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

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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1721 by gezelter, Thu May 24 14:17:42 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 Communicator<Row,RealType>(nAtoms);
90	<	AtomCommVectorI = new Communicator<Row,Vector3d>(nAtoms);
91	<	AtomCommMatrixI = new Communicator<Row,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 Communicator<Column,RealType>(nAtoms);
58	<	AtomCommVectorJ = new Communicator<Column,Vector3d>(nAtoms);
59	<	AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nAtoms);
106	>	massFactors = info_->getMassFactors();
107
108	<	cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
109	<	cgCommVectorJ = new Communicator<Column,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	>	#ifdef IS_MPI
114	>
115	>	MPI::Intracomm row = rowComm.getComm();
116	>	MPI::Intracomm col = colComm.getComm();
117	>
118	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
119	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
120	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
121	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
122	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
123	>
124	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
125	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
126	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
127	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
128	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
129	>
130	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
131	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
132	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
133	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
134	>
135	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
136	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
137	>	nGroupsInRow_ = cgPlanIntRow->getSize();
138	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
139	>
140	>	// Modify the data storage objects with the correct layouts and sizes:
141	>	atomRowData.resize(nAtomsInRow_);
142	>	atomRowData.setStorageLayout(storageLayout_);
143	>	atomColData.resize(nAtomsInCol_);
144	>	atomColData.setStorageLayout(storageLayout_);
145	>	cgRowData.resize(nGroupsInRow_);
146	>	cgRowData.setStorageLayout(DataStorage::dslPosition);
147	>	cgColData.resize(nGroupsInCol_);
148	>	cgColData.setStorageLayout(DataStorage::dslPosition);
149	>
150	>	identsRow.resize(nAtomsInRow_);
151	>	identsCol.resize(nAtomsInCol_);
152	>
153	>	AtomPlanIntRow->gather(idents, identsRow);
154	>	AtomPlanIntColumn->gather(idents, identsCol);
155	>
156	>	// allocate memory for the parallel objects
157	>	atypesRow.resize(nAtomsInRow_);
158	>	atypesCol.resize(nAtomsInCol_);
159	>
160	>	for (int i = 0; i < nAtomsInRow_; i++)
161	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
162	>	for (int i = 0; i < nAtomsInCol_; i++)
163	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
164	>
165	>	pot_row.resize(nAtomsInRow_);
166	>	pot_col.resize(nAtomsInCol_);
167	>
168	>	AtomRowToGlobal.resize(nAtomsInRow_);
169	>	AtomColToGlobal.resize(nAtomsInCol_);
170	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
171	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
172	>
173	>	cgRowToGlobal.resize(nGroupsInRow_);
174	>	cgColToGlobal.resize(nGroupsInCol_);
175	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177	>
178	>	massFactorsRow.resize(nAtomsInRow_);
179	>	massFactorsCol.resize(nAtomsInCol_);
180	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
181	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
182	>
183	>	groupListRow_.clear();
184	>	groupListRow_.resize(nGroupsInRow_);
185	>	for (int i = 0; i < nGroupsInRow_; i++) {
186	>	int gid = cgRowToGlobal[i];
187	>	for (int j = 0; j < nAtomsInRow_; j++) {
188	>	int aid = AtomRowToGlobal[j];
189	>	if (globalGroupMembership[aid] == gid)
190	>	groupListRow_[i].push_back(j);
191	>	}
192	>	}
193	>
194	>	groupListCol_.clear();
195	>	groupListCol_.resize(nGroupsInCol_);
196	>	for (int i = 0; i < nGroupsInCol_; i++) {
197	>	int gid = cgColToGlobal[i];
198	>	for (int j = 0; j < nAtomsInCol_; j++) {
199	>	int aid = AtomColToGlobal[j];
200	>	if (globalGroupMembership[aid] == gid)
201	>	groupListCol_[i].push_back(j);
202	>	}
203	>	}
204	>
205	>	excludesForAtom.clear();
206	>	excludesForAtom.resize(nAtomsInRow_);
207	>	toposForAtom.clear();
208	>	toposForAtom.resize(nAtomsInRow_);
209	>	topoDist.clear();
210	>	topoDist.resize(nAtomsInRow_);
211	>	for (int i = 0; i < nAtomsInRow_; i++) {
212	>	int iglob = AtomRowToGlobal[i];
213	>
214	>	for (int j = 0; j < nAtomsInCol_; j++) {
215	>	int jglob = AtomColToGlobal[j];
216	>
217	>	if (excludes->hasPair(iglob, jglob))
218	>	excludesForAtom[i].push_back(j);
219	>
220	>	if (oneTwo->hasPair(iglob, jglob)) {
221	>	toposForAtom[i].push_back(j);
222	>	topoDist[i].push_back(1);
223	>	} else {
224	>	if (oneThree->hasPair(iglob, jglob)) {
225	>	toposForAtom[i].push_back(j);
226	>	topoDist[i].push_back(2);
227	>	} else {
228	>	if (oneFour->hasPair(iglob, jglob)) {
229	>	toposForAtom[i].push_back(j);
230	>	topoDist[i].push_back(3);
231	>	}
232	>	}
233	>	}
234	>	}
235	>	}
236	>
237	>	#else
238	>	excludesForAtom.clear();
239	>	excludesForAtom.resize(nLocal_);
240	>	toposForAtom.clear();
241	>	toposForAtom.resize(nLocal_);
242	>	topoDist.clear();
243	>	topoDist.resize(nLocal_);
244	>
245	>	for (int i = 0; i < nLocal_; i++) {
246	>	int iglob = AtomLocalToGlobal[i];
247	>
248	>	for (int j = 0; j < nLocal_; j++) {
249	>	int jglob = AtomLocalToGlobal[j];
250	>
251	>	if (excludes->hasPair(iglob, jglob))
252	>	excludesForAtom[i].push_back(j);
253	>
254	>	if (oneTwo->hasPair(iglob, jglob)) {
255	>	toposForAtom[i].push_back(j);
256	>	topoDist[i].push_back(1);
257	>	} else {
258	>	if (oneThree->hasPair(iglob, jglob)) {
259	>	toposForAtom[i].push_back(j);
260	>	topoDist[i].push_back(2);
261	>	} else {
262	>	if (oneFour->hasPair(iglob, jglob)) {
263	>	toposForAtom[i].push_back(j);
264	>	topoDist[i].push_back(3);
265	>	}
266	>	}
267	>	}
268	>	}
269	>	}
270		#endif
271	+
272	+	// allocate memory for the parallel objects
273	+	atypesLocal.resize(nLocal_);
274	+
275	+	for (int i = 0; i < nLocal_; i++)
276	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
277	+
278	+	groupList_.clear();
279	+	groupList_.resize(nGroups_);
280	+	for (int i = 0; i < nGroups_; i++) {
281	+	int gid = cgLocalToGlobal[i];
282	+	for (int j = 0; j < nLocal_; j++) {
283	+	int aid = AtomLocalToGlobal[j];
284	+	if (globalGroupMembership[aid] == gid) {
285	+	groupList_[i].push_back(j);
286	+	}
287	+	}
288	+	}
289	+
290	+
291	+	createGtypeCutoffMap();
292	+
293		}
294	+
295	+	void ForceMatrixDecomposition::createGtypeCutoffMap() {
296
297	+	RealType tol = 1e-6;
298	+	largestRcut_ = 0.0;
299	+	RealType rc;
300	+	int atid;
301	+	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302	+
303	+	map<int, RealType> atypeCutoff;
304	+
305	+	for (set<AtomType*>::iterator at = atypes.begin();
306	+	at != atypes.end(); ++at){
307	+	atid = (*at)->getIdent();
308	+	if (userChoseCutoff_)
309	+	atypeCutoff[atid] = userCutoff_;
310	+	else
311	+	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312	+	}
313	+
314	+	vector<RealType> gTypeCutoffs;
315	+	// first we do a single loop over the cutoff groups to find the
316	+	// largest cutoff for any atypes present in this group.
317	+	#ifdef IS_MPI
318	+	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
319	+	groupRowToGtype.resize(nGroupsInRow_);
320	+	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
321	+	vector<int> atomListRow = getAtomsInGroupRow(cg1);
322	+	for (vector<int>::iterator ia = atomListRow.begin();
323	+	ia != atomListRow.end(); ++ia) {
324	+	int atom1 = (*ia);
325	+	atid = identsRow[atom1];
326	+	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
327	+	groupCutoffRow[cg1] = atypeCutoff[atid];
328	+	}
329	+	}
330
331	+	bool gTypeFound = false;
332	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
333	+	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
334	+	groupRowToGtype[cg1] = gt;
335	+	gTypeFound = true;
336	+	}
337	+	}
338	+	if (!gTypeFound) {
339	+	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
340	+	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
341	+	}
342	+
343	+	}
344	+	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
345	+	groupColToGtype.resize(nGroupsInCol_);
346	+	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
347	+	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
348	+	for (vector<int>::iterator jb = atomListCol.begin();
349	+	jb != atomListCol.end(); ++jb) {
350	+	int atom2 = (*jb);
351	+	atid = identsCol[atom2];
352	+	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
353	+	groupCutoffCol[cg2] = atypeCutoff[atid];
354	+	}
355	+	}
356	+	bool gTypeFound = false;
357	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
358	+	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
359	+	groupColToGtype[cg2] = gt;
360	+	gTypeFound = true;
361	+	}
362	+	}
363	+	if (!gTypeFound) {
364	+	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
365	+	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
366	+	}
367	+	}
368	+	#else
369
370	<	void ForceDecomposition::distributeData()  {
370	>	vector<RealType> groupCutoff(nGroups_, 0.0);
371	>	groupToGtype.resize(nGroups_);
372	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
373	>	groupCutoff[cg1] = 0.0;
374	>	vector<int> atomList = getAtomsInGroupRow(cg1);
375	>	for (vector<int>::iterator ia = atomList.begin();
376	>	ia != atomList.end(); ++ia) {
377	>	int atom1 = (*ia);
378	>	atid = idents[atom1];
379	>	if (atypeCutoff[atid] > groupCutoff[cg1])
380	>	groupCutoff[cg1] = atypeCutoff[atid];
381	>	}
382	>
383	>	bool gTypeFound = false;
384	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
386	>	groupToGtype[cg1] = gt;
387	>	gTypeFound = true;
388	>	}
389	>	}
390	>	if (!gTypeFound) {
391	>	gTypeCutoffs.push_back( groupCutoff[cg1] );
392	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393	>	}
394	>	}
395	>	#endif
396	>
397	>	// Now we find the maximum group cutoff value present in the simulation
398	>
399	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
400	>	gTypeCutoffs.end());
401	>
402		#ifdef IS_MPI
403	<	Snapshot* snap = sman_->getCurrentSnapshot();
403	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
404	>	MPI::MAX);
405	>	#endif
406
407	+	RealType tradRcut = groupMax;
408	+
409	+	for (int i = 0; i < gTypeCutoffs.size();  i++) {
410	+	for (int j = 0; j < gTypeCutoffs.size();  j++) {
411	+	RealType thisRcut;
412	+	switch(cutoffPolicy_) {
413	+	case TRADITIONAL:
414	+	thisRcut = tradRcut;
415	+	break;
416	+	case MIX:
417	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
418	+	break;
419	+	case MAX:
420	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
421	+	break;
422	+	default:
423	+	sprintf(painCave.errMsg,
424	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
425	+	"hit an unknown cutoff policy!\n");
426	+	painCave.severity = OPENMD_ERROR;
427	+	painCave.isFatal = 1;
428	+	simError();
429	+	break;
430	+	}
431	+
432	+	pair<int,int> key = make_pair(i,j);
433	+	gTypeCutoffMap[key].first = thisRcut;
434	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
435	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
436	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
437	+	// sanity check
438	+
439	+	if (userChoseCutoff_) {
440	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
441	+	sprintf(painCave.errMsg,
442	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
443	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
444	+	painCave.severity = OPENMD_ERROR;
445	+	painCave.isFatal = 1;
446	+	simError();
447	+	}
448	+	}
449	+	}
450	+	}
451	+	}
452	+
453	+
454	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
455	+	int i, j;
456	+	#ifdef IS_MPI
457	+	i = groupRowToGtype[cg1];
458	+	j = groupColToGtype[cg2];
459	+	#else
460	+	i = groupToGtype[cg1];
461	+	j = groupToGtype[cg2];
462	+	#endif
463	+	return gTypeCutoffMap[make_pair(i,j)];
464	+	}
465	+
466	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
467	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
468	+	if (toposForAtom[atom1][j] == atom2)
469	+	return topoDist[atom1][j];
470	+	}
471	+	return 0;
472	+	}
473	+
474	+	void ForceMatrixDecomposition::zeroWorkArrays() {
475	+	pairwisePot = 0.0;
476	+	embeddingPot = 0.0;
477	+
478	+	#ifdef IS_MPI
479	+	if (storageLayout_ & DataStorage::dslForce) {
480	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
481	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
482	+	}
483	+
484	+	if (storageLayout_ & DataStorage::dslTorque) {
485	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
486	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
487	+	}
488	+
489	+	fill(pot_row.begin(), pot_row.end(),
490	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
491	+
492	+	fill(pot_col.begin(), pot_col.end(),
493	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
494	+
495	+	if (storageLayout_ & DataStorage::dslParticlePot) {
496	+	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
497	+	0.0);
498	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
499	+	0.0);
500	+	}
501	+
502	+	if (storageLayout_ & DataStorage::dslDensity) {
503	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
504	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
505	+	}
506	+
507	+	if (storageLayout_ & DataStorage::dslFunctional) {
508	+	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
509	+	0.0);
510	+	fill(atomColData.functional.begin(), atomColData.functional.end(),
511	+	0.0);
512	+	}
513	+
514	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
515	+	fill(atomRowData.functionalDerivative.begin(),
516	+	atomRowData.functionalDerivative.end(), 0.0);
517	+	fill(atomColData.functionalDerivative.begin(),
518	+	atomColData.functionalDerivative.end(), 0.0);
519	+	}
520	+
521	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
522	+	fill(atomRowData.skippedCharge.begin(),
523	+	atomRowData.skippedCharge.end(), 0.0);
524	+	fill(atomColData.skippedCharge.begin(),
525	+	atomColData.skippedCharge.end(), 0.0);
526	+	}
527	+
528	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
529	+	fill(atomRowData.flucQFrc.begin(),
530	+	atomRowData.flucQFrc.end(), 0.0);
531	+	fill(atomColData.flucQFrc.begin(),
532	+	atomColData.flucQFrc.end(), 0.0);
533	+	}
534	+
535	+	if (storageLayout_ & DataStorage::dslElectricField) {
536	+	fill(atomRowData.electricField.begin(),
537	+	atomRowData.electricField.end(), V3Zero);
538	+	fill(atomColData.electricField.begin(),
539	+	atomColData.electricField.end(), V3Zero);
540	+	}
541	+
542	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
543	+	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
544	+	0.0);
545	+	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
546	+	0.0);
547	+	}
548	+
549	+	#endif
550	+	// even in parallel, we need to zero out the local arrays:
551	+
552	+	if (storageLayout_ & DataStorage::dslParticlePot) {
553	+	fill(snap_->atomData.particlePot.begin(),
554	+	snap_->atomData.particlePot.end(), 0.0);
555	+	}
556	+
557	+	if (storageLayout_ & DataStorage::dslDensity) {
558	+	fill(snap_->atomData.density.begin(),
559	+	snap_->atomData.density.end(), 0.0);
560	+	}
561	+
562	+	if (storageLayout_ & DataStorage::dslFunctional) {
563	+	fill(snap_->atomData.functional.begin(),
564	+	snap_->atomData.functional.end(), 0.0);
565	+	}
566	+
567	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
568	+	fill(snap_->atomData.functionalDerivative.begin(),
569	+	snap_->atomData.functionalDerivative.end(), 0.0);
570	+	}
571	+
572	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
573	+	fill(snap_->atomData.skippedCharge.begin(),
574	+	snap_->atomData.skippedCharge.end(), 0.0);
575	+	}
576	+
577	+	if (storageLayout_ & DataStorage::dslElectricField) {
578	+	fill(snap_->atomData.electricField.begin(),
579	+	snap_->atomData.electricField.end(), V3Zero);
580	+	}
581	+	}
582	+
583	+
584	+	void ForceMatrixDecomposition::distributeData()  {
585	+	snap_ = sman_->getCurrentSnapshot();
586	+	storageLayout_ = sman_->getStorageLayout();
587	+	#ifdef IS_MPI
588	+
589		// gather up the atomic positions
590	<	AtomCommVectorI->gather(snap->atomData.position,
591	<	snap->atomIData.position);
592	<	AtomCommVectorJ->gather(snap->atomData.position,
593	<	snap->atomJData.position);
590	>	AtomPlanVectorRow->gather(snap_->atomData.position,
591	>	atomRowData.position);
592	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
593	>	atomColData.position);
594
595		// gather up the cutoff group positions
596	<	cgCommVectorI->gather(snap->cgData.position,
597	<	snap->cgIData.position);
598	<	cgCommVectorJ->gather(snap->cgData.position,
599	<	snap->cgJData.position);
596	>
597	>	cgPlanVectorRow->gather(snap_->cgData.position,
598	>	cgRowData.position);
599	>
600	>	cgPlanVectorColumn->gather(snap_->cgData.position,
601	>	cgColData.position);
602	>
603
604		// if needed, gather the atomic rotation matrices
605	<	if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
606	<	AtomCommMatrixI->gather(snap->atomData.aMat,
607	<	snap->atomIData.aMat);
608	<	AtomCommMatrixJ->gather(snap->atomData.aMat,
609	<	snap->atomJData.aMat);
605	>	if (storageLayout_ & DataStorage::dslAmat) {
606	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
607	>	atomRowData.aMat);
608	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
609	>	atomColData.aMat);
610		}
611
612		// if needed, gather the atomic eletrostatic frames
613	<	if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
614	<	AtomCommMatrixI->gather(snap->atomData.electroFrame,
615	<	snap->atomIData.electroFrame);
616	<	AtomCommMatrixJ->gather(snap->atomData.electroFrame,
617	<	snap->atomJData.electroFrame);
613	>	if (storageLayout_ & DataStorage::dslElectroFrame) {
614	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
615	>	atomRowData.electroFrame);
616	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
617	>	atomColData.electroFrame);
618		}
619	+
620	+	// if needed, gather the atomic fluctuating charge values
621	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
622	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
623	+	atomRowData.flucQPos);
624	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
625	+	atomColData.flucQPos);
626	+	}
627	+
628		#endif
629		}
630
631	<	void ForceDecomposition::collectIntermediateData() {
631	>	/* collects information obtained during the pre-pair loop onto local
632	>	* data structures.
633	>	*/
634	>	void ForceMatrixDecomposition::collectIntermediateData() {
635	>	snap_ = sman_->getCurrentSnapshot();
636	>	storageLayout_ = sman_->getStorageLayout();
637		#ifdef IS_MPI
105	–	Snapshot* snap = sman_->getCurrentSnapshot();
638
639	<	if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
640	<	AtomCommRealI->scatter(snap->atomIData.density,
641	<	snap->atomData.density);
642	<	std::vector<RealType> rho_tmp;
643	<	int n = snap->getNumberOfAtoms();
644	<	rho_tmp.reserve( n );
645	<	AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
639	>	if (storageLayout_ & DataStorage::dslDensity) {
640	>
641	>	AtomPlanRealRow->scatter(atomRowData.density,
642	>	snap_->atomData.density);
643	>
644	>	int n = snap_->atomData.density.size();
645	>	vector<RealType> rho_tmp(n, 0.0);
646	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
647		for (int i = 0; i < n; i++)
648	<	snap->atomData.density[i] += rho_tmp[i];
648	>	snap_->atomData.density[i] += rho_tmp[i];
649		}
650	+
651	+	if (storageLayout_ & DataStorage::dslElectricField) {
652	+
653	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
654	+	snap_->atomData.electricField);
655	+
656	+	int n = snap_->atomData.electricField.size();
657	+	vector<Vector3d> field_tmp(n, V3Zero);
658	+	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
659	+	for (int i = 0; i < n; i++)
660	+	snap_->atomData.electricField[i] += field_tmp[i];
661	+	}
662		#endif
663		}
664	<
665	<	void ForceDecomposition::distributeIntermediateData() {
664	>
665	>	/*
666	>	* redistributes information obtained during the pre-pair loop out to
667	>	* row and column-indexed data structures
668	>	*/
669	>	void ForceMatrixDecomposition::distributeIntermediateData() {
670	>	snap_ = sman_->getCurrentSnapshot();
671	>	storageLayout_ = sman_->getStorageLayout();
672		#ifdef IS_MPI
673	<	Snapshot* snap = sman_->getCurrentSnapshot();
674	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
675	<	AtomCommRealI->gather(snap->atomData.functional,
676	<	snap->atomIData.functional);
677	<	AtomCommRealJ->gather(snap->atomData.functional,
127	<	snap->atomJData.functional);
673	>	if (storageLayout_ & DataStorage::dslFunctional) {
674	>	AtomPlanRealRow->gather(snap_->atomData.functional,
675	>	atomRowData.functional);
676	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
677	>	atomColData.functional);
678		}
679
680	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
681	<	AtomCommRealI->gather(snap->atomData.functionalDerivative,
682	<	snap->atomIData.functionalDerivative);
683	<	AtomCommRealJ->gather(snap->atomData.functionalDerivative,
684	<	snap->atomJData.functionalDerivative);
680	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
681	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
682	>	atomRowData.functionalDerivative);
683	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
684	>	atomColData.functionalDerivative);
685		}
686		#endif
687		}
688
689
690	<	void ForceDecomposition::collectData() {
691	<	#ifdef IS_MPI
692	<	Snapshot* snap = sman_->getCurrentSnapshot();
693	<	int n = snap->getNumberOfAtoms();
694	<
695	<	std::vector<Vector3d> frc_tmp;
146	<	frc_tmp.reserve( n );
690	>	void ForceMatrixDecomposition::collectData() {
691	>	snap_ = sman_->getCurrentSnapshot();
692	>	storageLayout_ = sman_->getStorageLayout();
693	>	#ifdef IS_MPI
694	>	int n = snap_->atomData.force.size();
695	>	vector<Vector3d> frc_tmp(n, V3Zero);
696
697	<	AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
698	<	for (int i = 0; i < n; i++)
699	<	snap->atomData.force[i] += frc_tmp[i];
700	<
701	<	AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
153	<	for (int i = 0; i < n; i++)
154	<	snap->atomData.force[i] += frc_tmp[i];
697	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
698	>	for (int i = 0; i < n; i++) {
699	>	snap_->atomData.force[i] += frc_tmp[i];
700	>	frc_tmp[i] = 0.0;
701	>	}
702
703	+	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
704	+	for (int i = 0; i < n; i++) {
705	+	snap_->atomData.force[i] += frc_tmp[i];
706	+	}
707	+
708	+	if (storageLayout_ & DataStorage::dslTorque) {
709	+
710	+	int nt = snap_->atomData.torque.size();
711	+	vector<Vector3d> trq_tmp(nt, V3Zero);
712	+
713	+	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
714	+	for (int i = 0; i < nt; i++) {
715	+	snap_->atomData.torque[i] += trq_tmp[i];
716	+	trq_tmp[i] = 0.0;
717	+	}
718	+
719	+	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
720	+	for (int i = 0; i < nt; i++)
721	+	snap_->atomData.torque[i] += trq_tmp[i];
722	+	}
723	+
724	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
725	+
726	+	int ns = snap_->atomData.skippedCharge.size();
727	+	vector<RealType> skch_tmp(ns, 0.0);
728	+
729	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
730	+	for (int i = 0; i < ns; i++) {
731	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
732	+	skch_tmp[i] = 0.0;
733	+	}
734	+
735	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
736	+	for (int i = 0; i < ns; i++)
737	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
738	+
739	+	}
740
741	<	if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
742	<	std::vector<Vector3d> trq_tmp;
743	<	trq_tmp.reserve( n );
741	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
742	>
743	>	int nq = snap_->atomData.flucQFrc.size();
744	>	vector<RealType> fqfrc_tmp(nq, 0.0);
745	>
746	>	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
747	>	for (int i = 0; i < nq; i++) {
748	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
749	>	fqfrc_tmp[i] = 0.0;
750	>	}
751
752	<	AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
753	<	for (int i = 0; i < n; i++)
754	<	snap->atomData.torque[i] += trq_tmp[i];
752	>	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
753	>	for (int i = 0; i < nq; i++)
754	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
755	>
756	>	}
757	>
758	>	nLocal_ = snap_->getNumberOfAtoms();
759	>
760	>	vector<potVec> pot_temp(nLocal_,
761	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
762	>
763	>	// scatter/gather pot_row into the members of my column
764	>
765	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
766	>
767	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
768	>	pairwisePot += pot_temp[ii];
769	>
770	>	fill(pot_temp.begin(), pot_temp.end(),
771	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
772
773	<	AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
774	<	for (int i = 0; i < n; i++)
775	<	snap->atomData.torque[i] += trq_tmp[i];
773	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
774	>
775	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
776	>	pairwisePot += pot_temp[ii];
777	>
778	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
779	>	RealType ploc1 = pairwisePot[ii];
780	>	RealType ploc2 = 0.0;
781	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
782	>	pairwisePot[ii] = ploc2;
783		}
784	+
785	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
786	+	RealType ploc1 = embeddingPot[ii];
787	+	RealType ploc2 = 0.0;
788	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
789	+	embeddingPot[ii] = ploc2;
790	+	}
791	+
792	+	#endif
793	+
794	+	}
795	+
796	+	int ForceMatrixDecomposition::getNAtomsInRow() {
797	+	#ifdef IS_MPI
798	+	return nAtomsInRow_;
799	+	#else
800	+	return nLocal_;
801	+	#endif
802	+	}
803	+
804	+	/**
805	+	* returns the list of atoms belonging to this group.
806	+	*/
807	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
808	+	#ifdef IS_MPI
809	+	return groupListRow_[cg1];
810	+	#else
811	+	return groupList_[cg1];
812	+	#endif
813	+	}
814	+
815	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
816	+	#ifdef IS_MPI
817	+	return groupListCol_[cg2];
818	+	#else
819	+	return groupList_[cg2];
820	+	#endif
821	+	}
822	+
823	+	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
824	+	Vector3d d;
825
826	<	// Still need pot!
826	>	#ifdef IS_MPI
827	>	d = cgColData.position[cg2] - cgRowData.position[cg1];
828	>	#else
829	>	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
830	>	#endif
831
832	+	snap_->wrapVector(d);
833	+	return d;
834	+	}
835	+
836	+
837	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
838	+
839	+	Vector3d d;
840	+
841	+	#ifdef IS_MPI
842	+	d = cgRowData.position[cg1] - atomRowData.position[atom1];
843	+	#else
844	+	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
845	+	#endif
846	+
847	+	snap_->wrapVector(d);
848	+	return d;
849	+	}
850	+
851	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
852	+	Vector3d d;
853	+
854	+	#ifdef IS_MPI
855	+	d = cgColData.position[cg2] - atomColData.position[atom2];
856	+	#else
857	+	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
858	+	#endif
859	+
860	+	snap_->wrapVector(d);
861	+	return d;
862	+	}
863	+
864	+	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
865	+	#ifdef IS_MPI
866	+	return massFactorsRow[atom1];
867	+	#else
868	+	return massFactors[atom1];
869	+	#endif
870	+	}
871	+
872	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
873	+	#ifdef IS_MPI
874	+	return massFactorsCol[atom2];
875	+	#else
876	+	return massFactors[atom2];
877	+	#endif
878	+
879	+	}
880	+
881	+	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
882	+	Vector3d d;
883	+
884	+	#ifdef IS_MPI
885	+	d = atomColData.position[atom2] - atomRowData.position[atom1];
886	+	#else
887	+	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
888	+	#endif
889	+
890	+	snap_->wrapVector(d);
891	+	return d;
892	+	}
893	+
894	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
895	+	return excludesForAtom[atom1];
896	+	}
897	+
898	+	/**
899	+	* We need to exclude some overcounted interactions that result from
900	+	* the parallel decomposition.
901	+	*/
902	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
903	+	int unique_id_1, unique_id_2;
904	+
905	+	#ifdef IS_MPI
906	+	// in MPI, we have to look up the unique IDs for each atom
907	+	unique_id_1 = AtomRowToGlobal[atom1];
908	+	unique_id_2 = AtomColToGlobal[atom2];
909	+	#else
910	+	unique_id_1 = AtomLocalToGlobal[atom1];
911	+	unique_id_2 = AtomLocalToGlobal[atom2];
912	+	#endif
913	+
914	+	if (unique_id_1 == unique_id_2) return true;
915	+
916	+	#ifdef IS_MPI
917	+	// this prevents us from doing the pair on multiple processors
918	+	if (unique_id_1 < unique_id_2) {
919	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
920	+	} else {
921	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
922	+	}
923	+	#endif
924	+
925	+	return false;
926	+	}
927	+
928	+	/**
929	+	* We need to handle the interactions for atoms who are involved in
930	+	* the same rigid body as well as some short range interactions
931	+	* (bonds, bends, torsions) differently from other interactions.
932	+	* We'll still visit the pairwise routines, but with a flag that
933	+	* tells those routines to exclude the pair from direct long range
934	+	* interactions.  Some indirect interactions (notably reaction
935	+	* field) must still be handled for these pairs.
936	+	*/
937	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
938	+
939	+	// excludesForAtom was constructed to use row/column indices in the MPI
940	+	// version, and to use local IDs in the non-MPI version:
941	+
942	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
943	+	i != excludesForAtom[atom1].end(); ++i) {
944	+	if ( (*i) == atom2 ) return true;
945	+	}
946	+
947	+	return false;
948	+	}
949	+
950	+
951	+	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
952	+	#ifdef IS_MPI
953	+	atomRowData.force[atom1] += fg;
954	+	#else
955	+	snap_->atomData.force[atom1] += fg;
956	+	#endif
957	+	}
958	+
959	+	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
960	+	#ifdef IS_MPI
961	+	atomColData.force[atom2] += fg;
962	+	#else
963	+	snap_->atomData.force[atom2] += fg;
964	+	#endif
965	+	}
966	+
967	+	// filling interaction blocks with pointers
968	+	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
969	+	int atom1, int atom2) {
970	+
971	+	idat.excluded = excludeAtomPair(atom1, atom2);
972	+
973	+	#ifdef IS_MPI
974	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
975	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
976	+	//                         ff_->getAtomType(identsCol[atom2]) );
977	+
978	+	if (storageLayout_ & DataStorage::dslAmat) {
979	+	idat.A1 = &(atomRowData.aMat[atom1]);
980	+	idat.A2 = &(atomColData.aMat[atom2]);
981	+	}
982	+
983	+	if (storageLayout_ & DataStorage::dslElectroFrame) {
984	+	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
985	+	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
986	+	}
987	+
988	+	if (storageLayout_ & DataStorage::dslTorque) {
989	+	idat.t1 = &(atomRowData.torque[atom1]);
990	+	idat.t2 = &(atomColData.torque[atom2]);
991	+	}
992	+
993	+	if (storageLayout_ & DataStorage::dslDensity) {
994	+	idat.rho1 = &(atomRowData.density[atom1]);
995	+	idat.rho2 = &(atomColData.density[atom2]);
996	+	}
997	+
998	+	if (storageLayout_ & DataStorage::dslFunctional) {
999	+	idat.frho1 = &(atomRowData.functional[atom1]);
1000	+	idat.frho2 = &(atomColData.functional[atom2]);
1001	+	}
1002	+
1003	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1004	+	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1005	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1006	+	}
1007	+
1008	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1009	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1010	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1011	+	}
1012	+
1013	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1014	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1015	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1016	+	}
1017	+
1018	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1019	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1020	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1021	+	}
1022	+
1023	+	#else
1024	+
1025	+
1026	+	// cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1027	+	// cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1028	+	// cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1029	+
1030	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1031	+	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1032	+	//                         ff_->getAtomType(idents[atom2]) );
1033	+
1034	+	if (storageLayout_ & DataStorage::dslAmat) {
1035	+	idat.A1 = &(snap_->atomData.aMat[atom1]);
1036	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1037	+	}
1038
1039	+	if (storageLayout_ & DataStorage::dslElectroFrame) {
1040	+	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1041	+	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1042	+	}
1043
1044	+	if (storageLayout_ & DataStorage::dslTorque) {
1045	+	idat.t1 = &(snap_->atomData.torque[atom1]);
1046	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1047	+	}
1048	+
1049	+	if (storageLayout_ & DataStorage::dslDensity) {
1050	+	idat.rho1 = &(snap_->atomData.density[atom1]);
1051	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1052	+	}
1053	+
1054	+	if (storageLayout_ & DataStorage::dslFunctional) {
1055	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1056	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1057	+	}
1058	+
1059	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1060	+	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1061	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1062	+	}
1063	+
1064	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1065	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1066	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1067	+	}
1068	+
1069	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1070	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1071	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1072	+	}
1073	+
1074	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1075	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1076	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1077	+	}
1078	+
1079		#endif
1080		}
1081	+
1082
1083	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1084	+	#ifdef IS_MPI
1085	+	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1086	+	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1087	+
1088	+	atomRowData.force[atom1] += *(idat.f1);
1089	+	atomColData.force[atom2] -= *(idat.f1);
1090	+
1091	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1092	+	atomRowData.flucQFrc[atom1] += *(idat.dVdFQ1);
1093	+	atomColData.flucQFrc[atom2] += *(idat.dVdFQ2);
1094	+	}
1095	+
1096	+	if (storageLayout_ & DataStorage::dslElectricField) {
1097	+	atomRowData.electricField[atom1] += *(idat.eField1);
1098	+	atomColData.electricField[atom2] += *(idat.eField2);
1099	+	}
1100	+
1101	+	// should particle pot be done here also?
1102	+	#else
1103	+	pairwisePot += *(idat.pot);
1104	+
1105	+	snap_->atomData.force[atom1] += *(idat.f1);
1106	+	snap_->atomData.force[atom2] -= *(idat.f1);
1107	+
1108	+	if (idat.doParticlePot) {
1109	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1110	+	snap_->atomData.particlePot[atom2] -= *(idat.vpair) * *(idat.sw);
1111	+	}
1112	+
1113	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1114	+	snap_->atomData.flucQFrc[atom1] += *(idat.dVdFQ1);
1115	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1116	+	}
1117	+
1118	+	if (storageLayout_ & DataStorage::dslElectricField) {
1119	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1120	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1121	+	}
1122	+
1123	+	#endif
1124	+
1125	+	}
1126	+
1127	+	/*
1128	+	* buildNeighborList
1129	+	*
1130	+	* first element of pair is row-indexed CutoffGroup
1131	+	* second element of pair is column-indexed CutoffGroup
1132	+	*/
1133	+	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1134	+
1135	+	vector<pair<int, int> > neighborList;
1136	+	groupCutoffs cuts;
1137	+	bool doAllPairs = false;
1138	+
1139	+	#ifdef IS_MPI
1140	+	cellListRow_.clear();
1141	+	cellListCol_.clear();
1142	+	#else
1143	+	cellList_.clear();
1144	+	#endif
1145	+
1146	+	RealType rList_ = (largestRcut_ + skinThickness_);
1147	+	RealType rl2 = rList_ * rList_;
1148	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1149	+	Mat3x3d Hmat = snap_->getHmat();
1150	+	Vector3d Hx = Hmat.getColumn(0);
1151	+	Vector3d Hy = Hmat.getColumn(1);
1152	+	Vector3d Hz = Hmat.getColumn(2);
1153	+
1154	+	nCells_.x() = (int) ( Hx.length() )/ rList_;
1155	+	nCells_.y() = (int) ( Hy.length() )/ rList_;
1156	+	nCells_.z() = (int) ( Hz.length() )/ rList_;
1157	+
1158	+	// handle small boxes where the cell offsets can end up repeating cells
1159	+
1160	+	if (nCells_.x() < 3) doAllPairs = true;
1161	+	if (nCells_.y() < 3) doAllPairs = true;
1162	+	if (nCells_.z() < 3) doAllPairs = true;
1163	+
1164	+	Mat3x3d invHmat = snap_->getInvHmat();
1165	+	Vector3d rs, scaled, dr;
1166	+	Vector3i whichCell;
1167	+	int cellIndex;
1168	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1169	+
1170	+	#ifdef IS_MPI
1171	+	cellListRow_.resize(nCtot);
1172	+	cellListCol_.resize(nCtot);
1173	+	#else
1174	+	cellList_.resize(nCtot);
1175	+	#endif
1176	+
1177	+	if (!doAllPairs) {
1178	+	#ifdef IS_MPI
1179	+
1180	+	for (int i = 0; i < nGroupsInRow_; i++) {
1181	+	rs = cgRowData.position[i];
1182	+
1183	+	// scaled positions relative to the box vectors
1184	+	scaled = invHmat * rs;
1185	+
1186	+	// wrap the vector back into the unit box by subtracting integer box
1187	+	// numbers
1188	+	for (int j = 0; j < 3; j++) {
1189	+	scaled[j] -= roundMe(scaled[j]);
1190	+	scaled[j] += 0.5;
1191	+	}
1192	+
1193	+	// find xyz-indices of cell that cutoffGroup is in.
1194	+	whichCell.x() = nCells_.x() * scaled.x();
1195	+	whichCell.y() = nCells_.y() * scaled.y();
1196	+	whichCell.z() = nCells_.z() * scaled.z();
1197	+
1198	+	// find single index of this cell:
1199	+	cellIndex = Vlinear(whichCell, nCells_);
1200	+
1201	+	// add this cutoff group to the list of groups in this cell;
1202	+	cellListRow_[cellIndex].push_back(i);
1203	+	}
1204	+	for (int i = 0; i < nGroupsInCol_; i++) {
1205	+	rs = cgColData.position[i];
1206	+
1207	+	// scaled positions relative to the box vectors
1208	+	scaled = invHmat * rs;
1209	+
1210	+	// wrap the vector back into the unit box by subtracting integer box
1211	+	// numbers
1212	+	for (int j = 0; j < 3; j++) {
1213	+	scaled[j] -= roundMe(scaled[j]);
1214	+	scaled[j] += 0.5;
1215	+	}
1216	+
1217	+	// find xyz-indices of cell that cutoffGroup is in.
1218	+	whichCell.x() = nCells_.x() * scaled.x();
1219	+	whichCell.y() = nCells_.y() * scaled.y();
1220	+	whichCell.z() = nCells_.z() * scaled.z();
1221	+
1222	+	// find single index of this cell:
1223	+	cellIndex = Vlinear(whichCell, nCells_);
1224	+
1225	+	// add this cutoff group to the list of groups in this cell;
1226	+	cellListCol_[cellIndex].push_back(i);
1227	+	}
1228	+
1229	+	#else
1230	+	for (int i = 0; i < nGroups_; i++) {
1231	+	rs = snap_->cgData.position[i];
1232	+
1233	+	// scaled positions relative to the box vectors
1234	+	scaled = invHmat * rs;
1235	+
1236	+	// wrap the vector back into the unit box by subtracting integer box
1237	+	// numbers
1238	+	for (int j = 0; j < 3; j++) {
1239	+	scaled[j] -= roundMe(scaled[j]);
1240	+	scaled[j] += 0.5;
1241	+	}
1242	+
1243	+	// find xyz-indices of cell that cutoffGroup is in.
1244	+	whichCell.x() = nCells_.x() * scaled.x();
1245	+	whichCell.y() = nCells_.y() * scaled.y();
1246	+	whichCell.z() = nCells_.z() * scaled.z();
1247	+
1248	+	// find single index of this cell:
1249	+	cellIndex = Vlinear(whichCell, nCells_);
1250	+
1251	+	// add this cutoff group to the list of groups in this cell;
1252	+	cellList_[cellIndex].push_back(i);
1253	+	}
1254	+
1255	+	#endif
1256	+
1257	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1258	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1259	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1260	+	Vector3i m1v(m1x, m1y, m1z);
1261	+	int m1 = Vlinear(m1v, nCells_);
1262	+
1263	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1264	+	os != cellOffsets_.end(); ++os) {
1265	+
1266	+	Vector3i m2v = m1v + (*os);
1267	+
1268	+
1269	+	if (m2v.x() >= nCells_.x()) {
1270	+	m2v.x() = 0;
1271	+	} else if (m2v.x() < 0) {
1272	+	m2v.x() = nCells_.x() - 1;
1273	+	}
1274	+
1275	+	if (m2v.y() >= nCells_.y()) {
1276	+	m2v.y() = 0;
1277	+	} else if (m2v.y() < 0) {
1278	+	m2v.y() = nCells_.y() - 1;
1279	+	}
1280	+
1281	+	if (m2v.z() >= nCells_.z()) {
1282	+	m2v.z() = 0;
1283	+	} else if (m2v.z() < 0) {
1284	+	m2v.z() = nCells_.z() - 1;
1285	+	}
1286	+
1287	+	int m2 = Vlinear (m2v, nCells_);
1288	+
1289	+	#ifdef IS_MPI
1290	+	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1291	+	j1 != cellListRow_[m1].end(); ++j1) {
1292	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1293	+	j2 != cellListCol_[m2].end(); ++j2) {
1294	+
1295	+	// In parallel, we need to visit *all* pairs of row
1296	+	// & column indicies and will divide labor in the
1297	+	// force evaluation later.
1298	+	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1299	+	snap_->wrapVector(dr);
1300	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1301	+	if (dr.lengthSquare() < cuts.third) {
1302	+	neighborList.push_back(make_pair((*j1), (*j2)));
1303	+	}
1304	+	}
1305	+	}
1306	+	#else
1307	+	for (vector<int>::iterator j1 = cellList_[m1].begin();
1308	+	j1 != cellList_[m1].end(); ++j1) {
1309	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1310	+	j2 != cellList_[m2].end(); ++j2) {
1311	+
1312	+	// Always do this if we're in different cells or if
1313	+	// we're in the same cell and the global index of
1314	+	// the j2 cutoff group is greater than or equal to
1315	+	// the j1 cutoff group.  Note that Rappaport's code
1316	+	// has a "less than" conditional here, but that
1317	+	// deals with atom-by-atom computation.  OpenMD
1318	+	// allows atoms within a single cutoff group to
1319	+	// interact with each other.
1320	+
1321	+
1322	+
1323	+	if (m2 != m1 || (*j2) >= (*j1) ) {
1324	+
1325	+	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1326	+	snap_->wrapVector(dr);
1327	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1328	+	if (dr.lengthSquare() < cuts.third) {
1329	+	neighborList.push_back(make_pair((*j1), (*j2)));
1330	+	}
1331	+	}
1332	+	}
1333	+	}
1334	+	#endif
1335	+	}
1336	+	}
1337	+	}
1338	+	}
1339	+	} else {
1340	+	// branch to do all cutoff group pairs
1341	+	#ifdef IS_MPI
1342	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1343	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1344	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1345	+	snap_->wrapVector(dr);
1346	+	cuts = getGroupCutoffs( j1, j2 );
1347	+	if (dr.lengthSquare() < cuts.third) {
1348	+	neighborList.push_back(make_pair(j1, j2));
1349	+	}
1350	+	}
1351	+	}
1352	+	#else
1353	+	// include all groups here.
1354	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1355	+	// include self group interactions j2 == j1
1356	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1357	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1358	+	snap_->wrapVector(dr);
1359	+	cuts = getGroupCutoffs( j1, j2 );
1360	+	if (dr.lengthSquare() < cuts.third) {
1361	+	neighborList.push_back(make_pair(j1, j2));
1362	+	}
1363	+	}
1364	+	}
1365	+	#endif
1366	+	}
1367	+
1368	+	// save the local cutoff group positions for the check that is
1369	+	// done on each loop:
1370	+	saved_CG_positions_.clear();
1371	+	for (int i = 0; i < nGroups_; i++)
1372	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1373	+
1374	+	return neighborList;
1375	+	}
1376		} //end namespace OpenMD

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