1473	+
1474	+
1475	+	if (m2 != m1 || (*j2) >= (*j1) ) {
1476	+
1477	+	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1478	+	snap_->wrapVector(dr);
1479	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1480	+	if (dr.lengthSquare() < cuts.third) {
1481	+	neighborList.push_back(make_pair((*j1), (*j2)));
1482	+	}
1483	+	}
1484	+	}
1485	+	}
1486	+	#endif
1487	+	}
1488	+	}
1489	+	}
1490	+	}
1491	+	} else {
1492	+	// branch to do all cutoff group pairs
1493	+	#ifdef IS_MPI
1494	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1495	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1496	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1497	+	snap_->wrapVector(dr);
1498	+	cuts = getGroupCutoffs( j1, j2 );
1499	+	if (dr.lengthSquare() < cuts.third) {
1500	+	neighborList.push_back(make_pair(j1, j2));
1501	+	}
1502	+	}
1503	+	}
1504	+	#else
1505	+	// include all groups here.
1506	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1507	+	// include self group interactions j2 == j1
1508	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1509	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1510	+	snap_->wrapVector(dr);
1511	+	cuts = getGroupCutoffs( j1, j2 );
1512	+	if (dr.lengthSquare() < cuts.third) {
1513	+	neighborList.push_back(make_pair(j1, j2));
1514	+	}
1515	+	}
1516	+	}
1517	+	#endif
1518	+	}
1519	+
1520	+	// save the local cutoff group positions for the check that is
1521	+	// done on each loop:
1522	+	saved_CG_positions_.clear();
1523	+	for (int i = 0; i < nGroups_; i++)
1524	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1525	+
1526	+	return neighborList;
1527	+	}
1528		} //end namespace OpenMD

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