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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
Revision 1713 by gezelter, Sat May 19 14:21:02 2012 UTC

#	Line 36 | Line 36
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/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	+	ff_ = info_->getForceField();
97		nLocal_ = snap_->getNumberOfAtoms();
98	<	nGroups_ = snap_->getNumberOfCutoffGroups();
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		#ifdef IS_MPI
114
115	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
116	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
64	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
65	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
115	>	MPI::Intracomm row = rowComm.getComm();
116	>	MPI::Intracomm col = colComm.getComm();
117
118	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
119	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
120	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
121	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
118	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
119	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
120	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
121	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
122	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
123
124	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
125	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
126	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
127	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
124	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
125	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
126	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
127	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
128	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
129
130	<	nAtomsInRow_ = AtomCommIntRow->getSize();
131	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
132	<	nGroupsInRow_ = cgCommIntRow->getSize();
133	<	nGroupsInCol_ = cgCommIntColumn->getSize();
130	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
131	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
132	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
133	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
134
135	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
136	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
137	+	nGroupsInRow_ = cgPlanIntRow->getSize();
138	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
139	+
140		// Modify the data storage objects with the correct layouts and sizes:
141		atomRowData.resize(nAtomsInRow_);
142		atomRowData.setStorageLayout(storageLayout_);
#	Line 88 | Line 146 | namespace OpenMD {
146		cgRowData.setStorageLayout(DataStorage::dslPosition);
147		cgColData.resize(nGroupsInCol_);
148		cgColData.setStorageLayout(DataStorage::dslPosition);
149	+
150	+	identsRow.resize(nAtomsInRow_);
151	+	identsCol.resize(nAtomsInCol_);
152
153	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
154	<	vector<RealType> (nAtomsInRow_, 0.0));
155	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
156	<	vector<RealType> (nAtomsInCol_, 0.0));
153	>	AtomPlanIntRow->gather(idents, identsRow);
154	>	AtomPlanIntColumn->gather(idents, identsCol);
155	>
156	>	// allocate memory for the parallel objects
157	>	atypesRow.resize(nAtomsInRow_);
158	>	atypesCol.resize(nAtomsInCol_);
159
160	+	for (int i = 0; i < nAtomsInRow_; i++)
161	+	atypesRow[i] = ff_->getAtomType(identsRow[i]);
162	+	for (int i = 0; i < nAtomsInCol_; i++)
163	+	atypesCol[i] = ff_->getAtomType(identsCol[i]);
164
165	<	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
165	>	pot_row.resize(nAtomsInRow_);
166	>	pot_col.resize(nAtomsInCol_);
167	>
168	>	AtomRowToGlobal.resize(nAtomsInRow_);
169	>	AtomColToGlobal.resize(nAtomsInCol_);
170	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
171	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
172	>
173	>	cgRowToGlobal.resize(nGroupsInRow_);
174	>	cgColToGlobal.resize(nGroupsInCol_);
175	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177	>
178	>	massFactorsRow.resize(nAtomsInRow_);
179	>	massFactorsCol.resize(nAtomsInCol_);
180	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
181	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
182	>
183	>	groupListRow_.clear();
184	>	groupListRow_.resize(nGroupsInRow_);
185	>	for (int i = 0; i < nGroupsInRow_; i++) {
186	>	int gid = cgRowToGlobal[i];
187	>	for (int j = 0; j < nAtomsInRow_; j++) {
188	>	int aid = AtomRowToGlobal[j];
189	>	if (globalGroupMembership[aid] == gid)
190	>	groupListRow_[i].push_back(j);
191	>	}
192	>	}
193	>
194	>	groupListCol_.clear();
195	>	groupListCol_.resize(nGroupsInCol_);
196	>	for (int i = 0; i < nGroupsInCol_; i++) {
197	>	int gid = cgColToGlobal[i];
198	>	for (int j = 0; j < nAtomsInCol_; j++) {
199	>	int aid = AtomColToGlobal[j];
200	>	if (globalGroupMembership[aid] == gid)
201	>	groupListCol_[i].push_back(j);
202	>	}
203	>	}
204	>
205	>	excludesForAtom.clear();
206	>	excludesForAtom.resize(nAtomsInRow_);
207	>	toposForAtom.clear();
208	>	toposForAtom.resize(nAtomsInRow_);
209	>	topoDist.clear();
210	>	topoDist.resize(nAtomsInRow_);
211	>	for (int i = 0; i < nAtomsInRow_; i++) {
212	>	int iglob = AtomRowToGlobal[i];
213	>
214	>	for (int j = 0; j < nAtomsInCol_; j++) {
215	>	int jglob = AtomColToGlobal[j];
216	>
217	>	if (excludes->hasPair(iglob, jglob))
218	>	excludesForAtom[i].push_back(j);
219	>
220	>	if (oneTwo->hasPair(iglob, jglob)) {
221	>	toposForAtom[i].push_back(j);
222	>	topoDist[i].push_back(1);
223	>	} else {
224	>	if (oneThree->hasPair(iglob, jglob)) {
225	>	toposForAtom[i].push_back(j);
226	>	topoDist[i].push_back(2);
227	>	} else {
228	>	if (oneFour->hasPair(iglob, jglob)) {
229	>	toposForAtom[i].push_back(j);
230	>	topoDist[i].push_back(3);
231	>	}
232	>	}
233	>	}
234	>	}
235	>	}
236	>
237	>	#else
238	>	excludesForAtom.clear();
239	>	excludesForAtom.resize(nLocal_);
240	>	toposForAtom.clear();
241	>	toposForAtom.resize(nLocal_);
242	>	topoDist.clear();
243	>	topoDist.resize(nLocal_);
244	>
245	>	for (int i = 0; i < nLocal_; i++) {
246	>	int iglob = AtomLocalToGlobal[i];
247	>
248	>	for (int j = 0; j < nLocal_; j++) {
249	>	int jglob = AtomLocalToGlobal[j];
250	>
251	>	if (excludes->hasPair(iglob, jglob))
252	>	excludesForAtom[i].push_back(j);
253	>
254	>	if (oneTwo->hasPair(iglob, jglob)) {
255	>	toposForAtom[i].push_back(j);
256	>	topoDist[i].push_back(1);
257	>	} else {
258	>	if (oneThree->hasPair(iglob, jglob)) {
259	>	toposForAtom[i].push_back(j);
260	>	topoDist[i].push_back(2);
261	>	} else {
262	>	if (oneFour->hasPair(iglob, jglob)) {
263	>	toposForAtom[i].push_back(j);
264	>	topoDist[i].push_back(3);
265	>	}
266	>	}
267	>	}
268	>	}
269	>	}
270	>	#endif
271	>
272	>	// allocate memory for the parallel objects
273	>	atypesLocal.resize(nLocal_);
274	>
275	>	for (int i = 0; i < nLocal_; i++)
276	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
277	>
278	>	groupList_.clear();
279	>	groupList_.resize(nGroups_);
280	>	for (int i = 0; i < nGroups_; i++) {
281	>	int gid = cgLocalToGlobal[i];
282	>	for (int j = 0; j < nLocal_; j++) {
283	>	int aid = AtomLocalToGlobal[j];
284	>	if (globalGroupMembership[aid] == gid) {
285	>	groupList_[i].push_back(j);
286	>	}
287	>	}
288	>	}
289	>
290	>
291	>	createGtypeCutoffMap();
292	>
293	>	}
294	>
295	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
296
297	<	// gather the information for atomtype IDs (atids):
298	<	vector<int> identsLocal = info_->getIdentArray();
299	<	identsRow.reserve(nAtomsInRow_);
300	<	identsCol.reserve(nAtomsInCol_);
297	>	RealType tol = 1e-6;
298	>	largestRcut_ = 0.0;
299	>	RealType rc;
300	>	int atid;
301	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302
303	<	AtomCommIntRow->gather(identsLocal, identsRow);
304	<	AtomCommIntColumn->gather(identsLocal, identsCol);
303	>	map<int, RealType> atypeCutoff;
304	>
305	>	for (set<AtomType*>::iterator at = atypes.begin();
306	>	at != atypes.end(); ++at){
307	>	atid = (*at)->getIdent();
308	>	if (userChoseCutoff_)
309	>	atypeCutoff[atid] = userCutoff_;
310	>	else
311	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312	>	}
313
314	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
315	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
316	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
317	<
318	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
319	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
320	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
314	>	vector<RealType> gTypeCutoffs;
315	>	// first we do a single loop over the cutoff groups to find the
316	>	// largest cutoff for any atypes present in this group.
317	>	#ifdef IS_MPI
318	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
319	>	groupRowToGtype.resize(nGroupsInRow_);
320	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
321	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
322	>	for (vector<int>::iterator ia = atomListRow.begin();
323	>	ia != atomListRow.end(); ++ia) {
324	>	int atom1 = (*ia);
325	>	atid = identsRow[atom1];
326	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
327	>	groupCutoffRow[cg1] = atypeCutoff[atid];
328	>	}
329	>	}
330
331	<	// still need:
332	<	// topoDist
333	<	// exclude
331	>	bool gTypeFound = false;
332	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
333	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
334	>	groupRowToGtype[cg1] = gt;
335	>	gTypeFound = true;
336	>	}
337	>	}
338	>	if (!gTypeFound) {
339	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
340	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
341	>	}
342	>
343	>	}
344	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
345	>	groupColToGtype.resize(nGroupsInCol_);
346	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
347	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
348	>	for (vector<int>::iterator jb = atomListCol.begin();
349	>	jb != atomListCol.end(); ++jb) {
350	>	int atom2 = (*jb);
351	>	atid = identsCol[atom2];
352	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
353	>	groupCutoffCol[cg2] = atypeCutoff[atid];
354	>	}
355	>	}
356	>	bool gTypeFound = false;
357	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
358	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
359	>	groupColToGtype[cg2] = gt;
360	>	gTypeFound = true;
361	>	}
362	>	}
363	>	if (!gTypeFound) {
364	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
365	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
366	>	}
367	>	}
368	>	#else
369	>
370	>	vector<RealType> groupCutoff(nGroups_, 0.0);
371	>	groupToGtype.resize(nGroups_);
372	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
373	>	groupCutoff[cg1] = 0.0;
374	>	vector<int> atomList = getAtomsInGroupRow(cg1);
375	>	for (vector<int>::iterator ia = atomList.begin();
376	>	ia != atomList.end(); ++ia) {
377	>	int atom1 = (*ia);
378	>	atid = idents[atom1];
379	>	if (atypeCutoff[atid] > groupCutoff[cg1])
380	>	groupCutoff[cg1] = atypeCutoff[atid];
381	>	}
382	>
383	>	bool gTypeFound = false;
384	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
386	>	groupToGtype[cg1] = gt;
387	>	gTypeFound = true;
388	>	}
389	>	}
390	>	if (!gTypeFound) {
391	>	gTypeCutoffs.push_back( groupCutoff[cg1] );
392	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393	>	}
394	>	}
395		#endif
396	+
397	+	// Now we find the maximum group cutoff value present in the simulation
398	+
399	+	RealType groupMax = *max_element(gTypeCutoffs.begin(),
400	+	gTypeCutoffs.end());
401	+
402	+	#ifdef IS_MPI
403	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
404	+	MPI::MAX);
405	+	#endif
406	+
407	+	RealType tradRcut = groupMax;
408	+
409	+	for (int i = 0; i < gTypeCutoffs.size();  i++) {
410	+	for (int j = 0; j < gTypeCutoffs.size();  j++) {
411	+	RealType thisRcut;
412	+	switch(cutoffPolicy_) {
413	+	case TRADITIONAL:
414	+	thisRcut = tradRcut;
415	+	break;
416	+	case MIX:
417	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
418	+	break;
419	+	case MAX:
420	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
421	+	break;
422	+	default:
423	+	sprintf(painCave.errMsg,
424	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
425	+	"hit an unknown cutoff policy!\n");
426	+	painCave.severity = OPENMD_ERROR;
427	+	painCave.isFatal = 1;
428	+	simError();
429	+	break;
430	+	}
431	+
432	+	pair<int,int> key = make_pair(i,j);
433	+	gTypeCutoffMap[key].first = thisRcut;
434	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
435	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
436	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
437	+	// sanity check
438	+
439	+	if (userChoseCutoff_) {
440	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
441	+	sprintf(painCave.errMsg,
442	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
443	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
444	+	painCave.severity = OPENMD_ERROR;
445	+	painCave.isFatal = 1;
446	+	simError();
447	+	}
448	+	}
449	+	}
450	+	}
451		}
452	+
453	+
454	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
455	+	int i, j;
456	+	#ifdef IS_MPI
457	+	i = groupRowToGtype[cg1];
458	+	j = groupColToGtype[cg2];
459	+	#else
460	+	i = groupToGtype[cg1];
461	+	j = groupToGtype[cg2];
462	+	#endif
463	+	return gTypeCutoffMap[make_pair(i,j)];
464	+	}
465	+
466	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
467	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
468	+	if (toposForAtom[atom1][j] == atom2)
469	+	return topoDist[atom1][j];
470	+	}
471	+	return 0;
472	+	}
473	+
474	+	void ForceMatrixDecomposition::zeroWorkArrays() {
475	+	pairwisePot = 0.0;
476	+	embeddingPot = 0.0;
477	+
478	+	#ifdef IS_MPI
479	+	if (storageLayout_ & DataStorage::dslForce) {
480	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
481	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
482	+	}
483	+
484	+	if (storageLayout_ & DataStorage::dslTorque) {
485	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
486	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
487	+	}
488
489	+	fill(pot_row.begin(), pot_row.end(),
490	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
491
492	+	fill(pot_col.begin(), pot_col.end(),
493	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
494
495	+	if (storageLayout_ & DataStorage::dslParticlePot) {
496	+	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
497	+	0.0);
498	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
499	+	0.0);
500	+	}
501	+
502	+	if (storageLayout_ & DataStorage::dslDensity) {
503	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
504	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
505	+	}
506	+
507	+	if (storageLayout_ & DataStorage::dslFunctional) {
508	+	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
509	+	0.0);
510	+	fill(atomColData.functional.begin(), atomColData.functional.end(),
511	+	0.0);
512	+	}
513	+
514	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
515	+	fill(atomRowData.functionalDerivative.begin(),
516	+	atomRowData.functionalDerivative.end(), 0.0);
517	+	fill(atomColData.functionalDerivative.begin(),
518	+	atomColData.functionalDerivative.end(), 0.0);
519	+	}
520	+
521	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
522	+	fill(atomRowData.skippedCharge.begin(),
523	+	atomRowData.skippedCharge.end(), 0.0);
524	+	fill(atomColData.skippedCharge.begin(),
525	+	atomColData.skippedCharge.end(), 0.0);
526	+	}
527	+
528	+	if (storageLayout_ & DataStorage::dslElectricField) {
529	+	fill(atomRowData.electricField.begin(),
530	+	atomRowData.electricField.end(), V3Zero);
531	+	fill(atomColData.electricField.begin(),
532	+	atomColData.electricField.end(), V3Zero);
533	+	}
534	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
535	+	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
536	+	0.0);
537	+	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
538	+	0.0);
539	+	}
540	+
541	+	#endif
542	+	// even in parallel, we need to zero out the local arrays:
543	+
544	+	if (storageLayout_ & DataStorage::dslParticlePot) {
545	+	fill(snap_->atomData.particlePot.begin(),
546	+	snap_->atomData.particlePot.end(), 0.0);
547	+	}
548	+
549	+	if (storageLayout_ & DataStorage::dslDensity) {
550	+	fill(snap_->atomData.density.begin(),
551	+	snap_->atomData.density.end(), 0.0);
552	+	}
553	+
554	+	if (storageLayout_ & DataStorage::dslFunctional) {
555	+	fill(snap_->atomData.functional.begin(),
556	+	snap_->atomData.functional.end(), 0.0);
557	+	}
558	+
559	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
560	+	fill(snap_->atomData.functionalDerivative.begin(),
561	+	snap_->atomData.functionalDerivative.end(), 0.0);
562	+	}
563	+
564	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
565	+	fill(snap_->atomData.skippedCharge.begin(),
566	+	snap_->atomData.skippedCharge.end(), 0.0);
567	+	}
568	+
569	+	if (storageLayout_ & DataStorage::dslElectricField) {
570	+	fill(snap_->atomData.electricField.begin(),
571	+	snap_->atomData.electricField.end(), V3Zero);
572	+	}
573	+	}
574	+
575	+
576		void ForceMatrixDecomposition::distributeData()  {
577		snap_ = sman_->getCurrentSnapshot();
578		storageLayout_ = sman_->getStorageLayout();
579		#ifdef IS_MPI
580
581		// gather up the atomic positions
582	<	AtomCommVectorRow->gather(snap_->atomData.position,
582	>	AtomPlanVectorRow->gather(snap_->atomData.position,
583		atomRowData.position);
584	<	AtomCommVectorColumn->gather(snap_->atomData.position,
584	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
585		atomColData.position);
586
587		// gather up the cutoff group positions
588	<	cgCommVectorRow->gather(snap_->cgData.position,
588	>
589	>	cgPlanVectorRow->gather(snap_->cgData.position,
590		cgRowData.position);
591	<	cgCommVectorColumn->gather(snap_->cgData.position,
591	>
592	>	cgPlanVectorColumn->gather(snap_->cgData.position,
593		cgColData.position);
594	+
595
596		// if needed, gather the atomic rotation matrices
597		if (storageLayout_ & DataStorage::dslAmat) {
598	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
598	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
599		atomRowData.aMat);
600	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
600	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
601		atomColData.aMat);
602		}
603
604		// if needed, gather the atomic eletrostatic frames
605		if (storageLayout_ & DataStorage::dslElectroFrame) {
606	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
606	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
607		atomRowData.electroFrame);
608	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
608	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
609		atomColData.electroFrame);
610		}
611	+
612	+	// if needed, gather the atomic fluctuating charge values
613	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
614	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
615	+	atomRowData.flucQPos);
616	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
617	+	atomColData.flucQPos);
618	+	}
619	+
620		#endif
621		}
622
623	+	/* collects information obtained during the pre-pair loop onto local
624	+	* data structures.
625	+	*/
626		void ForceMatrixDecomposition::collectIntermediateData() {
627		snap_ = sman_->getCurrentSnapshot();
628		storageLayout_ = sman_->getStorageLayout();
#	Line 163 | Line 630 | namespace OpenMD {
630
631		if (storageLayout_ & DataStorage::dslDensity) {
632
633	<	AtomCommRealRow->scatter(atomRowData.density,
633	>	AtomPlanRealRow->scatter(atomRowData.density,
634		snap_->atomData.density);
635
636		int n = snap_->atomData.density.size();
637	<	std::vector<RealType> rho_tmp(n, 0.0);
638	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
637	>	vector<RealType> rho_tmp(n, 0.0);
638	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
639		for (int i = 0; i < n; i++)
640		snap_->atomData.density[i] += rho_tmp[i];
641		}
642	+
643	+	if (storageLayout_ & DataStorage::dslElectricField) {
644	+
645	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
646	+	snap_->atomData.electricField);
647	+
648	+	int n = snap_->atomData.electricField.size();
649	+	vector<Vector3d> field_tmp(n, V3Zero);
650	+	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
651	+	for (int i = 0; i < n; i++)
652	+	snap_->atomData.electricField[i] += field_tmp[i];
653	+	}
654		#endif
655		}
656	<
656	>
657	>	/*
658	>	* redistributes information obtained during the pre-pair loop out to
659	>	* row and column-indexed data structures
660	>	*/
661		void ForceMatrixDecomposition::distributeIntermediateData() {
662		snap_ = sman_->getCurrentSnapshot();
663		storageLayout_ = sman_->getStorageLayout();
664		#ifdef IS_MPI
665		if (storageLayout_ & DataStorage::dslFunctional) {
666	<	AtomCommRealRow->gather(snap_->atomData.functional,
666	>	AtomPlanRealRow->gather(snap_->atomData.functional,
667		atomRowData.functional);
668	<	AtomCommRealColumn->gather(snap_->atomData.functional,
668	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
669		atomColData.functional);
670		}
671
672		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
673	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
673	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
674		atomRowData.functionalDerivative);
675	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
675	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
676		atomColData.functionalDerivative);
677		}
678		#endif
#	Line 203 | Line 686 | namespace OpenMD {
686		int n = snap_->atomData.force.size();
687		vector<Vector3d> frc_tmp(n, V3Zero);
688
689	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
689	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
690		for (int i = 0; i < n; i++) {
691		snap_->atomData.force[i] += frc_tmp[i];
692		frc_tmp[i] = 0.0;
693		}
694
695	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
696	<	for (int i = 0; i < n; i++)
695	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
696	>	for (int i = 0; i < n; i++) {
697		snap_->atomData.force[i] += frc_tmp[i];
698	<
699	<
698	>	}
699	>
700		if (storageLayout_ & DataStorage::dslTorque) {
701
702	<	int nt = snap_->atomData.force.size();
702	>	int nt = snap_->atomData.torque.size();
703		vector<Vector3d> trq_tmp(nt, V3Zero);
704
705	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
706	<	for (int i = 0; i < n; i++) {
705	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
706	>	for (int i = 0; i < nt; i++) {
707		snap_->atomData.torque[i] += trq_tmp[i];
708		trq_tmp[i] = 0.0;
709		}
710
711	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
712	<	for (int i = 0; i < n; i++)
711	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
712	>	for (int i = 0; i < nt; i++)
713		snap_->atomData.torque[i] += trq_tmp[i];
714		}
715	+
716	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
717	+
718	+	int ns = snap_->atomData.skippedCharge.size();
719	+	vector<RealType> skch_tmp(ns, 0.0);
720	+
721	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
722	+	for (int i = 0; i < ns; i++) {
723	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
724	+	skch_tmp[i] = 0.0;
725	+	}
726	+
727	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
728	+	for (int i = 0; i < ns; i++)
729	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
730	+
731	+	}
732
733	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
734	+
735	+	int nq = snap_->atomData.flucQFrc.size();
736	+	vector<RealType> fqfrc_tmp(nq, 0.0);
737	+
738	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
739	+	for (int i = 0; i < nq; i++) {
740	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
741	+	fqfrc_tmp[i] = 0.0;
742	+	}
743	+
744	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
745	+	for (int i = 0; i < nq; i++)
746	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
747	+
748	+	}
749	+
750		nLocal_ = snap_->getNumberOfAtoms();
751
752	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
753	<	vector<RealType> (nLocal_, 0.0));
752	>	vector<potVec> pot_temp(nLocal_,
753	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
754	>
755	>	// scatter/gather pot_row into the members of my column
756	>
757	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
758	>
759	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
760	>	pairwisePot += pot_temp[ii];
761
762	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
763	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
764	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
765	<	pot_local[i] += pot_temp[i][ii];
766	<	}
762	>	fill(pot_temp.begin(), pot_temp.end(),
763	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
764	>
765	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
766	>
767	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
768	>	pairwisePot += pot_temp[ii];
769	>
770	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
771	>	RealType ploc1 = pairwisePot[ii];
772	>	RealType ploc2 = 0.0;
773	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
774	>	pairwisePot[ii] = ploc2;
775		}
776	+
777	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
778	+	RealType ploc1 = embeddingPot[ii];
779	+	RealType ploc2 = 0.0;
780	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
781	+	embeddingPot[ii] = ploc2;
782	+	}
783	+
784		#endif
785	+
786		}
787
788	+	int ForceMatrixDecomposition::getNAtomsInRow() {
789	+	#ifdef IS_MPI
790	+	return nAtomsInRow_;
791	+	#else
792	+	return nLocal_;
793	+	#endif
794	+	}
795	+
796	+	/**
797	+	* returns the list of atoms belonging to this group.
798	+	*/
799	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
800	+	#ifdef IS_MPI
801	+	return groupListRow_[cg1];
802	+	#else
803	+	return groupList_[cg1];
804	+	#endif
805	+	}
806	+
807	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
808	+	#ifdef IS_MPI
809	+	return groupListCol_[cg2];
810	+	#else
811	+	return groupList_[cg2];
812	+	#endif
813	+	}
814
815		Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
816		Vector3d d;
#	Line 285 | Line 852 | namespace OpenMD {
852		snap_->wrapVector(d);
853		return d;
854		}
855	+
856	+	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
857	+	#ifdef IS_MPI
858	+	return massFactorsRow[atom1];
859	+	#else
860	+	return massFactors[atom1];
861	+	#endif
862	+	}
863	+
864	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
865	+	#ifdef IS_MPI
866	+	return massFactorsCol[atom2];
867	+	#else
868	+	return massFactors[atom2];
869	+	#endif
870	+
871	+	}
872
873		Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
874		Vector3d d;
#	Line 297 | Line 881 | namespace OpenMD {
881
882		snap_->wrapVector(d);
883		return d;
884	+	}
885	+
886	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
887	+	return excludesForAtom[atom1];
888	+	}
889	+
890	+	/**
891	+	* We need to exclude some overcounted interactions that result from
892	+	* the parallel decomposition.
893	+	*/
894	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
895	+	int unique_id_1, unique_id_2;
896	+
897	+	#ifdef IS_MPI
898	+	// in MPI, we have to look up the unique IDs for each atom
899	+	unique_id_1 = AtomRowToGlobal[atom1];
900	+	unique_id_2 = AtomColToGlobal[atom2];
901	+	#else
902	+	unique_id_1 = AtomLocalToGlobal[atom1];
903	+	unique_id_2 = AtomLocalToGlobal[atom2];
904	+	#endif
905	+
906	+	if (unique_id_1 == unique_id_2) return true;
907	+
908	+	#ifdef IS_MPI
909	+	// this prevents us from doing the pair on multiple processors
910	+	if (unique_id_1 < unique_id_2) {
911	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
912	+	} else {
913	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
914	+	}
915	+	#endif
916	+
917	+	return false;
918		}
919
920	+	/**
921	+	* We need to handle the interactions for atoms who are involved in
922	+	* the same rigid body as well as some short range interactions
923	+	* (bonds, bends, torsions) differently from other interactions.
924	+	* We'll still visit the pairwise routines, but with a flag that
925	+	* tells those routines to exclude the pair from direct long range
926	+	* interactions.  Some indirect interactions (notably reaction
927	+	* field) must still be handled for these pairs.
928	+	*/
929	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
930	+
931	+	// excludesForAtom was constructed to use row/column indices in the MPI
932	+	// version, and to use local IDs in the non-MPI version:
933	+
934	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
935	+	i != excludesForAtom[atom1].end(); ++i) {
936	+	if ( (*i) == atom2 ) return true;
937	+	}
938	+
939	+	return false;
940	+	}
941	+
942	+
943		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
944		#ifdef IS_MPI
945		atomRowData.force[atom1] += fg;
#	Line 316 | Line 957 | namespace OpenMD {
957		}
958
959		// filling interaction blocks with pointers
960	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
961	<	InteractionData idat;
960	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
961	>	int atom1, int atom2) {
962
963	+	idat.excluded = excludeAtomPair(atom1, atom2);
964	+
965		#ifdef IS_MPI
966	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
967	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
968	+	//                         ff_->getAtomType(identsCol[atom2]) );
969	+
970		if (storageLayout_ & DataStorage::dslAmat) {
971		idat.A1 = &(atomRowData.aMat[atom1]);
972		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 340 | Line 987 | namespace OpenMD {
987		idat.rho2 = &(atomColData.density[atom2]);
988		}
989
990	+	if (storageLayout_ & DataStorage::dslFunctional) {
991	+	idat.frho1 = &(atomRowData.functional[atom1]);
992	+	idat.frho2 = &(atomColData.functional[atom2]);
993	+	}
994	+
995		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
996		idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
997		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
998		}
999	+
1000	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1001	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1002	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1003	+	}
1004	+
1005	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1006	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1007	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1008	+	}
1009	+
1010		#else
1011	+
1012	+
1013	+	// cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1014	+	// cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1015	+	// cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1016	+
1017	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1018	+	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1019	+	//                         ff_->getAtomType(idents[atom2]) );
1020	+
1021		if (storageLayout_ & DataStorage::dslAmat) {
1022		idat.A1 = &(snap_->atomData.aMat[atom1]);
1023		idat.A2 = &(snap_->atomData.aMat[atom2]);
#	Line 360 | Line 1033 | namespace OpenMD {
1033		idat.t2 = &(snap_->atomData.torque[atom2]);
1034		}
1035
1036	<	if (storageLayout_ & DataStorage::dslDensity) {
1036	>	if (storageLayout_ & DataStorage::dslDensity) {
1037		idat.rho1 = &(snap_->atomData.density[atom1]);
1038		idat.rho2 = &(snap_->atomData.density[atom2]);
1039		}
1040
1041	+	if (storageLayout_ & DataStorage::dslFunctional) {
1042	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1043	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1044	+	}
1045	+
1046		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1047		idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1048		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1049		}
1050	+
1051	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1052	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1053	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1054	+	}
1055	+
1056	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1057	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1058	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1059	+	}
1060		#endif
373	–	return idat;
1061		}
1062
1063	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1064	<
378	<	InteractionData idat;
1063	>
1064	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1065		#ifdef IS_MPI
1066	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1067	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1068	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1069	<	}
1070	<	if (storageLayout_ & DataStorage::dslTorque) {
1071	<	idat.t1 = &(atomRowData.torque[atom1]);
1072	<	idat.t2 = &(atomColData.torque[atom2]);
387	<	}
388	<	if (storageLayout_ & DataStorage::dslForce) {
389	<	idat.t1 = &(atomRowData.force[atom1]);
390	<	idat.t2 = &(atomColData.force[atom2]);
391	<	}
1066	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1067	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1068	>
1069	>	atomRowData.force[atom1] += *(idat.f1);
1070	>	atomColData.force[atom2] -= *(idat.f1);
1071	>
1072	>	// should particle pot be done here also?
1073		#else
1074	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1075	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1076	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1074	>	pairwisePot += *(idat.pot);
1075	>
1076	>	snap_->atomData.force[atom1] += *(idat.f1);
1077	>	snap_->atomData.force[atom2] -= *(idat.f1);
1078	>
1079	>	if (idat.doParticlePot) {
1080	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1081	>	snap_->atomData.particlePot[atom2] -= *(idat.vpair) * *(idat.sw);
1082		}
1083	<	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	<	}
1083	>
1084		#endif
1085
1086		}
1087
409	–
410	–
411	–
1088		/*
1089		* buildNeighborList
1090		*
#	Line 418 | Line 1094 | namespace OpenMD {
1094		vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1095
1096		vector<pair<int, int> > neighborList;
1097	+	groupCutoffs cuts;
1098	+	bool doAllPairs = false;
1099	+
1100		#ifdef IS_MPI
1101		cellListRow_.clear();
1102		cellListCol_.clear();
#	Line 425 | Line 1104 | namespace OpenMD {
1104		cellList_.clear();
1105		#endif
1106
1107	<	// dangerous to not do error checking.
429	<	RealType rCut_;
430	<
431	<	RealType rList_ = (rCut_ + skinThickness_);
1107	>	RealType rList_ = (largestRcut_ + skinThickness_);
1108		RealType rl2 = rList_ * rList_;
1109		Snapshot* snap_ = sman_->getCurrentSnapshot();
1110		Mat3x3d Hmat = snap_->getHmat();
#	Line 440 | Line 1116 | namespace OpenMD {
1116		nCells_.y() = (int) ( Hy.length() )/ rList_;
1117		nCells_.z() = (int) ( Hz.length() )/ rList_;
1118
1119	+	// handle small boxes where the cell offsets can end up repeating cells
1120	+
1121	+	if (nCells_.x() < 3) doAllPairs = true;
1122	+	if (nCells_.y() < 3) doAllPairs = true;
1123	+	if (nCells_.z() < 3) doAllPairs = true;
1124	+
1125		Mat3x3d invHmat = snap_->getInvHmat();
1126		Vector3d rs, scaled, dr;
1127		Vector3i whichCell;
1128		int cellIndex;
1129	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1130
1131		#ifdef IS_MPI
1132	<	for (int i = 0; i < nGroupsInRow_; i++) {
1133	<	rs = cgRowData.position[i];
1134	<	// scaled positions relative to the box vectors
1135	<	scaled = invHmat * rs;
1136	<	// wrap the vector back into the unit box by subtracting integer box
454	<	// numbers
455	<	for (int j = 0; j < 3; j++)
456	<	scaled[j] -= roundMe(scaled[j]);
457	<
458	<	// find xyz-indices of cell that cutoffGroup is in.
459	<	whichCell.x() = nCells_.x() * scaled.x();
460	<	whichCell.y() = nCells_.y() * scaled.y();
461	<	whichCell.z() = nCells_.z() * scaled.z();
1132	>	cellListRow_.resize(nCtot);
1133	>	cellListCol_.resize(nCtot);
1134	>	#else
1135	>	cellList_.resize(nCtot);
1136	>	#endif
1137
1138	<	// find single index of this cell:
1139	<	cellIndex = Vlinear(whichCell, nCells_);
465	<	// add this cutoff group to the list of groups in this cell;
466	<	cellListRow_[cellIndex].push_back(i);
467	<	}
1138	>	if (!doAllPairs) {
1139	>	#ifdef IS_MPI
1140
1141	<	for (int i = 0; i < nGroupsInCol_; i++) {
1142	<	rs = cgColData.position[i];
1143	<	// scaled positions relative to the box vectors
1144	<	scaled = invHmat * rs;
1145	<	// wrap the vector back into the unit box by subtracting integer box
1146	<	// numbers
1147	<	for (int j = 0; j < 3; j++)
1148	<	scaled[j] -= roundMe(scaled[j]);
1149	<
1150	<	// find xyz-indices of cell that cutoffGroup is in.
1151	<	whichCell.x() = nCells_.x() * scaled.x();
1152	<	whichCell.y() = nCells_.y() * scaled.y();
1153	<	whichCell.z() = nCells_.z() * scaled.z();
1154	<
1155	<	// find single index of this cell:
1156	<	cellIndex = Vlinear(whichCell, nCells_);
1157	<	// add this cutoff group to the list of groups in this cell;
1158	<	cellListCol_[cellIndex].push_back(i);
1159	<	}
1141	>	for (int i = 0; i < nGroupsInRow_; i++) {
1142	>	rs = cgRowData.position[i];
1143	>
1144	>	// scaled positions relative to the box vectors
1145	>	scaled = invHmat * rs;
1146	>
1147	>	// wrap the vector back into the unit box by subtracting integer box
1148	>	// numbers
1149	>	for (int j = 0; j < 3; j++) {
1150	>	scaled[j] -= roundMe(scaled[j]);
1151	>	scaled[j] += 0.5;
1152	>	}
1153	>
1154	>	// find xyz-indices of cell that cutoffGroup is in.
1155	>	whichCell.x() = nCells_.x() * scaled.x();
1156	>	whichCell.y() = nCells_.y() * scaled.y();
1157	>	whichCell.z() = nCells_.z() * scaled.z();
1158	>
1159	>	// find single index of this cell:
1160	>	cellIndex = Vlinear(whichCell, nCells_);
1161	>
1162	>	// add this cutoff group to the list of groups in this cell;
1163	>	cellListRow_[cellIndex].push_back(i);
1164	>	}
1165	>	for (int i = 0; i < nGroupsInCol_; i++) {
1166	>	rs = cgColData.position[i];
1167	>
1168	>	// scaled positions relative to the box vectors
1169	>	scaled = invHmat * rs;
1170	>
1171	>	// wrap the vector back into the unit box by subtracting integer box
1172	>	// numbers
1173	>	for (int j = 0; j < 3; j++) {
1174	>	scaled[j] -= roundMe(scaled[j]);
1175	>	scaled[j] += 0.5;
1176	>	}
1177	>
1178	>	// find xyz-indices of cell that cutoffGroup is in.
1179	>	whichCell.x() = nCells_.x() * scaled.x();
1180	>	whichCell.y() = nCells_.y() * scaled.y();
1181	>	whichCell.z() = nCells_.z() * scaled.z();
1182	>
1183	>	// find single index of this cell:
1184	>	cellIndex = Vlinear(whichCell, nCells_);
1185	>
1186	>	// add this cutoff group to the list of groups in this cell;
1187	>	cellListCol_[cellIndex].push_back(i);
1188	>	}
1189	>
1190		#else
1191	<	for (int i = 0; i < nGroups_; i++) {
1192	<	rs = snap_->cgData.position[i];
1193	<	// scaled positions relative to the box vectors
1194	<	scaled = invHmat * rs;
1195	<	// wrap the vector back into the unit box by subtracting integer box
1196	<	// numbers
1197	<	for (int j = 0; j < 3; j++)
1198	<	scaled[j] -= roundMe(scaled[j]);
1191	>	for (int i = 0; i < nGroups_; i++) {
1192	>	rs = snap_->cgData.position[i];
1193	>
1194	>	// scaled positions relative to the box vectors
1195	>	scaled = invHmat * rs;
1196	>
1197	>	// wrap the vector back into the unit box by subtracting integer box
1198	>	// numbers
1199	>	for (int j = 0; j < 3; j++) {
1200	>	scaled[j] -= roundMe(scaled[j]);
1201	>	scaled[j] += 0.5;
1202	>	}
1203	>
1204	>	// find xyz-indices of cell that cutoffGroup is in.
1205	>	whichCell.x() = nCells_.x() * scaled.x();
1206	>	whichCell.y() = nCells_.y() * scaled.y();
1207	>	whichCell.z() = nCells_.z() * scaled.z();
1208	>
1209	>	// find single index of this cell:
1210	>	cellIndex = Vlinear(whichCell, nCells_);
1211	>
1212	>	// add this cutoff group to the list of groups in this cell;
1213	>	cellList_[cellIndex].push_back(i);
1214	>	}
1215
498	–	// find xyz-indices of cell that cutoffGroup is in.
499	–	whichCell.x() = nCells_.x() * scaled.x();
500	–	whichCell.y() = nCells_.y() * scaled.y();
501	–	whichCell.z() = nCells_.z() * scaled.z();
502	–
503	–	// find single index of this cell:
504	–	cellIndex = Vlinear(whichCell, nCells_);
505	–	// add this cutoff group to the list of groups in this cell;
506	–	cellList_[cellIndex].push_back(i);
507	–	}
1216		#endif
1217
1218	<
1219	<
1220	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1221	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1222	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
515	<	Vector3i m1v(m1x, m1y, m1z);
516	<	int m1 = Vlinear(m1v, nCells_);
517	<
518	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
519	<	os != cellOffsets_.end(); ++os) {
1218	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1219	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1220	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1221	>	Vector3i m1v(m1x, m1y, m1z);
1222	>	int m1 = Vlinear(m1v, nCells_);
1223
1224	<	Vector3i m2v = m1v + (*os);
1225	<
1226	<	if (m2v.x() >= nCells_.x()) {
1227	<	m2v.x() = 0;
1228	<	} else if (m2v.x() < 0) {
526	<	m2v.x() = nCells_.x() - 1;
527	<	}
528	<
529	<	if (m2v.y() >= nCells_.y()) {
530	<	m2v.y() = 0;
531	<	} else if (m2v.y() < 0) {
532	<	m2v.y() = nCells_.y() - 1;
533	<	}
534	<
535	<	if (m2v.z() >= nCells_.z()) {
536	<	m2v.z() = 0;
537	<	} else if (m2v.z() < 0) {
538	<	m2v.z() = nCells_.z() - 1;
539	<	}
540	<
541	<	int m2 = Vlinear (m2v, nCells_);
1224	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1225	>	os != cellOffsets_.end(); ++os) {
1226	>
1227	>	Vector3i m2v = m1v + (*os);
1228	>
1229
1230	<	#ifdef IS_MPI
1231	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1232	<	j1 != cellListRow_[m1].end(); ++j1) {
1233	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1234	<	j2 != cellListCol_[m2].end(); ++j2) {
1235	<
1236	<	// Always do this if we're in different cells or if
1237	<	// we're in the same cell and the global index of the
1238	<	// j2 cutoff group is less than the j1 cutoff group
1230	>	if (m2v.x() >= nCells_.x()) {
1231	>	m2v.x() = 0;
1232	>	} else if (m2v.x() < 0) {
1233	>	m2v.x() = nCells_.x() - 1;
1234	>	}
1235	>
1236	>	if (m2v.y() >= nCells_.y()) {
1237	>	m2v.y() = 0;
1238	>	} else if (m2v.y() < 0) {
1239	>	m2v.y() = nCells_.y() - 1;
1240	>	}
1241	>
1242	>	if (m2v.z() >= nCells_.z()) {
1243	>	m2v.z() = 0;
1244	>	} else if (m2v.z() < 0) {
1245	>	m2v.z() = nCells_.z() - 1;
1246	>	}
1247
1248	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1248	>	int m2 = Vlinear (m2v, nCells_);
1249	>
1250	>	#ifdef IS_MPI
1251	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1252	>	j1 != cellListRow_[m1].end(); ++j1) {
1253	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1254	>	j2 != cellListCol_[m2].end(); ++j2) {
1255	>
1256	>	// In parallel, we need to visit *all* pairs of row
1257	>	// & column indicies and will divide labor in the
1258	>	// force evaluation later.
1259		dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1260		snap_->wrapVector(dr);
1261	<	if (dr.lengthSquare() < rl2) {
1261	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1262	>	if (dr.lengthSquare() < cuts.third) {
1263		neighborList.push_back(make_pair((*j1), (*j2)));
1264	<	}
1264	>	}
1265		}
1266		}
561	–	}
1267		#else
1268	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1269	<	j1 != cellList_[m1].end(); ++j1) {
1270	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1271	<	j2 != cellList_[m2].end(); ++j2) {
1272	<
1273	<	// Always do this if we're in different cells or if
1274	<	// we're in the same cell and the global index of the
1275	<	// j2 cutoff group is less than the j1 cutoff group
1268	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1269	>	j1 != cellList_[m1].end(); ++j1) {
1270	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1271	>	j2 != cellList_[m2].end(); ++j2) {
1272	>
1273	>	// Always do this if we're in different cells or if
1274	>	// we're in the same cell and the global index of
1275	>	// the j2 cutoff group is greater than or equal to
1276	>	// the j1 cutoff group.  Note that Rappaport's code
1277	>	// has a "less than" conditional here, but that
1278	>	// deals with atom-by-atom computation.  OpenMD
1279	>	// allows atoms within a single cutoff group to
1280	>	// interact with each other.
1281
1282	<	if (m2 != m1 || (*j2) < (*j1)) {
1283	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1284	<	snap_->wrapVector(dr);
1285	<	if (dr.lengthSquare() < rl2) {
1286	<	neighborList.push_back(make_pair((*j1), (*j2)));
1282	>
1283	>
1284	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1285	>
1286	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1287	>	snap_->wrapVector(dr);
1288	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1289	>	if (dr.lengthSquare() < cuts.third) {
1290	>	neighborList.push_back(make_pair((*j1), (*j2)));
1291	>	}
1292		}
1293		}
1294		}
580	–	}
1295		#endif
1296	+	}
1297		}
1298		}
1299		}
1300	+	} else {
1301	+	// branch to do all cutoff group pairs
1302	+	#ifdef IS_MPI
1303	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1304	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1305	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1306	+	snap_->wrapVector(dr);
1307	+	cuts = getGroupCutoffs( j1, j2 );
1308	+	if (dr.lengthSquare() < cuts.third) {
1309	+	neighborList.push_back(make_pair(j1, j2));
1310	+	}
1311	+	}
1312	+	}
1313	+	#else
1314	+	// include all groups here.
1315	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1316	+	// include self group interactions j2 == j1
1317	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1318	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1319	+	snap_->wrapVector(dr);
1320	+	cuts = getGroupCutoffs( j1, j2 );
1321	+	if (dr.lengthSquare() < cuts.third) {
1322	+	neighborList.push_back(make_pair(j1, j2));
1323	+	}
1324	+	}
1325	+	}
1326	+	#endif
1327		}
1328	<
1328	>
1329		// save the local cutoff group positions for the check that is
1330		// done on each loop:
1331		saved_CG_positions_.clear();
1332		for (int i = 0; i < nGroups_; i++)
1333		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1334	<
1334	>
1335		return neighborList;
1336		}
1337		} //end namespace OpenMD

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