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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1567 by gezelter, Tue May 24 21:24:45 2011 UTC vs.
Revision 1593 by gezelter, Fri Jul 15 21:35:14 2011 UTC

#	Line 42 | Line 42
42		#include "math/SquareMatrix3.hpp"
43		#include "nonbonded/NonBondedInteraction.hpp"
44		#include "brains/SnapshotManager.hpp"
45	+	#include "brains/PairList.hpp"
46
47		using namespace std;
48		namespace OpenMD {
49
50	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
51	+
52	+	// In a parallel computation, row and colum scans must visit all
53	+	// surrounding cells (not just the 14 upper triangular blocks that
54	+	// are used when the processor can see all pairs)
55	+	#ifdef IS_MPI
56	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
57	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
58	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
59	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
60	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
62	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
63	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
64	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
66	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
68	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
69	+	#endif
70	+	}
71	+
72	+
73		/**
74		* distributeInitialData is essentially a copy of the older fortran
75		* SimulationSetup
76		*/
53	–
77		void ForceMatrixDecomposition::distributeInitialData() {
78		snap_ = sman_->getCurrentSnapshot();
79		storageLayout_ = sman_->getStorageLayout();
80	+	ff_ = info_->getForceField();
81		nLocal_ = snap_->getNumberOfAtoms();
82	<	nGroups_ = snap_->getNumberOfCutoffGroups();
82	>
83	>	nGroups_ = info_->getNLocalCutoffGroups();
84	>	// gather the information for atomtype IDs (atids):
85	>	idents = info_->getIdentArray();
86	>	AtomLocalToGlobal = info_->getGlobalAtomIndices();
87	>	cgLocalToGlobal = info_->getGlobalGroupIndices();
88	>	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
89
90	+	massFactors = info_->getMassFactors();
91	+
92	+	PairList* excludes = info_->getExcludedInteractions();
93	+	PairList* oneTwo = info_->getOneTwoInteractions();
94	+	PairList* oneThree = info_->getOneThreeInteractions();
95	+	PairList* oneFour = info_->getOneFourInteractions();
96	+
97		#ifdef IS_MPI
98
99	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
100	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
64	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
65	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
99	>	MPI::Intracomm row = rowComm.getComm();
100	>	MPI::Intracomm col = colComm.getComm();
101
102	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
103	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
104	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
105	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
102	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
103	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
104	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
105	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
106	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
107
108	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
109	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
110	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
111	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
108	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
109	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
110	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
111	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
112	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
113
114	<	nAtomsInRow_ = AtomCommIntRow->getSize();
115	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
116	<	nGroupsInRow_ = cgCommIntRow->getSize();
117	<	nGroupsInCol_ = cgCommIntColumn->getSize();
114	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
115	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
116	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
117	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
118
119	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
120	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
121	+	nGroupsInRow_ = cgPlanIntRow->getSize();
122	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
123	+
124		// Modify the data storage objects with the correct layouts and sizes:
125		atomRowData.resize(nAtomsInRow_);
126		atomRowData.setStorageLayout(storageLayout_);
#	Line 88 | Line 130 | namespace OpenMD {
130		cgRowData.setStorageLayout(DataStorage::dslPosition);
131		cgColData.resize(nGroupsInCol_);
132		cgColData.setStorageLayout(DataStorage::dslPosition);
133	+
134	+	identsRow.resize(nAtomsInRow_);
135	+	identsCol.resize(nAtomsInCol_);
136
137	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
138	<	vector<RealType> (nAtomsInRow_, 0.0));
139	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
140	<	vector<RealType> (nAtomsInCol_, 0.0));
137	>	AtomPlanIntRow->gather(idents, identsRow);
138	>	AtomPlanIntColumn->gather(idents, identsCol);
139	>
140	>	// allocate memory for the parallel objects
141	>	atypesRow.resize(nAtomsInRow_);
142	>	atypesCol.resize(nAtomsInCol_);
143
144	+	for (int i = 0; i < nAtomsInRow_; i++)
145	+	atypesRow[i] = ff_->getAtomType(identsRow[i]);
146	+	for (int i = 0; i < nAtomsInCol_; i++)
147	+	atypesCol[i] = ff_->getAtomType(identsCol[i]);
148
149	<	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
149	>	pot_row.resize(nAtomsInRow_);
150	>	pot_col.resize(nAtomsInCol_);
151	>
152	>	AtomRowToGlobal.resize(nAtomsInRow_);
153	>	AtomColToGlobal.resize(nAtomsInCol_);
154	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156	>
157	>	cerr << "Atoms in Local:\n";
158	>	for (int i = 0; i < AtomLocalToGlobal.size(); i++) {
159	>	cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
160	>	}
161	>	cerr << "Atoms in Row:\n";
162	>	for (int i = 0; i < AtomRowToGlobal.size(); i++) {
163	>	cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
164	>	}
165	>	cerr << "Atoms in Col:\n";
166	>	for (int i = 0; i < AtomColToGlobal.size(); i++) {
167	>	cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
168	>	}
169	>
170	>	cgRowToGlobal.resize(nGroupsInRow_);
171	>	cgColToGlobal.resize(nGroupsInCol_);
172	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
173	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
174	>
175	>	cerr << "Gruops in Local:\n";
176	>	for (int i = 0; i < cgLocalToGlobal.size(); i++) {
177	>	cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
178	>	}
179	>	cerr << "Groups in Row:\n";
180	>	for (int i = 0; i < cgRowToGlobal.size(); i++) {
181	>	cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
182	>	}
183	>	cerr << "Groups in Col:\n";
184	>	for (int i = 0; i < cgColToGlobal.size(); i++) {
185	>	cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
186	>	}
187	>
188	>
189	>	massFactorsRow.resize(nAtomsInRow_);
190	>	massFactorsCol.resize(nAtomsInCol_);
191	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
192	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
193	>
194	>	groupListRow_.clear();
195	>	groupListRow_.resize(nGroupsInRow_);
196	>	for (int i = 0; i < nGroupsInRow_; i++) {
197	>	int gid = cgRowToGlobal[i];
198	>	for (int j = 0; j < nAtomsInRow_; j++) {
199	>	int aid = AtomRowToGlobal[j];
200	>	if (globalGroupMembership[aid] == gid)
201	>	groupListRow_[i].push_back(j);
202	>	}
203	>	}
204	>
205	>	groupListCol_.clear();
206	>	groupListCol_.resize(nGroupsInCol_);
207	>	for (int i = 0; i < nGroupsInCol_; i++) {
208	>	int gid = cgColToGlobal[i];
209	>	for (int j = 0; j < nAtomsInCol_; j++) {
210	>	int aid = AtomColToGlobal[j];
211	>	if (globalGroupMembership[aid] == gid)
212	>	groupListCol_[i].push_back(j);
213	>	}
214	>	}
215	>
216	>	excludesForAtom.clear();
217	>	excludesForAtom.resize(nAtomsInRow_);
218	>	toposForAtom.clear();
219	>	toposForAtom.resize(nAtomsInRow_);
220	>	topoDist.clear();
221	>	topoDist.resize(nAtomsInRow_);
222	>	for (int i = 0; i < nAtomsInRow_; i++) {
223	>	int iglob = AtomRowToGlobal[i];
224	>
225	>	for (int j = 0; j < nAtomsInCol_; j++) {
226	>	int jglob = AtomColToGlobal[j];
227	>
228	>	if (excludes->hasPair(iglob, jglob))
229	>	excludesForAtom[i].push_back(j);
230	>
231	>	if (oneTwo->hasPair(iglob, jglob)) {
232	>	toposForAtom[i].push_back(j);
233	>	topoDist[i].push_back(1);
234	>	} else {
235	>	if (oneThree->hasPair(iglob, jglob)) {
236	>	toposForAtom[i].push_back(j);
237	>	topoDist[i].push_back(2);
238	>	} else {
239	>	if (oneFour->hasPair(iglob, jglob)) {
240	>	toposForAtom[i].push_back(j);
241	>	topoDist[i].push_back(3);
242	>	}
243	>	}
244	>	}
245	>	}
246	>	}
247	>
248	>	#endif
249	>
250	>	// allocate memory for the parallel objects
251	>	atypesLocal.resize(nLocal_);
252	>
253	>	for (int i = 0; i < nLocal_; i++)
254	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
255	>
256	>	groupList_.clear();
257	>	groupList_.resize(nGroups_);
258	>	for (int i = 0; i < nGroups_; i++) {
259	>	int gid = cgLocalToGlobal[i];
260	>	for (int j = 0; j < nLocal_; j++) {
261	>	int aid = AtomLocalToGlobal[j];
262	>	if (globalGroupMembership[aid] == gid) {
263	>	groupList_[i].push_back(j);
264	>	}
265	>	}
266	>	}
267	>
268	>	excludesForAtom.clear();
269	>	excludesForAtom.resize(nLocal_);
270	>	toposForAtom.clear();
271	>	toposForAtom.resize(nLocal_);
272	>	topoDist.clear();
273	>	topoDist.resize(nLocal_);
274	>
275	>	for (int i = 0; i < nLocal_; i++) {
276	>	int iglob = AtomLocalToGlobal[i];
277	>
278	>	for (int j = 0; j < nLocal_; j++) {
279	>	int jglob = AtomLocalToGlobal[j];
280	>
281	>	if (excludes->hasPair(iglob, jglob))
282	>	excludesForAtom[i].push_back(j);
283	>
284	>	if (oneTwo->hasPair(iglob, jglob)) {
285	>	toposForAtom[i].push_back(j);
286	>	topoDist[i].push_back(1);
287	>	} else {
288	>	if (oneThree->hasPair(iglob, jglob)) {
289	>	toposForAtom[i].push_back(j);
290	>	topoDist[i].push_back(2);
291	>	} else {
292	>	if (oneFour->hasPair(iglob, jglob)) {
293	>	toposForAtom[i].push_back(j);
294	>	topoDist[i].push_back(3);
295	>	}
296	>	}
297	>	}
298	>	}
299	>	}
300
301	<	// gather the information for atomtype IDs (atids):
302	<	vector<int> identsLocal = info_->getIdentArray();
303	<	identsRow.reserve(nAtomsInRow_);
304	<	identsCol.reserve(nAtomsInCol_);
301	>	createGtypeCutoffMap();
302	>
303	>	}
304	>
305	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
306
307	<	AtomCommIntRow->gather(identsLocal, identsRow);
308	<	AtomCommIntColumn->gather(identsLocal, identsCol);
307	>	RealType tol = 1e-6;
308	>	largestRcut_ = 0.0;
309	>	RealType rc;
310	>	int atid;
311	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
312
313	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
314	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
315	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
313	>	map<int, RealType> atypeCutoff;
314	>
315	>	for (set<AtomType*>::iterator at = atypes.begin();
316	>	at != atypes.end(); ++at){
317	>	atid = (*at)->getIdent();
318	>	if (userChoseCutoff_)
319	>	atypeCutoff[atid] = userCutoff_;
320	>	else
321	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
322	>	}
323
324	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
325	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
326	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
324	>	vector<RealType> gTypeCutoffs;
325	>	// first we do a single loop over the cutoff groups to find the
326	>	// largest cutoff for any atypes present in this group.
327	>	#ifdef IS_MPI
328	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
329	>	groupRowToGtype.resize(nGroupsInRow_);
330	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
331	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
332	>	for (vector<int>::iterator ia = atomListRow.begin();
333	>	ia != atomListRow.end(); ++ia) {
334	>	int atom1 = (*ia);
335	>	atid = identsRow[atom1];
336	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
337	>	groupCutoffRow[cg1] = atypeCutoff[atid];
338	>	}
339	>	}
340
341	<	// still need:
342	<	// topoDist
343	<	// exclude
341	>	bool gTypeFound = false;
342	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
343	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
344	>	groupRowToGtype[cg1] = gt;
345	>	gTypeFound = true;
346	>	}
347	>	}
348	>	if (!gTypeFound) {
349	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
350	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
351	>	}
352	>
353	>	}
354	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
355	>	groupColToGtype.resize(nGroupsInCol_);
356	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
357	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
358	>	for (vector<int>::iterator jb = atomListCol.begin();
359	>	jb != atomListCol.end(); ++jb) {
360	>	int atom2 = (*jb);
361	>	atid = identsCol[atom2];
362	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
363	>	groupCutoffCol[cg2] = atypeCutoff[atid];
364	>	}
365	>	}
366	>	bool gTypeFound = false;
367	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
368	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
369	>	groupColToGtype[cg2] = gt;
370	>	gTypeFound = true;
371	>	}
372	>	}
373	>	if (!gTypeFound) {
374	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
375	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
376	>	}
377	>	}
378	>	#else
379	>
380	>	vector<RealType> groupCutoff(nGroups_, 0.0);
381	>	groupToGtype.resize(nGroups_);
382	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
383	>	groupCutoff[cg1] = 0.0;
384	>	vector<int> atomList = getAtomsInGroupRow(cg1);
385	>	for (vector<int>::iterator ia = atomList.begin();
386	>	ia != atomList.end(); ++ia) {
387	>	int atom1 = (*ia);
388	>	atid = idents[atom1];
389	>	if (atypeCutoff[atid] > groupCutoff[cg1])
390	>	groupCutoff[cg1] = atypeCutoff[atid];
391	>	}
392	>
393	>	bool gTypeFound = false;
394	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
395	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
396	>	groupToGtype[cg1] = gt;
397	>	gTypeFound = true;
398	>	}
399	>	}
400	>	if (!gTypeFound) {
401	>	gTypeCutoffs.push_back( groupCutoff[cg1] );
402	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
403	>	}
404	>	}
405		#endif
406	+
407	+	// Now we find the maximum group cutoff value present in the simulation
408	+
409	+	RealType groupMax = *max_element(gTypeCutoffs.begin(),
410	+	gTypeCutoffs.end());
411	+
412	+	#ifdef IS_MPI
413	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
414	+	MPI::MAX);
415	+	#endif
416	+
417	+	RealType tradRcut = groupMax;
418	+
419	+	for (int i = 0; i < gTypeCutoffs.size();  i++) {
420	+	for (int j = 0; j < gTypeCutoffs.size();  j++) {
421	+	RealType thisRcut;
422	+	switch(cutoffPolicy_) {
423	+	case TRADITIONAL:
424	+	thisRcut = tradRcut;
425	+	break;
426	+	case MIX:
427	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
428	+	break;
429	+	case MAX:
430	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
431	+	break;
432	+	default:
433	+	sprintf(painCave.errMsg,
434	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
435	+	"hit an unknown cutoff policy!\n");
436	+	painCave.severity = OPENMD_ERROR;
437	+	painCave.isFatal = 1;
438	+	simError();
439	+	break;
440	+	}
441	+
442	+	pair<int,int> key = make_pair(i,j);
443	+	gTypeCutoffMap[key].first = thisRcut;
444	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
445	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
446	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
447	+	// sanity check
448	+
449	+	if (userChoseCutoff_) {
450	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
451	+	sprintf(painCave.errMsg,
452	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
453	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
454	+	painCave.severity = OPENMD_ERROR;
455	+	painCave.isFatal = 1;
456	+	simError();
457	+	}
458	+	}
459	+	}
460	+	}
461		}
462	+
463	+
464	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
465	+	int i, j;
466	+	#ifdef IS_MPI
467	+	i = groupRowToGtype[cg1];
468	+	j = groupColToGtype[cg2];
469	+	#else
470	+	i = groupToGtype[cg1];
471	+	j = groupToGtype[cg2];
472	+	#endif
473	+	return gTypeCutoffMap[make_pair(i,j)];
474	+	}
475	+
476	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
477	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
478	+	if (toposForAtom[atom1][j] == atom2)
479	+	return topoDist[atom1][j];
480	+	}
481	+	return 0;
482	+	}
483	+
484	+	void ForceMatrixDecomposition::zeroWorkArrays() {
485	+	pairwisePot = 0.0;
486	+	embeddingPot = 0.0;
487	+
488	+	#ifdef IS_MPI
489	+	if (storageLayout_ & DataStorage::dslForce) {
490	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
491	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
492	+	}
493	+
494	+	if (storageLayout_ & DataStorage::dslTorque) {
495	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
496	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
497	+	}
498
499	+	fill(pot_row.begin(), pot_row.end(),
500	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
501
502	+	fill(pot_col.begin(), pot_col.end(),
503	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
504
505	+	if (storageLayout_ & DataStorage::dslParticlePot) {
506	+	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
507	+	0.0);
508	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
509	+	0.0);
510	+	}
511	+
512	+	if (storageLayout_ & DataStorage::dslDensity) {
513	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
514	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
515	+	}
516	+
517	+	if (storageLayout_ & DataStorage::dslFunctional) {
518	+	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
519	+	0.0);
520	+	fill(atomColData.functional.begin(), atomColData.functional.end(),
521	+	0.0);
522	+	}
523	+
524	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
525	+	fill(atomRowData.functionalDerivative.begin(),
526	+	atomRowData.functionalDerivative.end(), 0.0);
527	+	fill(atomColData.functionalDerivative.begin(),
528	+	atomColData.functionalDerivative.end(), 0.0);
529	+	}
530	+
531	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
532	+	fill(atomRowData.skippedCharge.begin(),
533	+	atomRowData.skippedCharge.end(), 0.0);
534	+	fill(atomColData.skippedCharge.begin(),
535	+	atomColData.skippedCharge.end(), 0.0);
536	+	}
537	+
538	+	#endif
539	+	// even in parallel, we need to zero out the local arrays:
540	+
541	+	if (storageLayout_ & DataStorage::dslParticlePot) {
542	+	fill(snap_->atomData.particlePot.begin(),
543	+	snap_->atomData.particlePot.end(), 0.0);
544	+	}
545	+
546	+	if (storageLayout_ & DataStorage::dslDensity) {
547	+	fill(snap_->atomData.density.begin(),
548	+	snap_->atomData.density.end(), 0.0);
549	+	}
550	+	if (storageLayout_ & DataStorage::dslFunctional) {
551	+	fill(snap_->atomData.functional.begin(),
552	+	snap_->atomData.functional.end(), 0.0);
553	+	}
554	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
555	+	fill(snap_->atomData.functionalDerivative.begin(),
556	+	snap_->atomData.functionalDerivative.end(), 0.0);
557	+	}
558	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
559	+	fill(snap_->atomData.skippedCharge.begin(),
560	+	snap_->atomData.skippedCharge.end(), 0.0);
561	+	}
562	+
563	+	}
564	+
565	+
566		void ForceMatrixDecomposition::distributeData()  {
567		snap_ = sman_->getCurrentSnapshot();
568		storageLayout_ = sman_->getStorageLayout();
569		#ifdef IS_MPI
570
571		// gather up the atomic positions
572	<	AtomCommVectorRow->gather(snap_->atomData.position,
572	>	AtomPlanVectorRow->gather(snap_->atomData.position,
573		atomRowData.position);
574	<	AtomCommVectorColumn->gather(snap_->atomData.position,
574	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
575		atomColData.position);
576
577		// gather up the cutoff group positions
578	<	cgCommVectorRow->gather(snap_->cgData.position,
578	>
579	>	cerr  << "before gather\n";
580	>	for (int i = 0; i < snap_->cgData.position.size(); i++) {
581	>	cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
582	>	}
583	>
584	>	cgPlanVectorRow->gather(snap_->cgData.position,
585		cgRowData.position);
586	<	cgCommVectorColumn->gather(snap_->cgData.position,
586	>
587	>	cerr  << "after gather\n";
588	>	for (int i = 0; i < cgRowData.position.size(); i++) {
589	>	cerr << "cgRpos = " << cgRowData.position[i] << "\n";
590	>	}
591	>
592	>	cgPlanVectorColumn->gather(snap_->cgData.position,
593		cgColData.position);
594	+	for (int i = 0; i < cgColData.position.size(); i++) {
595	+	cerr << "cgCpos = " << cgColData.position[i] << "\n";
596	+	}
597	+
598
599		// if needed, gather the atomic rotation matrices
600		if (storageLayout_ & DataStorage::dslAmat) {
601	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
601	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
602		atomRowData.aMat);
603	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
603	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
604		atomColData.aMat);
605		}
606
607		// if needed, gather the atomic eletrostatic frames
608		if (storageLayout_ & DataStorage::dslElectroFrame) {
609	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
609	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
610		atomRowData.electroFrame);
611	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
611	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
612		atomColData.electroFrame);
613		}
614	+
615		#endif
616		}
617
618	+	/* collects information obtained during the pre-pair loop onto local
619	+	* data structures.
620	+	*/
621		void ForceMatrixDecomposition::collectIntermediateData() {
622		snap_ = sman_->getCurrentSnapshot();
623		storageLayout_ = sman_->getStorageLayout();
#	Line 163 | Line 625 | namespace OpenMD {
625
626		if (storageLayout_ & DataStorage::dslDensity) {
627
628	<	AtomCommRealRow->scatter(atomRowData.density,
628	>	AtomPlanRealRow->scatter(atomRowData.density,
629		snap_->atomData.density);
630
631		int n = snap_->atomData.density.size();
632	<	std::vector<RealType> rho_tmp(n, 0.0);
633	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
632	>	vector<RealType> rho_tmp(n, 0.0);
633	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
634		for (int i = 0; i < n; i++)
635		snap_->atomData.density[i] += rho_tmp[i];
636		}
637		#endif
638		}
639	<
639	>
640	>	/*
641	>	* redistributes information obtained during the pre-pair loop out to
642	>	* row and column-indexed data structures
643	>	*/
644		void ForceMatrixDecomposition::distributeIntermediateData() {
645		snap_ = sman_->getCurrentSnapshot();
646		storageLayout_ = sman_->getStorageLayout();
647		#ifdef IS_MPI
648		if (storageLayout_ & DataStorage::dslFunctional) {
649	<	AtomCommRealRow->gather(snap_->atomData.functional,
649	>	AtomPlanRealRow->gather(snap_->atomData.functional,
650		atomRowData.functional);
651	<	AtomCommRealColumn->gather(snap_->atomData.functional,
651	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
652		atomColData.functional);
653		}
654
655		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
656	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
656	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
657		atomRowData.functionalDerivative);
658	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
658	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
659		atomColData.functionalDerivative);
660		}
661		#endif
#	Line 203 | Line 669 | namespace OpenMD {
669		int n = snap_->atomData.force.size();
670		vector<Vector3d> frc_tmp(n, V3Zero);
671
672	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
672	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
673		for (int i = 0; i < n; i++) {
674		snap_->atomData.force[i] += frc_tmp[i];
675		frc_tmp[i] = 0.0;
676		}
677
678	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
679	<	for (int i = 0; i < n; i++)
678	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
679	>	for (int i = 0; i < n; i++) {
680		snap_->atomData.force[i] += frc_tmp[i];
681	<
682	<
681	>	}
682	>
683		if (storageLayout_ & DataStorage::dslTorque) {
684
685	<	int nt = snap_->atomData.force.size();
685	>	int nt = snap_->atomData.torque.size();
686		vector<Vector3d> trq_tmp(nt, V3Zero);
687
688	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
689	<	for (int i = 0; i < n; i++) {
688	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
689	>	for (int i = 0; i < nt; i++) {
690		snap_->atomData.torque[i] += trq_tmp[i];
691		trq_tmp[i] = 0.0;
692		}
693
694	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
695	<	for (int i = 0; i < n; i++)
694	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
695	>	for (int i = 0; i < nt; i++)
696		snap_->atomData.torque[i] += trq_tmp[i];
697		}
698	+
699	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
700	+
701	+	int ns = snap_->atomData.skippedCharge.size();
702	+	vector<RealType> skch_tmp(ns, 0.0);
703	+
704	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
705	+	for (int i = 0; i < ns; i++) {
706	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
707	+	skch_tmp[i] = 0.0;
708	+	}
709	+
710	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
711	+	for (int i = 0; i < ns; i++)
712	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
713	+	}
714
715		nLocal_ = snap_->getNumberOfAtoms();
716
717	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
718	<	vector<RealType> (nLocal_, 0.0));
717	>	vector<potVec> pot_temp(nLocal_,
718	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
719	>
720	>	// scatter/gather pot_row into the members of my column
721	>
722	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
723	>
724	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
725	>	pairwisePot += pot_temp[ii];
726
727	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
728	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
729	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
730	<	pot_local[i] += pot_temp[i][ii];
731	<	}
732	<	}
727	>	fill(pot_temp.begin(), pot_temp.end(),
728	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
729	>
730	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
731	>
732	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
733	>	pairwisePot += pot_temp[ii];
734		#endif
735	+
736	+	cerr << "pairwisePot = " <<  pairwisePot << "\n";
737		}
738
739	+	int ForceMatrixDecomposition::getNAtomsInRow() {
740	+	#ifdef IS_MPI
741	+	return nAtomsInRow_;
742	+	#else
743	+	return nLocal_;
744	+	#endif
745	+	}
746	+
747	+	/**
748	+	* returns the list of atoms belonging to this group.
749	+	*/
750	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
751	+	#ifdef IS_MPI
752	+	return groupListRow_[cg1];
753	+	#else
754	+	return groupList_[cg1];
755	+	#endif
756	+	}
757	+
758	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
759	+	#ifdef IS_MPI
760	+	return groupListCol_[cg2];
761	+	#else
762	+	return groupList_[cg2];
763	+	#endif
764	+	}
765
766		Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
767		Vector3d d;
768
769		#ifdef IS_MPI
770		d = cgColData.position[cg2] - cgRowData.position[cg1];
771	+	cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
772	+	cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
773		#else
774		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
775	+	cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
776	+	cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
777		#endif
778
779		snap_->wrapVector(d);
#	Line 285 | Line 807 | namespace OpenMD {
807		snap_->wrapVector(d);
808		return d;
809		}
810	+
811	+	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
812	+	#ifdef IS_MPI
813	+	return massFactorsRow[atom1];
814	+	#else
815	+	return massFactors[atom1];
816	+	#endif
817	+	}
818	+
819	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
820	+	#ifdef IS_MPI
821	+	return massFactorsCol[atom2];
822	+	#else
823	+	return massFactors[atom2];
824	+	#endif
825	+
826	+	}
827
828		Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
829		Vector3d d;
#	Line 299 | Line 838 | namespace OpenMD {
838		return d;
839		}
840
841	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
842	+	return excludesForAtom[atom1];
843	+	}
844	+
845	+	/**
846	+	* We need to exclude some overcounted interactions that result from
847	+	* the parallel decomposition.
848	+	*/
849	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
850	+	int unique_id_1, unique_id_2;
851	+
852	+
853	+	cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
854	+	#ifdef IS_MPI
855	+	// in MPI, we have to look up the unique IDs for each atom
856	+	unique_id_1 = AtomRowToGlobal[atom1];
857	+	unique_id_2 = AtomColToGlobal[atom2];
858	+
859	+	cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
860	+	// this situation should only arise in MPI simulations
861	+	if (unique_id_1 == unique_id_2) return true;
862	+
863	+	// this prevents us from doing the pair on multiple processors
864	+	if (unique_id_1 < unique_id_2) {
865	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
866	+	} else {
867	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
868	+	}
869	+	#endif
870	+	return false;
871	+	}
872	+
873	+	/**
874	+	* We need to handle the interactions for atoms who are involved in
875	+	* the same rigid body as well as some short range interactions
876	+	* (bonds, bends, torsions) differently from other interactions.
877	+	* We'll still visit the pairwise routines, but with a flag that
878	+	* tells those routines to exclude the pair from direct long range
879	+	* interactions.  Some indirect interactions (notably reaction
880	+	* field) must still be handled for these pairs.
881	+	*/
882	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
883	+	int unique_id_2;
884	+	#ifdef IS_MPI
885	+	// in MPI, we have to look up the unique IDs for the row atom.
886	+	unique_id_2 = AtomColToGlobal[atom2];
887	+	#else
888	+	// in the normal loop, the atom numbers are unique
889	+	unique_id_2 = atom2;
890	+	#endif
891	+
892	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
893	+	i != excludesForAtom[atom1].end(); ++i) {
894	+	if ( (*i) == unique_id_2 ) return true;
895	+	}
896	+
897	+	return false;
898	+	}
899	+
900	+
901		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
902		#ifdef IS_MPI
903		atomRowData.force[atom1] += fg;
#	Line 316 | Line 915 | namespace OpenMD {
915		}
916
917		// filling interaction blocks with pointers
918	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
919	<	InteractionData idat;
918	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
919	>	int atom1, int atom2) {
920
921	+	idat.excluded = excludeAtomPair(atom1, atom2);
922	+
923		#ifdef IS_MPI
924	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
925	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
926	+	//                         ff_->getAtomType(identsCol[atom2]) );
927	+
928		if (storageLayout_ & DataStorage::dslAmat) {
929		idat.A1 = &(atomRowData.aMat[atom1]);
930		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 340 | Line 945 | namespace OpenMD {
945		idat.rho2 = &(atomColData.density[atom2]);
946		}
947
948	+	if (storageLayout_ & DataStorage::dslFunctional) {
949	+	idat.frho1 = &(atomRowData.functional[atom1]);
950	+	idat.frho2 = &(atomColData.functional[atom2]);
951	+	}
952	+
953		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
954		idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
955		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
956		}
957	+
958	+	if (storageLayout_ & DataStorage::dslParticlePot) {
959	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
960	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
961	+	}
962	+
963	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
964	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
965	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
966	+	}
967	+
968		#else
969	+
970	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
971	+	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
972	+	//                         ff_->getAtomType(idents[atom2]) );
973	+
974		if (storageLayout_ & DataStorage::dslAmat) {
975		idat.A1 = &(snap_->atomData.aMat[atom1]);
976		idat.A2 = &(snap_->atomData.aMat[atom2]);
#	Line 360 | Line 986 | namespace OpenMD {
986		idat.t2 = &(snap_->atomData.torque[atom2]);
987		}
988
989	<	if (storageLayout_ & DataStorage::dslDensity) {
989	>	if (storageLayout_ & DataStorage::dslDensity) {
990		idat.rho1 = &(snap_->atomData.density[atom1]);
991		idat.rho2 = &(snap_->atomData.density[atom2]);
992		}
993
994	+	if (storageLayout_ & DataStorage::dslFunctional) {
995	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
996	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
997	+	}
998	+
999		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1000		idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1001		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1002		}
1003	+
1004	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1005	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1006	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1007	+	}
1008	+
1009	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1010	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1011	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1012	+	}
1013		#endif
373	–	return idat;
1014		}
1015
1016	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1017	<
378	<	InteractionData idat;
1016	>
1017	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1018		#ifdef IS_MPI
1019	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1020	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1021	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1022	<	}
1023	<	if (storageLayout_ & DataStorage::dslTorque) {
385	<	idat.t1 = &(atomRowData.torque[atom1]);
386	<	idat.t2 = &(atomColData.torque[atom2]);
387	<	}
388	<	if (storageLayout_ & DataStorage::dslForce) {
389	<	idat.t1 = &(atomRowData.force[atom1]);
390	<	idat.t2 = &(atomColData.force[atom2]);
391	<	}
1019	>	pot_row[atom1] += 0.5 *  *(idat.pot);
1020	>	pot_col[atom2] += 0.5 *  *(idat.pot);
1021	>
1022	>	atomRowData.force[atom1] += *(idat.f1);
1023	>	atomColData.force[atom2] -= *(idat.f1);
1024		#else
1025	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1026	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1027	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1028	<	}
397	<	if (storageLayout_ & DataStorage::dslTorque) {
398	<	idat.t1 = &(snap_->atomData.torque[atom1]);
399	<	idat.t2 = &(snap_->atomData.torque[atom2]);
400	<	}
401	<	if (storageLayout_ & DataStorage::dslForce) {
402	<	idat.t1 = &(snap_->atomData.force[atom1]);
403	<	idat.t2 = &(snap_->atomData.force[atom2]);
404	<	}
1025	>	pairwisePot += *(idat.pot);
1026	>
1027	>	snap_->atomData.force[atom1] += *(idat.f1);
1028	>	snap_->atomData.force[atom2] -= *(idat.f1);
1029		#endif
1030
1031		}
1032
409	–	SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
410	–	SelfData sdat;
411	–	// Still Missing atype, skippedCharge, potVec pot,
412	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
413	–	sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
414	–	}
415	–
416	–	if (storageLayout_ & DataStorage::dslTorque) {
417	–	sdat.t = &(snap_->atomData.torque[atom1]);
418	–	}
419	–
420	–	if (storageLayout_ & DataStorage::dslDensity) {
421	–	sdat.rho = &(snap_->atomData.density[atom1]);
422	–	}
423	–
424	–	if (storageLayout_ & DataStorage::dslFunctional) {
425	–	sdat.frho = &(snap_->atomData.functional[atom1]);
426	–	}
427	–
428	–	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
429	–	sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
430	–	}
431	–
432	–	return sdat;
433	–	}
434	–
435	–
436	–
1033		/*
1034		* buildNeighborList
1035		*
#	Line 443 | Line 1039 | namespace OpenMD {
1039		vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1040
1041		vector<pair<int, int> > neighborList;
1042	+	groupCutoffs cuts;
1043	+	bool doAllPairs = false;
1044	+
1045		#ifdef IS_MPI
1046	<	CellListRow.clear();
1047	<	CellListCol.clear();
1046	>	cellListRow_.clear();
1047	>	cellListCol_.clear();
1048		#else
1049	<	CellList.clear();
1049	>	cellList_.clear();
1050		#endif
1051
1052	<	// dangerous to not do error checking.
454	<	RealType skinThickness_ = info_->getSimParams()->getSkinThickness();
455	<	RealType rCut_;
456	<
457	<	RealType rList_ = (rCut_ + skinThickness_);
1052	>	RealType rList_ = (largestRcut_ + skinThickness_);
1053		RealType rl2 = rList_ * rList_;
1054		Snapshot* snap_ = sman_->getCurrentSnapshot();
1055		Mat3x3d Hmat = snap_->getHmat();
1056		Vector3d Hx = Hmat.getColumn(0);
1057		Vector3d Hy = Hmat.getColumn(1);
1058		Vector3d Hz = Hmat.getColumn(2);
464	–	Vector3i nCells;
1059
1060	<	nCells.x() = (int) ( Hx.length() )/ rList_;
1061	<	nCells.y() = (int) ( Hy.length() )/ rList_;
1062	<	nCells.z() = (int) ( Hz.length() )/ rList_;
1060	>	nCells_.x() = (int) ( Hx.length() )/ rList_;
1061	>	nCells_.y() = (int) ( Hy.length() )/ rList_;
1062	>	nCells_.z() = (int) ( Hz.length() )/ rList_;
1063
1064	+	// handle small boxes where the cell offsets can end up repeating cells
1065	+
1066	+	if (nCells_.x() < 3) doAllPairs = true;
1067	+	if (nCells_.y() < 3) doAllPairs = true;
1068	+	if (nCells_.z() < 3) doAllPairs = true;
1069	+
1070		Mat3x3d invHmat = snap_->getInvHmat();
1071		Vector3d rs, scaled, dr;
1072		Vector3i whichCell;
1073		int cellIndex;
1074	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1075
1076		#ifdef IS_MPI
1077	<	for (int i = 0; i < nGroupsInRow_; i++) {
1078	<	rs = cgRowData.position[i];
478	<	// scaled positions relative to the box vectors
479	<	scaled = invHmat * rs;
480	<	// wrap the vector back into the unit box by subtracting integer box
481	<	// numbers
482	<	for (int j = 0; j < 3; j++)
483	<	scaled[j] -= roundMe(scaled[j]);
484	<
485	<	// find xyz-indices of cell that cutoffGroup is in.
486	<	whichCell.x() = nCells.x() * scaled.x();
487	<	whichCell.y() = nCells.y() * scaled.y();
488	<	whichCell.z() = nCells.z() * scaled.z();
489	<
490	<	// find single index of this cell:
491	<	cellIndex = Vlinear(whichCell, nCells);
492	<	// add this cutoff group to the list of groups in this cell;
493	<	CellListRow[cellIndex].push_back(i);
494	<	}
495	<
496	<	for (int i = 0; i < nGroupsInCol_; i++) {
497	<	rs = cgColData.position[i];
498	<	// scaled positions relative to the box vectors
499	<	scaled = invHmat * rs;
500	<	// wrap the vector back into the unit box by subtracting integer box
501	<	// numbers
502	<	for (int j = 0; j < 3; j++)
503	<	scaled[j] -= roundMe(scaled[j]);
504	<
505	<	// find xyz-indices of cell that cutoffGroup is in.
506	<	whichCell.x() = nCells.x() * scaled.x();
507	<	whichCell.y() = nCells.y() * scaled.y();
508	<	whichCell.z() = nCells.z() * scaled.z();
509	<
510	<	// find single index of this cell:
511	<	cellIndex = Vlinear(whichCell, nCells);
512	<	// add this cutoff group to the list of groups in this cell;
513	<	CellListCol[cellIndex].push_back(i);
514	<	}
1077	>	cellListRow_.resize(nCtot);
1078	>	cellListCol_.resize(nCtot);
1079		#else
1080	<	for (int i = 0; i < nGroups_; i++) {
1081	<	rs = snap_->cgData.position[i];
518	<	// scaled positions relative to the box vectors
519	<	scaled = invHmat * rs;
520	<	// wrap the vector back into the unit box by subtracting integer box
521	<	// numbers
522	<	for (int j = 0; j < 3; j++)
523	<	scaled[j] -= roundMe(scaled[j]);
1080	>	cellList_.resize(nCtot);
1081	>	#endif
1082
1083	<	// find xyz-indices of cell that cutoffGroup is in.
1084	<	whichCell.x() = nCells.x() * scaled.x();
527	<	whichCell.y() = nCells.y() * scaled.y();
528	<	whichCell.z() = nCells.z() * scaled.z();
1083	>	if (!doAllPairs) {
1084	>	#ifdef IS_MPI
1085
1086	<	// find single index of this cell:
1087	<	cellIndex = Vlinear(whichCell, nCells);
1088	<	// add this cutoff group to the list of groups in this cell;
1089	<	CellList[cellIndex].push_back(i);
1090	<	}
1086	>	for (int i = 0; i < nGroupsInRow_; i++) {
1087	>	rs = cgRowData.position[i];
1088	>
1089	>	// scaled positions relative to the box vectors
1090	>	scaled = invHmat * rs;
1091	>
1092	>	// wrap the vector back into the unit box by subtracting integer box
1093	>	// numbers
1094	>	for (int j = 0; j < 3; j++) {
1095	>	scaled[j] -= roundMe(scaled[j]);
1096	>	scaled[j] += 0.5;
1097	>	}
1098	>
1099	>	// find xyz-indices of cell that cutoffGroup is in.
1100	>	whichCell.x() = nCells_.x() * scaled.x();
1101	>	whichCell.y() = nCells_.y() * scaled.y();
1102	>	whichCell.z() = nCells_.z() * scaled.z();
1103	>
1104	>	// find single index of this cell:
1105	>	cellIndex = Vlinear(whichCell, nCells_);
1106	>
1107	>	// add this cutoff group to the list of groups in this cell;
1108	>	cellListRow_[cellIndex].push_back(i);
1109	>	}
1110	>	for (int i = 0; i < nGroupsInCol_; i++) {
1111	>	rs = cgColData.position[i];
1112	>
1113	>	// scaled positions relative to the box vectors
1114	>	scaled = invHmat * rs;
1115	>
1116	>	// wrap the vector back into the unit box by subtracting integer box
1117	>	// numbers
1118	>	for (int j = 0; j < 3; j++) {
1119	>	scaled[j] -= roundMe(scaled[j]);
1120	>	scaled[j] += 0.5;
1121	>	}
1122	>
1123	>	// find xyz-indices of cell that cutoffGroup is in.
1124	>	whichCell.x() = nCells_.x() * scaled.x();
1125	>	whichCell.y() = nCells_.y() * scaled.y();
1126	>	whichCell.z() = nCells_.z() * scaled.z();
1127	>
1128	>	// find single index of this cell:
1129	>	cellIndex = Vlinear(whichCell, nCells_);
1130	>
1131	>	// add this cutoff group to the list of groups in this cell;
1132	>	cellListCol_[cellIndex].push_back(i);
1133	>	}
1134	>	#else
1135	>	for (int i = 0; i < nGroups_; i++) {
1136	>	rs = snap_->cgData.position[i];
1137	>
1138	>	// scaled positions relative to the box vectors
1139	>	scaled = invHmat * rs;
1140	>
1141	>	// wrap the vector back into the unit box by subtracting integer box
1142	>	// numbers
1143	>	for (int j = 0; j < 3; j++) {
1144	>	scaled[j] -= roundMe(scaled[j]);
1145	>	scaled[j] += 0.5;
1146	>	}
1147	>
1148	>	// find xyz-indices of cell that cutoffGroup is in.
1149	>	whichCell.x() = nCells_.x() * scaled.x();
1150	>	whichCell.y() = nCells_.y() * scaled.y();
1151	>	whichCell.z() = nCells_.z() * scaled.z();
1152	>
1153	>	// find single index of this cell:
1154	>	cellIndex = Vlinear(whichCell, nCells_);
1155	>
1156	>	// add this cutoff group to the list of groups in this cell;
1157	>	cellList_[cellIndex].push_back(i);
1158	>	}
1159		#endif
1160
1161	<
1162	<
1163	<	for (int m1z = 0; m1z < nCells.z(); m1z++) {
1164	<	for (int m1y = 0; m1y < nCells.y(); m1y++) {
1165	<	for (int m1x = 0; m1x < nCells.x(); m1x++) {
1166	<	Vector3i m1v(m1x, m1y, m1z);
1167	<	int m1 = Vlinear(m1v, nCells);
1168	<	for (int offset = 0; offset < nOffset_; offset++) {
1169	<	Vector3i m2v = m1v + cellOffsets_[offset];
1170	<
1171	<	if (m2v.x() >= nCells.x()) {
1172	<	m2v.x() = 0;
1173	<	} else if (m2v.x() < 0) {
1174	<	m2v.x() = nCells.x() - 1;
1175	<	}
1176	<
1177	<	if (m2v.y() >= nCells.y()) {
1178	<	m2v.y() = 0;
1179	<	} else if (m2v.y() < 0) {
1180	<	m2v.y() = nCells.y() - 1;
1181	<	}
1182	<
1183	<	if (m2v.z() >= nCells.z()) {
1184	<	m2v.z() = 0;
1185	<	} else if (m2v.z() < 0) {
1186	<	m2v.z() = nCells.z() - 1;
1187	<	}
1188	<
1189	<	int m2 = Vlinear (m2v, nCells);
1190	<
1161	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1162	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1163	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1164	>	Vector3i m1v(m1x, m1y, m1z);
1165	>	int m1 = Vlinear(m1v, nCells_);
1166	>
1167	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1168	>	os != cellOffsets_.end(); ++os) {
1169	>
1170	>	Vector3i m2v = m1v + (*os);
1171	>
1172	>	if (m2v.x() >= nCells_.x()) {
1173	>	m2v.x() = 0;
1174	>	} else if (m2v.x() < 0) {
1175	>	m2v.x() = nCells_.x() - 1;
1176	>	}
1177	>
1178	>	if (m2v.y() >= nCells_.y()) {
1179	>	m2v.y() = 0;
1180	>	} else if (m2v.y() < 0) {
1181	>	m2v.y() = nCells_.y() - 1;
1182	>	}
1183	>
1184	>	if (m2v.z() >= nCells_.z()) {
1185	>	m2v.z() = 0;
1186	>	} else if (m2v.z() < 0) {
1187	>	m2v.z() = nCells_.z() - 1;
1188	>	}
1189	>
1190	>	int m2 = Vlinear (m2v, nCells_);
1191	>
1192		#ifdef IS_MPI
1193	<	for (vector<int>::iterator j1 = CellListRow[m1].begin();
1194	<	j1 != CellListRow[m1].end(); ++j1) {
1195	<	for (vector<int>::iterator j2 = CellListCol[m2].begin();
1196	<	j2 != CellListCol[m2].end(); ++j2) {
1197	<
1198	<	// Always do this if we're in different cells or if
1199	<	// we're in the same cell and the global index of the
575	<	// j2 cutoff group is less than the j1 cutoff group
576	<
577	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1193	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1194	>	j1 != cellListRow_[m1].end(); ++j1) {
1195	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1196	>	j2 != cellListCol_[m2].end(); ++j2) {
1197	>
1198	>	// In parallel, we need to visit *all* pairs of row &
1199	>	// column indicies and will truncate later on.
1200		dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1201		snap_->wrapVector(dr);
1202	<	if (dr.lengthSquare() < rl2) {
1202	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1203	>	if (dr.lengthSquare() < cuts.third) {
1204		neighborList.push_back(make_pair((*j1), (*j2)));
1205	<	}
1205	>	}
1206		}
1207		}
585	–	}
1208		#else
1209	<	for (vector<int>::iterator j1 = CellList[m1].begin();
1210	<	j1 != CellList[m1].end(); ++j1) {
1211	<	for (vector<int>::iterator j2 = CellList[m2].begin();
1212	<	j2 != CellList[m2].end(); ++j2) {
1213	<
1214	<	// Always do this if we're in different cells or if
1215	<	// we're in the same cell and the global index of the
1216	<	// j2 cutoff group is less than the j1 cutoff group
1217	<
1218	<	if (m2 != m1 || (*j2) < (*j1)) {
1219	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1220	<	snap_->wrapVector(dr);
1221	<	if (dr.lengthSquare() < rl2) {
1222	<	neighborList.push_back(make_pair((*j1), (*j2)));
1209	>
1210	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1211	>	j1 != cellList_[m1].end(); ++j1) {
1212	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1213	>	j2 != cellList_[m2].end(); ++j2) {
1214	>
1215	>	// Always do this if we're in different cells or if
1216	>	// we're in the same cell and the global index of the
1217	>	// j2 cutoff group is less than the j1 cutoff group
1218	>
1219	>	if (m2 != m1 || (*j2) < (*j1)) {
1220	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1221	>	snap_->wrapVector(dr);
1222	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1223	>	if (dr.lengthSquare() < cuts.third) {
1224	>	neighborList.push_back(make_pair((*j1), (*j2)));
1225	>	}
1226		}
1227		}
1228		}
604	–	}
1229		#endif
1230	+	}
1231		}
1232		}
1233		}
1234	+	} else {
1235	+	// branch to do all cutoff group pairs
1236	+	#ifdef IS_MPI
1237	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1238	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1239	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1240	+	snap_->wrapVector(dr);
1241	+	cuts = getGroupCutoffs( j1, j2 );
1242	+	if (dr.lengthSquare() < cuts.third) {
1243	+	neighborList.push_back(make_pair(j1, j2));
1244	+	}
1245	+	}
1246	+	}
1247	+	#else
1248	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1249	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1250	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1251	+	snap_->wrapVector(dr);
1252	+	cuts = getGroupCutoffs( j1, j2 );
1253	+	if (dr.lengthSquare() < cuts.third) {
1254	+	neighborList.push_back(make_pair(j1, j2));
1255	+	}
1256	+	}
1257	+	}
1258	+	#endif
1259		}
1260	+
1261	+	// save the local cutoff group positions for the check that is
1262	+	// done on each loop:
1263	+	saved_CG_positions_.clear();
1264	+	for (int i = 0; i < nGroups_; i++)
1265	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1266	+
1267		return neighborList;
1268		}
1269		} //end namespace OpenMD

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