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

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1562 by gezelter, Thu May 12 17:00:14 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1896 by gezelter, Tue Jul 2 20:02:31 2013 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
44		#include "nonbonded/NonBondedInteraction.hpp"
45		#include "brains/SnapshotManager.hpp"
46	+	#include "brains/PairList.hpp"
47
48		using namespace std;
49		namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	+
53	+	// 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	+
88	+
89		/**
90		* distributeInitialData is essentially a copy of the older fortran
91		* SimulationSetup
92		*/
53	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96	<	#ifdef IS_MPI
97	<	int nLocal = snap_->getNumberOfAtoms();
98	<	int nGroups = snap_->getNumberOfCutoffGroups();
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	>	massFactors = info_->getMassFactors();
107	>
108	>	PairList* excludes = info_->getExcludedInteractions();
109	>	PairList* oneTwo = info_->getOneTwoInteractions();
110	>	PairList* oneThree = info_->getOneThreeInteractions();
111	>	PairList* oneFour = info_->getOneFourInteractions();
112
113	<	AtomCommIntRow = new Communicator<Row,int>(nLocal);
114	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
115	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
116	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
113	>	if (needVelocities_)
114	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
115	>	DataStorage::dslVelocity);
116	>	else
117	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118	>
119	>	#ifdef IS_MPI
120	>
121	>	MPI::Intracomm row = rowComm.getComm();
122	>	MPI::Intracomm col = colComm.getComm();
123
124	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal);
125	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
126	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
127	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
124	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
125	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
126	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
127	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
128	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
129
130	<	cgCommIntRow = new Communicator<Row,int>(nGroups);
131	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
132	<	cgCommIntColumn = new Communicator<Column,int>(nGroups);
133	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
130	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
131	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
132	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
133	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
134	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
135
136	<	int nAtomsInRow = AtomCommIntRow->getSize();
137	<	int nAtomsInCol = AtomCommIntColumn->getSize();
138	<	int nGroupsInRow = cgCommIntRow->getSize();
139	<	int nGroupsInCol = cgCommIntColumn->getSize();
136	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
137	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
138	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
139	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
140
141	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
142	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
143	+	nGroupsInRow_ = cgPlanIntRow->getSize();
144	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
145	+
146		// Modify the data storage objects with the correct layouts and sizes:
147	<	atomRowData.resize(nAtomsInRow);
147	>	atomRowData.resize(nAtomsInRow_);
148		atomRowData.setStorageLayout(storageLayout_);
149	<	atomColData.resize(nAtomsInCol);
149	>	atomColData.resize(nAtomsInCol_);
150		atomColData.setStorageLayout(storageLayout_);
151	<	cgRowData.resize(nGroupsInRow);
151	>	cgRowData.resize(nGroupsInRow_);
152		cgRowData.setStorageLayout(DataStorage::dslPosition);
153	<	cgColData.resize(nGroupsInCol);
154	<	cgColData.setStorageLayout(DataStorage::dslPosition);
153	>	cgColData.resize(nGroupsInCol_);
154	>	if (needVelocities_)
155	>	// we only need column velocities if we need them.
156	>	cgColData.setStorageLayout(DataStorage::dslPosition |
157	>	DataStorage::dslVelocity);
158	>	else
159	>	cgColData.setStorageLayout(DataStorage::dslPosition);
160	>
161	>	identsRow.resize(nAtomsInRow_);
162	>	identsCol.resize(nAtomsInCol_);
163
164	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
165	<	vector<RealType> (nAtomsInRow, 0.0));
166	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
167	<	vector<RealType> (nAtomsInCol, 0.0));
164	>	AtomPlanIntRow->gather(idents, identsRow);
165	>	AtomPlanIntColumn->gather(idents, identsCol);
166	>
167	>	// allocate memory for the parallel objects
168	>	atypesRow.resize(nAtomsInRow_);
169	>	atypesCol.resize(nAtomsInCol_);
170
171	+	for (int i = 0; i < nAtomsInRow_; i++)
172	+	atypesRow[i] = ff_->getAtomType(identsRow[i]);
173	+	for (int i = 0; i < nAtomsInCol_; i++)
174	+	atypesCol[i] = ff_->getAtomType(identsCol[i]);
175
176	<	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
177	<
99	<	// gather the information for atomtype IDs (atids):
100	<	vector<int> identsLocal = info_->getIdentArray();
101	<	identsRow.reserve(nAtomsInRow);
102	<	identsCol.reserve(nAtomsInCol);
103	<
104	<	AtomCommIntRow->gather(identsLocal, identsRow);
105	<	AtomCommIntColumn->gather(identsLocal, identsCol);
106	<
107	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
108	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
109	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
110	<
111	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
112	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
113	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
176	>	pot_row.resize(nAtomsInRow_);
177	>	pot_col.resize(nAtomsInCol_);
178
179	<	// still need:
180	<	// topoDist
181	<	// exclude
179	>	expot_row.resize(nAtomsInRow_);
180	>	expot_col.resize(nAtomsInCol_);
181	>
182	>	AtomRowToGlobal.resize(nAtomsInRow_);
183	>	AtomColToGlobal.resize(nAtomsInCol_);
184	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
185	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
186	>
187	>	cgRowToGlobal.resize(nGroupsInRow_);
188	>	cgColToGlobal.resize(nGroupsInCol_);
189	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
190	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
191	>
192	>	massFactorsRow.resize(nAtomsInRow_);
193	>	massFactorsCol.resize(nAtomsInCol_);
194	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
195	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
196	>
197	>	groupListRow_.clear();
198	>	groupListRow_.resize(nGroupsInRow_);
199	>	for (int i = 0; i < nGroupsInRow_; i++) {
200	>	int gid = cgRowToGlobal[i];
201	>	for (int j = 0; j < nAtomsInRow_; j++) {
202	>	int aid = AtomRowToGlobal[j];
203	>	if (globalGroupMembership[aid] == gid)
204	>	groupListRow_[i].push_back(j);
205	>	}
206	>	}
207	>
208	>	groupListCol_.clear();
209	>	groupListCol_.resize(nGroupsInCol_);
210	>	for (int i = 0; i < nGroupsInCol_; i++) {
211	>	int gid = cgColToGlobal[i];
212	>	for (int j = 0; j < nAtomsInCol_; j++) {
213	>	int aid = AtomColToGlobal[j];
214	>	if (globalGroupMembership[aid] == gid)
215	>	groupListCol_[i].push_back(j);
216	>	}
217	>	}
218	>
219	>	excludesForAtom.clear();
220	>	excludesForAtom.resize(nAtomsInRow_);
221	>	toposForAtom.clear();
222	>	toposForAtom.resize(nAtomsInRow_);
223	>	topoDist.clear();
224	>	topoDist.resize(nAtomsInRow_);
225	>	for (int i = 0; i < nAtomsInRow_; i++) {
226	>	int iglob = AtomRowToGlobal[i];
227	>
228	>	for (int j = 0; j < nAtomsInCol_; j++) {
229	>	int jglob = AtomColToGlobal[j];
230	>
231	>	if (excludes->hasPair(iglob, jglob))
232	>	excludesForAtom[i].push_back(j);
233	>
234	>	if (oneTwo->hasPair(iglob, jglob)) {
235	>	toposForAtom[i].push_back(j);
236	>	topoDist[i].push_back(1);
237	>	} else {
238	>	if (oneThree->hasPair(iglob, jglob)) {
239	>	toposForAtom[i].push_back(j);
240	>	topoDist[i].push_back(2);
241	>	} else {
242	>	if (oneFour->hasPair(iglob, jglob)) {
243	>	toposForAtom[i].push_back(j);
244	>	topoDist[i].push_back(3);
245	>	}
246	>	}
247	>	}
248	>	}
249	>	}
250	>
251	>	#else
252	>	excludesForAtom.clear();
253	>	excludesForAtom.resize(nLocal_);
254	>	toposForAtom.clear();
255	>	toposForAtom.resize(nLocal_);
256	>	topoDist.clear();
257	>	topoDist.resize(nLocal_);
258	>
259	>	for (int i = 0; i < nLocal_; i++) {
260	>	int iglob = AtomLocalToGlobal[i];
261	>
262	>	for (int j = 0; j < nLocal_; j++) {
263	>	int jglob = AtomLocalToGlobal[j];
264	>
265	>	if (excludes->hasPair(iglob, jglob))
266	>	excludesForAtom[i].push_back(j);
267	>
268	>	if (oneTwo->hasPair(iglob, jglob)) {
269	>	toposForAtom[i].push_back(j);
270	>	topoDist[i].push_back(1);
271	>	} else {
272	>	if (oneThree->hasPair(iglob, jglob)) {
273	>	toposForAtom[i].push_back(j);
274	>	topoDist[i].push_back(2);
275	>	} else {
276	>	if (oneFour->hasPair(iglob, jglob)) {
277	>	toposForAtom[i].push_back(j);
278	>	topoDist[i].push_back(3);
279	>	}
280	>	}
281	>	}
282	>	}
283	>	}
284	>	#endif
285	>
286	>	// allocate memory for the parallel objects
287	>	atypesLocal.resize(nLocal_);
288	>
289	>	for (int i = 0; i < nLocal_; i++)
290	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
291	>
292	>	groupList_.clear();
293	>	groupList_.resize(nGroups_);
294	>	for (int i = 0; i < nGroups_; i++) {
295	>	int gid = cgLocalToGlobal[i];
296	>	for (int j = 0; j < nLocal_; j++) {
297	>	int aid = AtomLocalToGlobal[j];
298	>	if (globalGroupMembership[aid] == gid) {
299	>	groupList_[i].push_back(j);
300	>	}
301	>	}
302	>	}
303	>
304	>
305	>	createGtypeCutoffMap();
306	>
307	>	}
308	>
309	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
310	>
311	>	GrCut.clear();
312	>	GrCutSq.clear();
313	>	GrlistSq.clear();
314	>
315	>	RealType tol = 1e-6;
316	>	largestRcut_ = 0.0;
317	>	int atid;
318	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
319	>
320	>	map<int, RealType> atypeCutoff;
321	>
322	>	for (set<AtomType*>::iterator at = atypes.begin();
323	>	at != atypes.end(); ++at){
324	>	atid = (*at)->getIdent();
325	>	if (userChoseCutoff_)
326	>	atypeCutoff[atid] = userCutoff_;
327	>	else
328	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
329	>	}
330	>
331	>	vector<RealType> gTypeCutoffs;
332	>	// first we do a single loop over the cutoff groups to find the
333	>	// largest cutoff for any atypes present in this group.
334	>	#ifdef IS_MPI
335	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
336	>	groupRowToGtype.resize(nGroupsInRow_);
337	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
338	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
339	>	for (vector<int>::iterator ia = atomListRow.begin();
340	>	ia != atomListRow.end(); ++ia) {
341	>	int atom1 = (*ia);
342	>	atid = identsRow[atom1];
343	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
344	>	groupCutoffRow[cg1] = atypeCutoff[atid];
345	>	}
346	>	}
347	>
348	>	bool gTypeFound = false;
349	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
350	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
351	>	groupRowToGtype[cg1] = gt;
352	>	gTypeFound = true;
353	>	}
354	>	}
355	>	if (!gTypeFound) {
356	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
357	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
358	>	}
359	>
360	>	}
361	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
362	>	groupColToGtype.resize(nGroupsInCol_);
363	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
364	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
365	>	for (vector<int>::iterator jb = atomListCol.begin();
366	>	jb != atomListCol.end(); ++jb) {
367	>	int atom2 = (*jb);
368	>	atid = identsCol[atom2];
369	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
370	>	groupCutoffCol[cg2] = atypeCutoff[atid];
371	>	}
372	>	}
373	>	bool gTypeFound = false;
374	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
375	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
376	>	groupColToGtype[cg2] = gt;
377	>	gTypeFound = true;
378	>	}
379	>	}
380	>	if (!gTypeFound) {
381	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
382	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
383	>	}
384	>	}
385	>	#else
386	>
387	>	vector<RealType> groupCutoff(nGroups_, 0.0);
388	>	groupToGtype.resize(nGroups_);
389	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
390	>	groupCutoff[cg1] = 0.0;
391	>	vector<int> atomList = getAtomsInGroupRow(cg1);
392	>	for (vector<int>::iterator ia = atomList.begin();
393	>	ia != atomList.end(); ++ia) {
394	>	int atom1 = (*ia);
395	>	atid = idents[atom1];
396	>	if (atypeCutoff[atid] > groupCutoff[cg1])
397	>	groupCutoff[cg1] = atypeCutoff[atid];
398	>	}
399	>
400	>	bool gTypeFound = false;
401	>	for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
402	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
403	>	groupToGtype[cg1] = gt;
404	>	gTypeFound = true;
405	>	}
406	>	}
407	>	if (!gTypeFound) {
408	>	gTypeCutoffs.push_back( groupCutoff[cg1] );
409	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
410	>	}
411	>	}
412	>	#endif
413	>
414	>	// Now we find the maximum group cutoff value present in the simulation
415	>
416	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
417	>	gTypeCutoffs.end());
418	>
419	>	#ifdef IS_MPI
420	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
421	>	MPI::MAX);
422		#endif
423	+
424	+	RealType tradRcut = groupMax;
425	+
426	+	GrCut.resize( gTypeCutoffs.size() );
427	+	GrCutSq.resize( gTypeCutoffs.size() );
428	+	GrlistSq.resize( gTypeCutoffs.size() );
429	+
430	+
431	+	for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
432	+	GrCut[i].resize( gTypeCutoffs.size() , 0.0);
433	+	GrCutSq[i].resize( gTypeCutoffs.size(), 0.0 );
434	+	GrlistSq[i].resize( gTypeCutoffs.size(), 0.0 );
435	+
436	+	for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {
437	+	RealType thisRcut;
438	+	switch(cutoffPolicy_) {
439	+	case TRADITIONAL:
440	+	thisRcut = tradRcut;
441	+	break;
442	+	case MIX:
443	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
444	+	break;
445	+	case MAX:
446	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
447	+	break;
448	+	default:
449	+	sprintf(painCave.errMsg,
450	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
451	+	"hit an unknown cutoff policy!\n");
452	+	painCave.severity = OPENMD_ERROR;
453	+	painCave.isFatal = 1;
454	+	simError();
455	+	break;
456	+	}
457	+
458	+	GrCut[i][j] = thisRcut;
459	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
460	+	GrCutSq[i][j] = thisRcut * thisRcut;
461	+	GrlistSq[i][j] = pow(thisRcut + skinThickness_, 2);
462	+
463	+	// pair<int,int> key = make_pair(i,j);
464	+	// gTypeCutoffMap[key].first = thisRcut;
465	+	// gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
466	+	// sanity check
467	+
468	+	if (userChoseCutoff_) {
469	+	if (abs(GrCut[i][j] - userCutoff_) > 0.0001) {
470	+	sprintf(painCave.errMsg,
471	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
472	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
473	+	painCave.severity = OPENMD_ERROR;
474	+	painCave.isFatal = 1;
475	+	simError();
476	+	}
477	+	}
478	+	}
479	+	}
480		}
481	+
482	+	void ForceMatrixDecomposition::getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) {
483	+	int i, j;
484	+	#ifdef IS_MPI
485	+	i = groupRowToGtype[cg1];
486	+	j = groupColToGtype[cg2];
487	+	#else
488	+	i = groupToGtype[cg1];
489	+	j = groupToGtype[cg2];
490	+	#endif
491	+	rcut = GrCut[i][j];
492	+	rcutsq = GrCutSq[i][j];
493	+	rlistsq = GrlistSq[i][j];
494	+	return;
495	+	//return gTypeCutoffMap[make_pair(i,j)];
496	+	}
497	+
498	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
499	+	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
500	+	if (toposForAtom[atom1][j] == atom2)
501	+	return topoDist[atom1][j];
502	+	}
503	+	return 0;
504	+	}
505	+
506	+	void ForceMatrixDecomposition::zeroWorkArrays() {
507	+	pairwisePot = 0.0;
508	+	embeddingPot = 0.0;
509	+	excludedPot = 0.0;
510	+	excludedSelfPot = 0.0;
511	+
512	+	#ifdef IS_MPI
513	+	if (storageLayout_ & DataStorage::dslForce) {
514	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
515	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
516	+	}
517	+
518	+	if (storageLayout_ & DataStorage::dslTorque) {
519	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
520	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
521	+	}
522
523	+	fill(pot_row.begin(), pot_row.end(),
524	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
525
526	+	fill(pot_col.begin(), pot_col.end(),
527	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
528
529	+	fill(expot_row.begin(), expot_row.end(),
530	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
531	+
532	+	fill(expot_col.begin(), expot_col.end(),
533	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
534	+
535	+	if (storageLayout_ & DataStorage::dslParticlePot) {
536	+	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
537	+	0.0);
538	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
539	+	0.0);
540	+	}
541	+
542	+	if (storageLayout_ & DataStorage::dslDensity) {
543	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
544	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
545	+	}
546	+
547	+	if (storageLayout_ & DataStorage::dslFunctional) {
548	+	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
549	+	0.0);
550	+	fill(atomColData.functional.begin(), atomColData.functional.end(),
551	+	0.0);
552	+	}
553	+
554	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
555	+	fill(atomRowData.functionalDerivative.begin(),
556	+	atomRowData.functionalDerivative.end(), 0.0);
557	+	fill(atomColData.functionalDerivative.begin(),
558	+	atomColData.functionalDerivative.end(), 0.0);
559	+	}
560	+
561	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
562	+	fill(atomRowData.skippedCharge.begin(),
563	+	atomRowData.skippedCharge.end(), 0.0);
564	+	fill(atomColData.skippedCharge.begin(),
565	+	atomColData.skippedCharge.end(), 0.0);
566	+	}
567	+
568	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
569	+	fill(atomRowData.flucQFrc.begin(),
570	+	atomRowData.flucQFrc.end(), 0.0);
571	+	fill(atomColData.flucQFrc.begin(),
572	+	atomColData.flucQFrc.end(), 0.0);
573	+	}
574	+
575	+	if (storageLayout_ & DataStorage::dslElectricField) {
576	+	fill(atomRowData.electricField.begin(),
577	+	atomRowData.electricField.end(), V3Zero);
578	+	fill(atomColData.electricField.begin(),
579	+	atomColData.electricField.end(), V3Zero);
580	+	}
581	+
582	+	#endif
583	+	// even in parallel, we need to zero out the local arrays:
584	+
585	+	if (storageLayout_ & DataStorage::dslParticlePot) {
586	+	fill(snap_->atomData.particlePot.begin(),
587	+	snap_->atomData.particlePot.end(), 0.0);
588	+	}
589	+
590	+	if (storageLayout_ & DataStorage::dslDensity) {
591	+	fill(snap_->atomData.density.begin(),
592	+	snap_->atomData.density.end(), 0.0);
593	+	}
594	+
595	+	if (storageLayout_ & DataStorage::dslFunctional) {
596	+	fill(snap_->atomData.functional.begin(),
597	+	snap_->atomData.functional.end(), 0.0);
598	+	}
599	+
600	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
601	+	fill(snap_->atomData.functionalDerivative.begin(),
602	+	snap_->atomData.functionalDerivative.end(), 0.0);
603	+	}
604	+
605	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
606	+	fill(snap_->atomData.skippedCharge.begin(),
607	+	snap_->atomData.skippedCharge.end(), 0.0);
608	+	}
609	+
610	+	if (storageLayout_ & DataStorage::dslElectricField) {
611	+	fill(snap_->atomData.electricField.begin(),
612	+	snap_->atomData.electricField.end(), V3Zero);
613	+	}
614	+	}
615	+
616	+
617		void ForceMatrixDecomposition::distributeData()  {
618		snap_ = sman_->getCurrentSnapshot();
619		storageLayout_ = sman_->getStorageLayout();
620		#ifdef IS_MPI
621
622		// gather up the atomic positions
623	<	AtomCommVectorRow->gather(snap_->atomData.position,
623	>	AtomPlanVectorRow->gather(snap_->atomData.position,
624		atomRowData.position);
625	<	AtomCommVectorColumn->gather(snap_->atomData.position,
625	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
626		atomColData.position);
627
628		// gather up the cutoff group positions
629	<	cgCommVectorRow->gather(snap_->cgData.position,
629	>
630	>	cgPlanVectorRow->gather(snap_->cgData.position,
631		cgRowData.position);
632	<	cgCommVectorColumn->gather(snap_->cgData.position,
632	>
633	>	cgPlanVectorColumn->gather(snap_->cgData.position,
634		cgColData.position);
635	+
636	+
637	+
638	+	if (needVelocities_) {
639	+	// gather up the atomic velocities
640	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
641	+	atomColData.velocity);
642	+
643	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
644	+	cgColData.velocity);
645	+	}
646	+
647
648		// if needed, gather the atomic rotation matrices
649		if (storageLayout_ & DataStorage::dslAmat) {
650	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
650	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
651		atomRowData.aMat);
652	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
652	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
653		atomColData.aMat);
654		}
655	<
656	<	// if needed, gather the atomic eletrostatic frames
657	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
658	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
659	<	atomRowData.electroFrame);
660	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
661	<	atomColData.electroFrame);
655	>
656	>	// if needed, gather the atomic eletrostatic information
657	>	if (storageLayout_ & DataStorage::dslDipole) {
658	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
659	>	atomRowData.dipole);
660	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
661	>	atomColData.dipole);
662		}
663	+
664	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
665	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
666	+	atomRowData.quadrupole);
667	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
668	+	atomColData.quadrupole);
669	+	}
670	+
671	+	// if needed, gather the atomic fluctuating charge values
672	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
673	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
674	+	atomRowData.flucQPos);
675	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
676	+	atomColData.flucQPos);
677	+	}
678	+
679		#endif
680		}
681
682	+	/* collects information obtained during the pre-pair loop onto local
683	+	* data structures.
684	+	*/
685		void ForceMatrixDecomposition::collectIntermediateData() {
686		snap_ = sman_->getCurrentSnapshot();
687		storageLayout_ = sman_->getStorageLayout();
#	Line 162 | Line 689 | namespace OpenMD {
689
690		if (storageLayout_ & DataStorage::dslDensity) {
691
692	<	AtomCommRealRow->scatter(atomRowData.density,
692	>	AtomPlanRealRow->scatter(atomRowData.density,
693		snap_->atomData.density);
694
695		int n = snap_->atomData.density.size();
696	<	std::vector<RealType> rho_tmp(n, 0.0);
697	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
696	>	vector<RealType> rho_tmp(n, 0.0);
697	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
698		for (int i = 0; i < n; i++)
699		snap_->atomData.density[i] += rho_tmp[i];
700		}
701	+
702	+	// this isn't necessary if we don't have polarizable atoms, but
703	+	// we'll leave it here for now.
704	+	if (storageLayout_ & DataStorage::dslElectricField) {
705	+
706	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
707	+	snap_->atomData.electricField);
708	+
709	+	int n = snap_->atomData.electricField.size();
710	+	vector<Vector3d> field_tmp(n, V3Zero);
711	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
712	+	field_tmp);
713	+	for (int i = 0; i < n; i++)
714	+	snap_->atomData.electricField[i] += field_tmp[i];
715	+	}
716		#endif
717		}
718	<
718	>
719	>	/*
720	>	* redistributes information obtained during the pre-pair loop out to
721	>	* row and column-indexed data structures
722	>	*/
723		void ForceMatrixDecomposition::distributeIntermediateData() {
724		snap_ = sman_->getCurrentSnapshot();
725		storageLayout_ = sman_->getStorageLayout();
726		#ifdef IS_MPI
727		if (storageLayout_ & DataStorage::dslFunctional) {
728	<	AtomCommRealRow->gather(snap_->atomData.functional,
728	>	AtomPlanRealRow->gather(snap_->atomData.functional,
729		atomRowData.functional);
730	<	AtomCommRealColumn->gather(snap_->atomData.functional,
730	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
731		atomColData.functional);
732		}
733
734		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
735	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
735	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
736		atomRowData.functionalDerivative);
737	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
737	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
738		atomColData.functionalDerivative);
739		}
740		#endif
#	Line 202 | Line 748 | namespace OpenMD {
748		int n = snap_->atomData.force.size();
749		vector<Vector3d> frc_tmp(n, V3Zero);
750
751	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
751	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
752		for (int i = 0; i < n; i++) {
753		snap_->atomData.force[i] += frc_tmp[i];
754		frc_tmp[i] = 0.0;
755		}
756
757	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
758	<	for (int i = 0; i < n; i++)
757	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
758	>	for (int i = 0; i < n; i++) {
759		snap_->atomData.force[i] += frc_tmp[i];
760	<
761	<
760	>	}
761	>
762		if (storageLayout_ & DataStorage::dslTorque) {
763
764	<	int nt = snap_->atomData.force.size();
764	>	int nt = snap_->atomData.torque.size();
765		vector<Vector3d> trq_tmp(nt, V3Zero);
766
767	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
768	<	for (int i = 0; i < n; i++) {
767	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
768	>	for (int i = 0; i < nt; i++) {
769		snap_->atomData.torque[i] += trq_tmp[i];
770		trq_tmp[i] = 0.0;
771		}
772
773	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
774	<	for (int i = 0; i < n; i++)
773	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
774	>	for (int i = 0; i < nt; i++)
775		snap_->atomData.torque[i] += trq_tmp[i];
776		}
231	–
232	–	int nLocal = snap_->getNumberOfAtoms();
777
778	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
779	<	vector<RealType> (nLocal, 0.0));
778	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
779	>
780	>	int ns = snap_->atomData.skippedCharge.size();
781	>	vector<RealType> skch_tmp(ns, 0.0);
782	>
783	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
784	>	for (int i = 0; i < ns; i++) {
785	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
786	>	skch_tmp[i] = 0.0;
787	>	}
788	>
789	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
790	>	for (int i = 0; i < ns; i++)
791	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
792	>
793	>	}
794
795	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
796	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
797	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
798	<	pot_local[i] += pot_temp[i][ii];
795	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
796	>
797	>	int nq = snap_->atomData.flucQFrc.size();
798	>	vector<RealType> fqfrc_tmp(nq, 0.0);
799	>
800	>	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
801	>	for (int i = 0; i < nq; i++) {
802	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
803	>	fqfrc_tmp[i] = 0.0;
804	>	}
805	>
806	>	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
807	>	for (int i = 0; i < nq; i++)
808	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
809	>
810	>	}
811	>
812	>	if (storageLayout_ & DataStorage::dslElectricField) {
813	>
814	>	int nef = snap_->atomData.electricField.size();
815	>	vector<Vector3d> efield_tmp(nef, V3Zero);
816	>
817	>	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
818	>	for (int i = 0; i < nef; i++) {
819	>	snap_->atomData.electricField[i] += efield_tmp[i];
820	>	efield_tmp[i] = 0.0;
821	>	}
822	>
823	>	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
824	>	for (int i = 0; i < nef; i++)
825	>	snap_->atomData.electricField[i] += efield_tmp[i];
826	>	}
827	>
828	>
829	>	nLocal_ = snap_->getNumberOfAtoms();
830	>
831	>	vector<potVec> pot_temp(nLocal_,
832	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
833	>	vector<potVec> expot_temp(nLocal_,
834	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
835	>
836	>	// scatter/gather pot_row into the members of my column
837	>
838	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
839	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
840	>
841	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
842	>	pairwisePot += pot_temp[ii];
843	>
844	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
845	>	excludedPot += expot_temp[ii];
846	>
847	>	if (storageLayout_ & DataStorage::dslParticlePot) {
848	>	// This is the pairwise contribution to the particle pot.  The
849	>	// embedding contribution is added in each of the low level
850	>	// non-bonded routines.  In single processor, this is done in
851	>	// unpackInteractionData, not in collectData.
852	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
853	>	for (int i = 0; i < nLocal_; i++) {
854	>	// factor of two is because the total potential terms are divided
855	>	// by 2 in parallel due to row/ column scatter
856	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
857	>	}
858		}
859		}
860	+
861	+	fill(pot_temp.begin(), pot_temp.end(),
862	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
863	+	fill(expot_temp.begin(), expot_temp.end(),
864	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
865	+
866	+	AtomPlanPotColumn->scatter(pot_col, pot_temp);
867	+	AtomPlanPotColumn->scatter(expot_col, expot_temp);
868	+
869	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
870	+	pairwisePot += pot_temp[ii];
871	+
872	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
873	+	excludedPot += expot_temp[ii];
874	+
875	+	if (storageLayout_ & DataStorage::dslParticlePot) {
876	+	// This is the pairwise contribution to the particle pot.  The
877	+	// embedding contribution is added in each of the low level
878	+	// non-bonded routines.  In single processor, this is done in
879	+	// unpackInteractionData, not in collectData.
880	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
881	+	for (int i = 0; i < nLocal_; i++) {
882	+	// factor of two is because the total potential terms are divided
883	+	// by 2 in parallel due to row/ column scatter
884	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
885	+	}
886	+	}
887	+	}
888	+
889	+	if (storageLayout_ & DataStorage::dslParticlePot) {
890	+	int npp = snap_->atomData.particlePot.size();
891	+	vector<RealType> ppot_temp(npp, 0.0);
892	+
893	+	// This is the direct or embedding contribution to the particle
894	+	// pot.
895	+
896	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
897	+	for (int i = 0; i < npp; i++) {
898	+	snap_->atomData.particlePot[i] += ppot_temp[i];
899	+	}
900	+
901	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
902	+
903	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
904	+	for (int i = 0; i < npp; i++) {
905	+	snap_->atomData.particlePot[i] += ppot_temp[i];
906	+	}
907	+	}
908	+
909	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
910	+	RealType ploc1 = pairwisePot[ii];
911	+	RealType ploc2 = 0.0;
912	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
913	+	pairwisePot[ii] = ploc2;
914	+	}
915	+
916	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
917	+	RealType ploc1 = excludedPot[ii];
918	+	RealType ploc2 = 0.0;
919	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
920	+	excludedPot[ii] = ploc2;
921	+	}
922	+
923	+	// Here be dragons.
924	+	MPI::Intracomm col = colComm.getComm();
925	+
926	+	col.Allreduce(MPI::IN_PLACE,
927	+	&snap_->frameData.conductiveHeatFlux[0], 3,
928	+	MPI::REALTYPE, MPI::SUM);
929	+
930	+
931		#endif
932	+
933		}
934
935	+	/**
936	+	* Collects information obtained during the post-pair (and embedding
937	+	* functional) loops onto local data structures.
938	+	*/
939	+	void ForceMatrixDecomposition::collectSelfData() {
940	+	snap_ = sman_->getCurrentSnapshot();
941	+	storageLayout_ = sman_->getStorageLayout();
942	+
943	+	#ifdef IS_MPI
944	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
945	+	RealType ploc1 = embeddingPot[ii];
946	+	RealType ploc2 = 0.0;
947	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
948	+	embeddingPot[ii] = ploc2;
949	+	}
950	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
951	+	RealType ploc1 = excludedSelfPot[ii];
952	+	RealType ploc2 = 0.0;
953	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
954	+	excludedSelfPot[ii] = ploc2;
955	+	}
956	+	#endif
957	+
958	+	}
959	+
960	+
961	+
962	+	int& ForceMatrixDecomposition::getNAtomsInRow() {
963	+	#ifdef IS_MPI
964	+	return nAtomsInRow_;
965	+	#else
966	+	return nLocal_;
967	+	#endif
968	+	}
969	+
970	+	/**
971	+	* returns the list of atoms belonging to this group.
972	+	*/
973	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
974	+	#ifdef IS_MPI
975	+	return groupListRow_[cg1];
976	+	#else
977	+	return groupList_[cg1];
978	+	#endif
979	+	}
980	+
981	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
982	+	#ifdef IS_MPI
983	+	return groupListCol_[cg2];
984	+	#else
985	+	return groupList_[cg2];
986	+	#endif
987	+	}
988
989		Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
990		Vector3d d;
#	Line 253 | Line 995 | namespace OpenMD {
995		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
996		#endif
997
998	<	snap_->wrapVector(d);
998	>	if (usePeriodicBoundaryConditions_) {
999	>	snap_->wrapVector(d);
1000	>	}
1001		return d;
1002		}
1003
1004	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
1005	+	#ifdef IS_MPI
1006	+	return cgColData.velocity[cg2];
1007	+	#else
1008	+	return snap_->cgData.velocity[cg2];
1009	+	#endif
1010	+	}
1011
1012	+	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
1013	+	#ifdef IS_MPI
1014	+	return atomColData.velocity[atom2];
1015	+	#else
1016	+	return snap_->atomData.velocity[atom2];
1017	+	#endif
1018	+	}
1019	+
1020	+
1021		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
1022
1023		Vector3d d;
#	Line 267 | Line 1027 | namespace OpenMD {
1027		#else
1028		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1029		#endif
1030	<
1031	<	snap_->wrapVector(d);
1030	>	if (usePeriodicBoundaryConditions_) {
1031	>	snap_->wrapVector(d);
1032	>	}
1033		return d;
1034		}
1035
#	Line 280 | Line 1041 | namespace OpenMD {
1041		#else
1042		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1043		#endif
1044	<
1045	<	snap_->wrapVector(d);
1044	>	if (usePeriodicBoundaryConditions_) {
1045	>	snap_->wrapVector(d);
1046	>	}
1047		return d;
1048		}
1049	+
1050	+	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1051	+	#ifdef IS_MPI
1052	+	return massFactorsRow[atom1];
1053	+	#else
1054	+	return massFactors[atom1];
1055	+	#endif
1056	+	}
1057	+
1058	+	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1059	+	#ifdef IS_MPI
1060	+	return massFactorsCol[atom2];
1061	+	#else
1062	+	return massFactors[atom2];
1063	+	#endif
1064	+
1065	+	}
1066
1067		Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
1068		Vector3d d;
#	Line 293 | Line 1072 | namespace OpenMD {
1072		#else
1073		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1074		#endif
1075	<
1076	<	snap_->wrapVector(d);
1075	>	if (usePeriodicBoundaryConditions_) {
1076	>	snap_->wrapVector(d);
1077	>	}
1078		return d;
1079		}
1080
1081	+	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1082	+	return excludesForAtom[atom1];
1083	+	}
1084	+
1085	+	/**
1086	+	* We need to exclude some overcounted interactions that result from
1087	+	* the parallel decomposition.
1088	+	*/
1089	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1090	+	int unique_id_1, unique_id_2;
1091	+
1092	+	#ifdef IS_MPI
1093	+	// in MPI, we have to look up the unique IDs for each atom
1094	+	unique_id_1 = AtomRowToGlobal[atom1];
1095	+	unique_id_2 = AtomColToGlobal[atom2];
1096	+	// group1 = cgRowToGlobal[cg1];
1097	+	// group2 = cgColToGlobal[cg2];
1098	+	#else
1099	+	unique_id_1 = AtomLocalToGlobal[atom1];
1100	+	unique_id_2 = AtomLocalToGlobal[atom2];
1101	+	int group1 = cgLocalToGlobal[cg1];
1102	+	int group2 = cgLocalToGlobal[cg2];
1103	+	#endif
1104	+
1105	+	if (unique_id_1 == unique_id_2) return true;
1106	+
1107	+	#ifdef IS_MPI
1108	+	// this prevents us from doing the pair on multiple processors
1109	+	if (unique_id_1 < unique_id_2) {
1110	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1111	+	} else {
1112	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1113	+	}
1114	+	#endif
1115	+
1116	+	#ifndef IS_MPI
1117	+	if (group1 == group2) {
1118	+	if (unique_id_1 < unique_id_2) return true;
1119	+	}
1120	+	#endif
1121	+
1122	+	return false;
1123	+	}
1124	+
1125	+	/**
1126	+	* We need to handle the interactions for atoms who are involved in
1127	+	* the same rigid body as well as some short range interactions
1128	+	* (bonds, bends, torsions) differently from other interactions.
1129	+	* We'll still visit the pairwise routines, but with a flag that
1130	+	* tells those routines to exclude the pair from direct long range
1131	+	* interactions.  Some indirect interactions (notably reaction
1132	+	* field) must still be handled for these pairs.
1133	+	*/
1134	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1135	+
1136	+	// excludesForAtom was constructed to use row/column indices in the MPI
1137	+	// version, and to use local IDs in the non-MPI version:
1138	+
1139	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1140	+	i != excludesForAtom[atom1].end(); ++i) {
1141	+	if ( (*i) == atom2 ) return true;
1142	+	}
1143	+
1144	+	return false;
1145	+	}
1146	+
1147	+
1148		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1149		#ifdef IS_MPI
1150		atomRowData.force[atom1] += fg;
#	Line 312 | Line 1159 | namespace OpenMD {
1159		#else
1160		snap_->atomData.force[atom2] += fg;
1161		#endif
315	–
1162		}
1163
1164		// filling interaction blocks with pointers
1165	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1165	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1166	>	int atom1, int atom2) {
1167
1168	<	InteractionData idat;
1168	>	idat.excluded = excludeAtomPair(atom1, atom2);
1169	>
1170		#ifdef IS_MPI
1171	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1172	+	idat.atid1 = identsRow[atom1];
1173	+	idat.atid2 = identsCol[atom2];
1174	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1175	+	//                         ff_->getAtomType(identsCol[atom2]) );
1176	+
1177		if (storageLayout_ & DataStorage::dslAmat) {
1178		idat.A1 = &(atomRowData.aMat[atom1]);
1179		idat.A2 = &(atomColData.aMat[atom2]);
1180		}
1181	<
328	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
329	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
330	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
331	<	}
332	<
1181	>
1182		if (storageLayout_ & DataStorage::dslTorque) {
1183		idat.t1 = &(atomRowData.torque[atom1]);
1184		idat.t2 = &(atomColData.torque[atom2]);
1185		}
1186
1187	+	if (storageLayout_ & DataStorage::dslDipole) {
1188	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1189	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1190	+	}
1191	+
1192	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1193	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1194	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1195	+	}
1196	+
1197		if (storageLayout_ & DataStorage::dslDensity) {
1198		idat.rho1 = &(atomRowData.density[atom1]);
1199		idat.rho2 = &(atomColData.density[atom2]);
1200		}
1201
1202	+	if (storageLayout_ & DataStorage::dslFunctional) {
1203	+	idat.frho1 = &(atomRowData.functional[atom1]);
1204	+	idat.frho2 = &(atomColData.functional[atom2]);
1205	+	}
1206	+
1207		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1208		idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1209		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1210		}
1211	+
1212	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1213	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1214	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1215	+	}
1216	+
1217	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1218	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1219	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1220	+	}
1221	+
1222	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1223	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1224	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1225	+	}
1226	+
1227		#else
1228	+
1229	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1230	+	idat.atid1 = idents[atom1];
1231	+	idat.atid2 = idents[atom2];
1232	+
1233		if (storageLayout_ & DataStorage::dslAmat) {
1234		idat.A1 = &(snap_->atomData.aMat[atom1]);
1235		idat.A2 = &(snap_->atomData.aMat[atom2]);
1236		}
1237
353	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
354	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
355	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
356	–	}
357	–
1238		if (storageLayout_ & DataStorage::dslTorque) {
1239		idat.t1 = &(snap_->atomData.torque[atom1]);
1240		idat.t2 = &(snap_->atomData.torque[atom2]);
1241		}
1242
1243	<	if (storageLayout_ & DataStorage::dslDensity) {
1243	>	if (storageLayout_ & DataStorage::dslDipole) {
1244	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1245	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1246	>	}
1247	>
1248	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1249	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1250	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1251	>	}
1252	>
1253	>	if (storageLayout_ & DataStorage::dslDensity) {
1254		idat.rho1 = &(snap_->atomData.density[atom1]);
1255		idat.rho2 = &(snap_->atomData.density[atom2]);
1256		}
1257
1258	+	if (storageLayout_ & DataStorage::dslFunctional) {
1259	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1260	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1261	+	}
1262	+
1263		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1264		idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1265		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1266		}
1267	+
1268	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1269	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1270	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1271	+	}
1272	+
1273	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1274	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1275	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1276	+	}
1277	+
1278	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1279	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1280	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1281	+	}
1282	+
1283		#endif
373	–
1284		}
1285	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1286	<	InteractionData idat;
1287	<	skippedCharge1
378	<	skippedCharge2
379	<	rij
380	<	d
381	<	electroMult
382	<	sw
383	<	f
1285	>
1286	>
1287	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1288		#ifdef IS_MPI
1289	+	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1290	+	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1291	+	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1292	+	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1293
1294	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1295	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1296	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1294	>	atomRowData.force[atom1] += *(idat.f1);
1295	>	atomColData.force[atom2] -= *(idat.f1);
1296	>
1297	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1298	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1299	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1300		}
1301	<	if (storageLayout_ & DataStorage::dslTorque) {
1302	<	idat.t1 = &(atomRowData.torque[atom1]);
1303	<	idat.t2 = &(atomColData.torque[atom2]);
1301	>
1302	>	if (storageLayout_ & DataStorage::dslElectricField) {
1303	>	atomRowData.electricField[atom1] += *(idat.eField1);
1304	>	atomColData.electricField[atom2] += *(idat.eField2);
1305		}
1306
1307	+	#else
1308	+	pairwisePot += *(idat.pot);
1309	+	excludedPot += *(idat.excludedPot);
1310	+
1311	+	snap_->atomData.force[atom1] += *(idat.f1);
1312	+	snap_->atomData.force[atom2] -= *(idat.f1);
1313	+
1314	+	if (idat.doParticlePot) {
1315	+	// This is the pairwise contribution to the particle pot.  The
1316	+	// embedding contribution is added in each of the low level
1317	+	// non-bonded routines.  In parallel, this calculation is done
1318	+	// in collectData, not in unpackInteractionData.
1319	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1320	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1321	+	}
1322
1323	<	}
1324	<	SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
1325	<	}
1323	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1324	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1325	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1326	>	}
1327
1328	+	if (storageLayout_ & DataStorage::dslElectricField) {
1329	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1330	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1331	+	}
1332
1333	+	#endif
1334	+
1335	+	}
1336	+
1337		/*
1338		* buildNeighborList
1339		*
1340		* first element of pair is row-indexed CutoffGroup
1341		* second element of pair is column-indexed CutoffGroup
1342		*/
1343	<	vector<pair<int, int> >  buildNeighborList() {
1344	<	Vector3d dr, invWid, rs, shift;
1345	<	Vector3i cc, m1v, m2s;
1346	<	RealType rrNebr;
1347	<	int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;
1343	>	void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1344	>
1345	>	neighborList.clear();
1346	>	groupCutoffs cuts;
1347	>	bool doAllPairs = false;
1348
1349	+	RealType rList_ = (largestRcut_ + skinThickness_);
1350	+	RealType rcut, rcutsq, rlistsq;
1351	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1352	+	Mat3x3d box;
1353	+	Mat3x3d invBox;
1354
1355	<	vector<pair<int, int> > neighborList;
1356	<	Vector3i nCells;
1357	<	Vector3d invWid, r;
1355	>	Vector3d rs, scaled, dr;
1356	>	Vector3i whichCell;
1357	>	int cellIndex;
1358
1359	<	rList_ = (rCut_ + skinThickness_);
1360	<	rl2 = rList_ * rList_;
1361	<
1362	<	snap_ = sman_->getCurrentSnapshot();
1363	<	Mat3x3d Hmat = snap_->getHmat();
1364	<	Vector3d Hx = Hmat.getColumn(0);
1365	<	Vector3d Hy = Hmat.getColumn(1);
1366	<	Vector3d Hz = Hmat.getColumn(2);
1367	<
1368	<	nCells.x() = (int) ( Hx.length() )/ rList_;
1369	<	nCells.y() = (int) ( Hy.length() )/ rList_;
1370	<	nCells.z() = (int) ( Hz.length() )/ rList_;
1371	<
431	<	for (i = 0; i < nGroupsInRow; i++) {
432	<	rs = cgRowData.position[i];
433	<	snap_->scaleVector(rs);
1359	>	#ifdef IS_MPI
1360	>	cellListRow_.clear();
1361	>	cellListCol_.clear();
1362	>	#else
1363	>	cellList_.clear();
1364	>	#endif
1365	>
1366	>	if (!usePeriodicBoundaryConditions_) {
1367	>	box = snap_->getBoundingBox();
1368	>	invBox = snap_->getInvBoundingBox();
1369	>	} else {
1370	>	box = snap_->getHmat();
1371	>	invBox = snap_->getInvHmat();
1372		}
1373
1374	+	Vector3d boxX = box.getColumn(0);
1375	+	Vector3d boxY = box.getColumn(1);
1376	+	Vector3d boxZ = box.getColumn(2);
1377	+
1378	+	nCells_.x() = (int) ( boxX.length() )/ rList_;
1379	+	nCells_.y() = (int) ( boxY.length() )/ rList_;
1380	+	nCells_.z() = (int) ( boxZ.length() )/ rList_;
1381	+
1382	+	// handle small boxes where the cell offsets can end up repeating cells
1383	+
1384	+	if (nCells_.x() < 3) doAllPairs = true;
1385	+	if (nCells_.y() < 3) doAllPairs = true;
1386	+	if (nCells_.z() < 3) doAllPairs = true;
1387	+
1388	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1389	+
1390	+	#ifdef IS_MPI
1391	+	cellListRow_.resize(nCtot);
1392	+	cellListCol_.resize(nCtot);
1393	+	#else
1394	+	cellList_.resize(nCtot);
1395	+	#endif
1396	+
1397	+	if (!doAllPairs) {
1398	+	#ifdef IS_MPI
1399	+
1400	+	for (int i = 0; i < nGroupsInRow_; i++) {
1401	+	rs = cgRowData.position[i];
1402	+
1403	+	// scaled positions relative to the box vectors
1404	+	scaled = invBox * rs;
1405	+
1406	+	// wrap the vector back into the unit box by subtracting integer box
1407	+	// numbers
1408	+	for (int j = 0; j < 3; j++) {
1409	+	scaled[j] -= roundMe(scaled[j]);
1410	+	scaled[j] += 0.5;
1411	+	// Handle the special case when an object is exactly on the
1412	+	// boundary (a scaled coordinate of 1.0 is the same as
1413	+	// scaled coordinate of 0.0)
1414	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1415	+	}
1416	+
1417	+	// find xyz-indices of cell that cutoffGroup is in.
1418	+	whichCell.x() = nCells_.x() * scaled.x();
1419	+	whichCell.y() = nCells_.y() * scaled.y();
1420	+	whichCell.z() = nCells_.z() * scaled.z();
1421	+
1422	+	// find single index of this cell:
1423	+	cellIndex = Vlinear(whichCell, nCells_);
1424	+
1425	+	// add this cutoff group to the list of groups in this cell;
1426	+	cellListRow_[cellIndex].push_back(i);
1427	+	}
1428	+	for (int i = 0; i < nGroupsInCol_; i++) {
1429	+	rs = cgColData.position[i];
1430	+
1431	+	// scaled positions relative to the box vectors
1432	+	scaled = invBox * rs;
1433	+
1434	+	// wrap the vector back into the unit box by subtracting integer box
1435	+	// numbers
1436	+	for (int j = 0; j < 3; j++) {
1437	+	scaled[j] -= roundMe(scaled[j]);
1438	+	scaled[j] += 0.5;
1439	+	// Handle the special case when an object is exactly on the
1440	+	// boundary (a scaled coordinate of 1.0 is the same as
1441	+	// scaled coordinate of 0.0)
1442	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1443	+	}
1444	+
1445	+	// find xyz-indices of cell that cutoffGroup is in.
1446	+	whichCell.x() = nCells_.x() * scaled.x();
1447	+	whichCell.y() = nCells_.y() * scaled.y();
1448	+	whichCell.z() = nCells_.z() * scaled.z();
1449	+
1450	+	// find single index of this cell:
1451	+	cellIndex = Vlinear(whichCell, nCells_);
1452	+
1453	+	// add this cutoff group to the list of groups in this cell;
1454	+	cellListCol_[cellIndex].push_back(i);
1455	+	}
1456	+
1457	+	#else
1458	+	for (int i = 0; i < nGroups_; i++) {
1459	+	rs = snap_->cgData.position[i];
1460	+
1461	+	// scaled positions relative to the box vectors
1462	+	scaled = invBox * rs;
1463	+
1464	+	// wrap the vector back into the unit box by subtracting integer box
1465	+	// numbers
1466	+	for (int j = 0; j < 3; j++) {
1467	+	scaled[j] -= roundMe(scaled[j]);
1468	+	scaled[j] += 0.5;
1469	+	// Handle the special case when an object is exactly on the
1470	+	// boundary (a scaled coordinate of 1.0 is the same as
1471	+	// scaled coordinate of 0.0)
1472	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1473	+	}
1474	+
1475	+	// find xyz-indices of cell that cutoffGroup is in.
1476	+	whichCell.x() = nCells_.x() * scaled.x();
1477	+	whichCell.y() = nCells_.y() * scaled.y();
1478	+	whichCell.z() = nCells_.z() * scaled.z();
1479	+
1480	+	// find single index of this cell:
1481	+	cellIndex = Vlinear(whichCell, nCells_);
1482	+
1483	+	// add this cutoff group to the list of groups in this cell;
1484	+	cellList_[cellIndex].push_back(i);
1485	+	}
1486
1487	<	VDiv (invWid, cells, region);
438	<	for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
439	<	for (n = 0; n < nMol; n ++) {
440	<	VSAdd (rs, mol[n].r, 0.5, region);
441	<	VMul (cc, rs, invWid);
442	<	c = VLinear (cc, cells) + nMol;
443	<	cellList[n] = cellList[c];
444	<	cellList[c] = n;
445	<	}
446	<	nebrTabLen = 0;
447	<	for (m1z = 0; m1z < cells.z(); m1z++) {
448	<	for (m1y = 0; m1y < cells.y(); m1y++) {
449	<	for (m1x = 0; m1x < cells.x(); m1x++) {
450	<	Vector3i m1v(m1x, m1y, m1z);
451	<	m1 = VLinear(m1v, cells) + nMol;
452	<	for (offset = 0; offset < nOffset_; offset++) {
453	<	m2v = m1v + cellOffsets_[offset];
454	<	shift = V3Zero();
1487	>	#endif
1488
1489	<	if (m2v.x() >= cells.x) {
1490	<	m2v.x() = 0;
1491	<	shift.x() = region.x();
1492	<	} else if (m2v.x() < 0) {
1493	<	m2v.x() = cells.x() - 1;
1494	<	shift.x() = - region.x();
1495	<	}
1489	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1490	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1491	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1492	>	Vector3i m1v(m1x, m1y, m1z);
1493	>	int m1 = Vlinear(m1v, nCells_);
1494	>
1495	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1496	>	os != cellOffsets_.end(); ++os) {
1497	>
1498	>	Vector3i m2v = m1v + (*os);
1499	>
1500
1501	<	if (m2v.y() >= cells.y()) {
1502	<	m2v.y() = 0;
1503	<	shift.y() = region.y();
1504	<	} else if (m2v.y() < 0) {
1505	<	m2v.y() = cells.y() - 1;
1506	<	shift.y() = - region.y();
1507	<	}
1501	>	if (m2v.x() >= nCells_.x()) {
1502	>	m2v.x() = 0;
1503	>	} else if (m2v.x() < 0) {
1504	>	m2v.x() = nCells_.x() - 1;
1505	>	}
1506	>
1507	>	if (m2v.y() >= nCells_.y()) {
1508	>	m2v.y() = 0;
1509	>	} else if (m2v.y() < 0) {
1510	>	m2v.y() = nCells_.y() - 1;
1511	>	}
1512	>
1513	>	if (m2v.z() >= nCells_.z()) {
1514	>	m2v.z() = 0;
1515	>	} else if (m2v.z() < 0) {
1516	>	m2v.z() = nCells_.z() - 1;
1517	>	}
1518
1519	<	m2 = VLinear (m2v, cells) + nMol;
1520	<	for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
1521	<	for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
1522	<	if (m1 != m2 || j2 < j1) {
1523	<	dr = mol[j1].r - mol[j2].r;
1524	<	VSub (dr, mol[j1].r, mol[j2].r);
1525	<	VVSub (dr, shift);
1526	<	if (VLenSq (dr) < rrNebr) {
1527	<	neighborList.push_back(make_pair(j1, j2));
1519	>	int m2 = Vlinear (m2v, nCells_);
1520	>
1521	>	#ifdef IS_MPI
1522	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1523	>	j1 != cellListRow_[m1].end(); ++j1) {
1524	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1525	>	j2 != cellListCol_[m2].end(); ++j2) {
1526	>
1527	>	// In parallel, we need to visit *all* pairs of row
1528	>	// & column indicies and will divide labor in the
1529	>	// force evaluation later.
1530	>	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1531	>	if (usePeriodicBoundaryConditions_) {
1532	>	snap_->wrapVector(dr);
1533		}
1534	+	getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1535	+	if (dr.lengthSquare() < rlistsq) {
1536	+	neighborList.push_back(make_pair((*j1), (*j2)));
1537	+	}
1538		}
1539		}
1540	+	#else
1541	+	for (vector<int>::iterator j1 = cellList_[m1].begin();
1542	+	j1 != cellList_[m1].end(); ++j1) {
1543	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1544	+	j2 != cellList_[m2].end(); ++j2) {
1545	+
1546	+	// Always do this if we're in different cells or if
1547	+	// we're in the same cell and the global index of
1548	+	// the j2 cutoff group is greater than or equal to
1549	+	// the j1 cutoff group.  Note that Rappaport's code
1550	+	// has a "less than" conditional here, but that
1551	+	// deals with atom-by-atom computation.  OpenMD
1552	+	// allows atoms within a single cutoff group to
1553	+	// interact with each other.
1554	+
1555	+	if (m2 != m1 || (*j2) >= (*j1) ) {
1556	+
1557	+	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1558	+	if (usePeriodicBoundaryConditions_) {
1559	+	snap_->wrapVector(dr);
1560	+	}
1561	+	getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1562	+	if (dr.lengthSquare() < rlistsq) {
1563	+	neighborList.push_back(make_pair((*j1), (*j2)));
1564	+	}
1565	+	}
1566	+	}
1567	+	}
1568	+	#endif
1569		}
1570		}
1571		}
1572		}
1573	+	} else {
1574	+	// branch to do all cutoff group pairs
1575	+	#ifdef IS_MPI
1576	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1577	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1578	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1579	+	if (usePeriodicBoundaryConditions_) {
1580	+	snap_->wrapVector(dr);
1581	+	}
1582	+	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1583	+	if (dr.lengthSquare() < rlistsq) {
1584	+	neighborList.push_back(make_pair(j1, j2));
1585	+	}
1586	+	}
1587	+	}
1588	+	#else
1589	+	// include all groups here.
1590	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1591	+	// include self group interactions j2 == j1
1592	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1593	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1594	+	if (usePeriodicBoundaryConditions_) {
1595	+	snap_->wrapVector(dr);
1596	+	}
1597	+	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1598	+	if (dr.lengthSquare() < rlistsq) {
1599	+	neighborList.push_back(make_pair(j1, j2));
1600	+	}
1601	+	}
1602	+	}
1603	+	#endif
1604		}
1605	+
1606	+	// save the local cutoff group positions for the check that is
1607	+	// done on each loop:
1608	+	saved_CG_positions_.clear();
1609	+	for (int i = 0; i < nGroups_; i++)
1610	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1611		}
490	–
491	–
1612		} //end namespace OpenMD

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