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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs.
Revision 1721 by gezelter, Thu May 24 14:17:42 2012 UTC

#	Line 36 | Line 36
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
#	Line 47 | Line 48 | namespace OpenMD {
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		*/
54	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96		ff_ = info_->getForceField();
97		nLocal_ = snap_->getNumberOfAtoms();
98	<
98	>
99		nGroups_ = info_->getNLocalCutoffGroups();
100		// gather the information for atomtype IDs (atids):
101	<	identsLocal = info_->getIdentArray();
101	>	idents = info_->getIdentArray();
102		AtomLocalToGlobal = info_->getGlobalAtomIndices();
103		cgLocalToGlobal = info_->getGlobalGroupIndices();
104		vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67	–	vector<RealType> massFactorsLocal = info_->getMassFactors();
68	–	PairList excludes = info_->getExcludedInteractions();
69	–	PairList oneTwo = info_->getOneTwoInteractions();
70	–	PairList oneThree = info_->getOneThreeInteractions();
71	–	PairList oneFour = info_->getOneFourInteractions();
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_);
77	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
78	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
79	<	AtomCommPotRow = new Communicator<Row,potVec>(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_);
122	<	AtomCommPotColumn = new Communicator<Column,potVec>(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 107 | Line 150 | namespace OpenMD {
150		identsRow.resize(nAtomsInRow_);
151		identsCol.resize(nAtomsInCol_);
152
153	<	AtomCommIntRow->gather(identsLocal, identsRow);
154	<	AtomCommIntColumn->gather(identsLocal, identsCol);
153	>	AtomPlanIntRow->gather(idents, identsRow);
154	>	AtomPlanIntColumn->gather(idents, identsCol);
155
156	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
157	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
158	<
116	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
117	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
156	>	// allocate memory for the parallel objects
157	>	atypesRow.resize(nAtomsInRow_);
158	>	atypesCol.resize(nAtomsInCol_);
159
160	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
161	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
160	>	for (int i = 0; i < nAtomsInRow_; i++)
161	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
162	>	for (int i = 0; i < nAtomsInCol_; i++)
163	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
164
165	+	pot_row.resize(nAtomsInRow_);
166	+	pot_col.resize(nAtomsInCol_);
167	+
168	+	AtomRowToGlobal.resize(nAtomsInRow_);
169	+	AtomColToGlobal.resize(nAtomsInCol_);
170	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
171	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
172	+
173	+	cgRowToGlobal.resize(nGroupsInRow_);
174	+	cgColToGlobal.resize(nGroupsInCol_);
175	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177	+
178	+	massFactorsRow.resize(nAtomsInRow_);
179	+	massFactorsCol.resize(nAtomsInCol_);
180	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
181	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
182	+
183		groupListRow_.clear();
184		groupListRow_.resize(nGroupsInRow_);
185		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 141 | Line 202 | namespace OpenMD {
202		}
203		}
204
205	<	skipsForRowAtom.clear();
206	<	skipsForRowAtom.resize(nAtomsInRow_);
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	<	if (excludes.hasPair(iglob, jglob))
217	<	skipsForRowAtom[i].push_back(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	<	toposForRowAtom.clear();
238	<	toposForRowAtom.resize(nAtomsInRow_);
239	<	for (int i = 0; i < nAtomsInRow_; i++) {
240	<	int iglob = AtomRowToGlobal[i];
241	<	int nTopos = 0;
242	<	for (int j = 0; j < nAtomsInCol_; j++) {
243	<	int jglob = AtomColToGlobal[j];
244	<	if (oneTwo.hasPair(iglob, jglob)) {
245	<	toposForRowAtom[i].push_back(j);
246	<	topoDistRow[i][nTopos] = 1;
247	<	nTopos++;
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		}
167	–	if (oneThree.hasPair(iglob, jglob)) {
168	–	toposForRowAtom[i].push_back(j);
169	–	topoDistRow[i][nTopos] = 2;
170	–	nTopos++;
171	–	}
172	–	if (oneFour.hasPair(iglob, jglob)) {
173	–	toposForRowAtom[i].push_back(j);
174	–	topoDistRow[i][nTopos] = 3;
175	–	nTopos++;
176	–	}
268		}
269		}
179	–
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++) {
#	Line 186 | Line 283 | namespace OpenMD {
283		int aid = AtomLocalToGlobal[j];
284		if (globalGroupMembership[aid] == gid) {
285		groupList_[i].push_back(j);
189	–
286		}
287		}
288		}
289
194	–	skipsForLocalAtom.clear();
195	–	skipsForLocalAtom.resize(nLocal_);
290
291	<	for (int i = 0; i < nLocal_; i++) {
198	<	int iglob = AtomLocalToGlobal[i];
199	<	for (int j = 0; j < nLocal_; j++) {
200	<	int jglob = AtomLocalToGlobal[j];
201	<	if (excludes.hasPair(iglob, jglob))
202	<	skipsForLocalAtom[i].push_back(j);
203	<	}
204	<	}
205	<	toposForLocalAtom.clear();
206	<	toposForLocalAtom.resize(nLocal_);
207	<	for (int i = 0; i < nLocal_; i++) {
208	<	int iglob = AtomLocalToGlobal[i];
209	<	int nTopos = 0;
210	<	for (int j = 0; j < nLocal_; j++) {
211	<	int jglob = AtomLocalToGlobal[j];
212	<	if (oneTwo.hasPair(iglob, jglob)) {
213	<	toposForLocalAtom[i].push_back(j);
214	<	topoDistLocal[i][nTopos] = 1;
215	<	nTopos++;
216	<	}
217	<	if (oneThree.hasPair(iglob, jglob)) {
218	<	toposForLocalAtom[i].push_back(j);
219	<	topoDistLocal[i][nTopos] = 2;
220	<	nTopos++;
221	<	}
222	<	if (oneFour.hasPair(iglob, jglob)) {
223	<	toposForLocalAtom[i].push_back(j);
224	<	topoDistLocal[i][nTopos] = 3;
225	<	nTopos++;
226	<	}
227	<	}
228	<	}
291	>	createGtypeCutoffMap();
292
293		}
294
295		void ForceMatrixDecomposition::createGtypeCutoffMap() {
296	<
296	>
297		RealType tol = 1e-6;
298	+	largestRcut_ = 0.0;
299		RealType rc;
300		int atid;
301		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302	<	vector<RealType> atypeCutoff;
303	<	atypeCutoff.resize( atypes.size() );
304	<
305	<	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
306	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
302	>
303	>	map<int, RealType> atypeCutoff;
304	>
305	>	for (set<AtomType*>::iterator at = atypes.begin();
306	>	at != atypes.end(); ++at){
307		atid = (*at)->getIdent();
308	<	atypeCutoff[atid] = rc;
308	>	if (userChoseCutoff_)
309	>	atypeCutoff[atid] = userCutoff_;
310	>	else
311	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312		}
313	<
313	>
314		vector<RealType> gTypeCutoffs;
248	–
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();
#	Line 275 | Line 342 | namespace OpenMD {
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();
#	Line 298 | Line 366 | namespace OpenMD {
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 = identsLocal[atom1];
379	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
378	>	atid = idents[atom1];
379	>	if (atypeCutoff[atid] > groupCutoff[cg1])
380		groupCutoff[cg1] = atypeCutoff[atid];
311	–	}
381		}
382	<
382	>
383		bool gTypeFound = false;
384		for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
#	Line 318 | Line 387 | namespace OpenMD {
387		gTypeFound = true;
388		}
389		}
390	<	if (!gTypeFound) {
390	>	if (!gTypeFound) {
391		gTypeCutoffs.push_back( groupCutoff[cg1] );
392		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393		}
#	Line 327 | Line 396 | namespace OpenMD {
396
397		// Now we find the maximum group cutoff value present in the simulation
398
399	<	vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
400	<	RealType groupMax = *groupMaxLoc;
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, MPI::MAX);
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++) {
341	<
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();
428	>	simError();
429	>	break;
430		}
431
432		pair<int,int> key = make_pair(i,j);
433		gTypeCutoffMap[key].first = thisRcut;
361	–
434		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
363	–
435		gTypeCutoffMap[key].second = thisRcut*thisRcut;
365	–
436		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
367	–
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 does not match computed group Cutoff\n");
443	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
444		painCave.severity = OPENMD_ERROR;
445		painCave.isFatal = 1;
446		simError();
#	Line 383 | Line 452 | namespace OpenMD {
452
453
454		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
455	<	int i, j;
387	<
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
395	<
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
402	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403	–	longRangePot_[j] = 0.0;
404	–	}
405	–
478		#ifdef IS_MPI
479		if (storageLayout_ & DataStorage::dslForce) {
480		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 418 | Line 490 | namespace OpenMD {
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));
422	<
423	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
493	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
494
495		if (storageLayout_ & DataStorage::dslParticlePot) {
496	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
497	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
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) {
#	Line 433 | Line 505 | namespace OpenMD {
505		}
506
507		if (storageLayout_ & DataStorage::dslFunctional) {
508	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
509	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
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) {
#	Line 444 | Line 518 | namespace OpenMD {
518		atomColData.functionalDerivative.end(), 0.0);
519		}
520
521	<	#else
522	<
521	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
522	>	fill(atomRowData.skippedCharge.begin(),
523	>	atomRowData.skippedCharge.end(), 0.0);
524	>	fill(atomColData.skippedCharge.begin(),
525	>	atomColData.skippedCharge.end(), 0.0);
526	>	}
527	>
528	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
529	>	fill(atomRowData.flucQFrc.begin(),
530	>	atomRowData.flucQFrc.end(), 0.0);
531	>	fill(atomColData.flucQFrc.begin(),
532	>	atomColData.flucQFrc.end(), 0.0);
533	>	}
534	>
535	>	if (storageLayout_ & DataStorage::dslElectricField) {
536	>	fill(atomRowData.electricField.begin(),
537	>	atomRowData.electricField.end(), V3Zero);
538	>	fill(atomColData.electricField.begin(),
539	>	atomColData.electricField.end(), V3Zero);
540	>	}
541	>
542	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
543	>	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
544	>	0.0);
545	>	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
546	>	0.0);
547	>	}
548	>
549	>	#endif
550	>	// even in parallel, we need to zero out the local arrays:
551	>
552		if (storageLayout_ & DataStorage::dslParticlePot) {
553		fill(snap_->atomData.particlePot.begin(),
554		snap_->atomData.particlePot.end(), 0.0);
#	Line 455 | Line 558 | namespace OpenMD {
558		fill(snap_->atomData.density.begin(),
559		snap_->atomData.density.end(), 0.0);
560		}
561	+
562		if (storageLayout_ & DataStorage::dslFunctional) {
563		fill(snap_->atomData.functional.begin(),
564		snap_->atomData.functional.end(), 0.0);
565		}
566	+
567		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
568		fill(snap_->atomData.functionalDerivative.begin(),
569		snap_->atomData.functionalDerivative.end(), 0.0);
570		}
571	<	#endif
572	<
571	>
572	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
573	>	fill(snap_->atomData.skippedCharge.begin(),
574	>	snap_->atomData.skippedCharge.end(), 0.0);
575	>	}
576	>
577	>	if (storageLayout_ & DataStorage::dslElectricField) {
578	>	fill(snap_->atomData.electricField.begin(),
579	>	snap_->atomData.electricField.end(), V3Zero);
580	>	}
581		}
582
583
#	Line 474 | Line 587 | namespace OpenMD {
587		#ifdef IS_MPI
588
589		// gather up the atomic positions
590	<	AtomCommVectorRow->gather(snap_->atomData.position,
590	>	AtomPlanVectorRow->gather(snap_->atomData.position,
591		atomRowData.position);
592	<	AtomCommVectorColumn->gather(snap_->atomData.position,
592	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
593		atomColData.position);
594
595		// gather up the cutoff group positions
596	<	cgCommVectorRow->gather(snap_->cgData.position,
596	>
597	>	cgPlanVectorRow->gather(snap_->cgData.position,
598		cgRowData.position);
599	<	cgCommVectorColumn->gather(snap_->cgData.position,
599	>
600	>	cgPlanVectorColumn->gather(snap_->cgData.position,
601		cgColData.position);
602	+
603
604		// if needed, gather the atomic rotation matrices
605		if (storageLayout_ & DataStorage::dslAmat) {
606	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
606	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
607		atomRowData.aMat);
608	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
608	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
609		atomColData.aMat);
610		}
611
612		// if needed, gather the atomic eletrostatic frames
613		if (storageLayout_ & DataStorage::dslElectroFrame) {
614	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
614	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
615		atomRowData.electroFrame);
616	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
616	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
617		atomColData.electroFrame);
618		}
619	+
620	+	// if needed, gather the atomic fluctuating charge values
621	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
622	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
623	+	atomRowData.flucQPos);
624	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
625	+	atomColData.flucQPos);
626	+	}
627	+
628		#endif
629		}
630
#	Line 513 | Line 638 | namespace OpenMD {
638
639		if (storageLayout_ & DataStorage::dslDensity) {
640
641	<	AtomCommRealRow->scatter(atomRowData.density,
641	>	AtomPlanRealRow->scatter(atomRowData.density,
642		snap_->atomData.density);
643
644		int n = snap_->atomData.density.size();
645		vector<RealType> rho_tmp(n, 0.0);
646	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
646	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
647		for (int i = 0; i < n; i++)
648		snap_->atomData.density[i] += rho_tmp[i];
649		}
650	+
651	+	if (storageLayout_ & DataStorage::dslElectricField) {
652	+
653	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
654	+	snap_->atomData.electricField);
655	+
656	+	int n = snap_->atomData.electricField.size();
657	+	vector<Vector3d> field_tmp(n, V3Zero);
658	+	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
659	+	for (int i = 0; i < n; i++)
660	+	snap_->atomData.electricField[i] += field_tmp[i];
661	+	}
662		#endif
663		}
664
#	Line 534 | Line 671 | namespace OpenMD {
671		storageLayout_ = sman_->getStorageLayout();
672		#ifdef IS_MPI
673		if (storageLayout_ & DataStorage::dslFunctional) {
674	<	AtomCommRealRow->gather(snap_->atomData.functional,
674	>	AtomPlanRealRow->gather(snap_->atomData.functional,
675		atomRowData.functional);
676	<	AtomCommRealColumn->gather(snap_->atomData.functional,
676	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
677		atomColData.functional);
678		}
679
680		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
681	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
681	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
682		atomRowData.functionalDerivative);
683	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
683	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
684		atomColData.functionalDerivative);
685		}
686		#endif
#	Line 557 | Line 694 | namespace OpenMD {
694		int n = snap_->atomData.force.size();
695		vector<Vector3d> frc_tmp(n, V3Zero);
696
697	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
697	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
698		for (int i = 0; i < n; i++) {
699		snap_->atomData.force[i] += frc_tmp[i];
700		frc_tmp[i] = 0.0;
701		}
702
703	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
704	<	for (int i = 0; i < n; i++)
703	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
704	>	for (int i = 0; i < n; i++) {
705		snap_->atomData.force[i] += frc_tmp[i];
706	<
707	<
706	>	}
707	>
708		if (storageLayout_ & DataStorage::dslTorque) {
709
710	<	int nt = snap_->atomData.force.size();
710	>	int nt = snap_->atomData.torque.size();
711		vector<Vector3d> trq_tmp(nt, V3Zero);
712
713	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
714	<	for (int i = 0; i < n; i++) {
713	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
714	>	for (int i = 0; i < nt; i++) {
715		snap_->atomData.torque[i] += trq_tmp[i];
716		trq_tmp[i] = 0.0;
717		}
718
719	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
720	<	for (int i = 0; i < n; i++)
719	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
720	>	for (int i = 0; i < nt; i++)
721		snap_->atomData.torque[i] += trq_tmp[i];
722		}
723	+
724	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
725	+
726	+	int ns = snap_->atomData.skippedCharge.size();
727	+	vector<RealType> skch_tmp(ns, 0.0);
728	+
729	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
730	+	for (int i = 0; i < ns; i++) {
731	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
732	+	skch_tmp[i] = 0.0;
733	+	}
734	+
735	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
736	+	for (int i = 0; i < ns; i++)
737	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
738	+
739	+	}
740
741	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
742	+
743	+	int nq = snap_->atomData.flucQFrc.size();
744	+	vector<RealType> fqfrc_tmp(nq, 0.0);
745	+
746	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
747	+	for (int i = 0; i < nq; i++) {
748	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
749	+	fqfrc_tmp[i] = 0.0;
750	+	}
751	+
752	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
753	+	for (int i = 0; i < nq; i++)
754	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
755	+
756	+	}
757	+
758		nLocal_ = snap_->getNumberOfAtoms();
759
760		vector<potVec> pot_temp(nLocal_,
#	Line 591 | Line 762 | namespace OpenMD {
762
763		// scatter/gather pot_row into the members of my column
764
765	<	AtomCommPotRow->scatter(pot_row, pot_temp);
765	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
766
767		for (int ii = 0;  ii < pot_temp.size(); ii++ )
768	<	pot_local += pot_temp[ii];
768	>	pairwisePot += pot_temp[ii];
769
770		fill(pot_temp.begin(), pot_temp.end(),
771		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
772
773	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
773	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
774
775		for (int ii = 0;  ii < pot_temp.size(); ii++ )
776	<	pot_local += pot_temp[ii];
776	>	pairwisePot += pot_temp[ii];
777
778	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
779	+	RealType ploc1 = pairwisePot[ii];
780	+	RealType ploc2 = 0.0;
781	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
782	+	pairwisePot[ii] = ploc2;
783	+	}
784	+
785	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
786	+	RealType ploc1 = embeddingPot[ii];
787	+	RealType ploc2 = 0.0;
788	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
789	+	embeddingPot[ii] = ploc2;
790	+	}
791	+
792		#endif
793	+
794		}
795
796		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 679 | Line 865 | namespace OpenMD {
865		#ifdef IS_MPI
866		return massFactorsRow[atom1];
867		#else
868	<	return massFactorsLocal[atom1];
868	>	return massFactors[atom1];
869		#endif
870		}
871
#	Line 687 | Line 873 | namespace OpenMD {
873		#ifdef IS_MPI
874		return massFactorsCol[atom2];
875		#else
876	<	return massFactorsLocal[atom2];
876	>	return massFactors[atom2];
877		#endif
878
879		}
#	Line 705 | Line 891 | namespace OpenMD {
891		return d;
892		}
893
894	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
895	<	#ifdef IS_MPI
710	<	return skipsForRowAtom[atom1];
711	<	#else
712	<	return skipsForLocalAtom[atom1];
713	<	#endif
894	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
895	>	return excludesForAtom[atom1];
896		}
897
898		/**
899	<	* There are a number of reasons to skip a pair or a
718	<	* particle. Mostly we do this to exclude atoms who are involved in
719	<	* short range interactions (bonds, bends, torsions), but we also
720	<	* need to exclude some overcounted interactions that result from
899	>	* We need to exclude some overcounted interactions that result from
900		* the parallel decomposition.
901		*/
902		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
903		int unique_id_1, unique_id_2;
904	<
904	>
905		#ifdef IS_MPI
906		// in MPI, we have to look up the unique IDs for each atom
907		unique_id_1 = AtomRowToGlobal[atom1];
908		unique_id_2 = AtomColToGlobal[atom2];
909	+	#else
910	+	unique_id_1 = AtomLocalToGlobal[atom1];
911	+	unique_id_2 = AtomLocalToGlobal[atom2];
912	+	#endif
913
731	–	// this situation should only arise in MPI simulations
914		if (unique_id_1 == unique_id_2) return true;
915	<
915	>
916	>	#ifdef IS_MPI
917		// this prevents us from doing the pair on multiple processors
918		if (unique_id_1 < unique_id_2) {
919		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
920		} else {
921	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
921	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
922		}
740	–	#else
741	–	// in the normal loop, the atom numbers are unique
742	–	unique_id_1 = atom1;
743	–	unique_id_2 = atom2;
923		#endif
924
925	<	#ifdef IS_MPI
747	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748	<	i != skipsForRowAtom[atom1].end(); ++i) {
749	<	if ( (*i) == unique_id_2 ) return true;
750	<	}
751	<	#else
752	<	for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
753	<	i != skipsForLocalAtom[atom1].end(); ++i) {
754	<	if ( (*i) == unique_id_2 ) return true;
755	<	}
756	<	#endif
925	>	return false;
926		}
927
928	<	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
929	<
930	<	#ifdef IS_MPI
931	<	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
932	<	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
933	<	}
934	<	#else
935	<	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
936	<	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
928	>	/**
929	>	* We need to handle the interactions for atoms who are involved in
930	>	* the same rigid body as well as some short range interactions
931	>	* (bonds, bends, torsions) differently from other interactions.
932	>	* We'll still visit the pairwise routines, but with a flag that
933	>	* tells those routines to exclude the pair from direct long range
934	>	* interactions.  Some indirect interactions (notably reaction
935	>	* field) must still be handled for these pairs.
936	>	*/
937	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
938	>
939	>	// excludesForAtom was constructed to use row/column indices in the MPI
940	>	// version, and to use local IDs in the non-MPI version:
941	>
942	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
943	>	i != excludesForAtom[atom1].end(); ++i) {
944	>	if ( (*i) == atom2 ) return true;
945		}
769	–	#endif
946
947	<	// zero is default for unconnected (i.e. normal) pair interactions
772	<	return 0;
947	>	return false;
948		}
949
950	+
951		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
952		#ifdef IS_MPI
953		atomRowData.force[atom1] += fg;
#	Line 789 | Line 965 | namespace OpenMD {
965		}
966
967		// filling interaction blocks with pointers
968	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
969	<	InteractionData idat;
968	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
969	>	int atom1, int atom2) {
970
971	+	idat.excluded = excludeAtomPair(atom1, atom2);
972	+
973		#ifdef IS_MPI
974	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
975	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
976	+	//                         ff_->getAtomType(identsCol[atom2]) );
977
797	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
798	–	ff_->getAtomType(identsCol[atom2]) );
799	–
800	–
978		if (storageLayout_ & DataStorage::dslAmat) {
979		idat.A1 = &(atomRowData.aMat[atom1]);
980		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 833 | Line 1010 | namespace OpenMD {
1010		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1011		}
1012
1013	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1014	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1015	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1016	+	}
1017	+
1018	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1019	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1020	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1021	+	}
1022	+
1023		#else
1024	+
1025
1026	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
1027	<	ff_->getAtomType(identsLocal[atom2]) );
1026	>	// cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1027	>	// cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1028	>	// cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1029
1030	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1031	+	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1032	+	//                         ff_->getAtomType(idents[atom2]) );
1033	+
1034		if (storageLayout_ & DataStorage::dslAmat) {
1035		idat.A1 = &(snap_->atomData.aMat[atom1]);
1036		idat.A2 = &(snap_->atomData.aMat[atom2]);
#	Line 853 | Line 1046 | namespace OpenMD {
1046		idat.t2 = &(snap_->atomData.torque[atom2]);
1047		}
1048
1049	<	if (storageLayout_ & DataStorage::dslDensity) {
1049	>	if (storageLayout_ & DataStorage::dslDensity) {
1050		idat.rho1 = &(snap_->atomData.density[atom1]);
1051		idat.rho2 = &(snap_->atomData.density[atom2]);
1052		}
#	Line 873 | Line 1066 | namespace OpenMD {
1066		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1067		}
1068
1069	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1070	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1071	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1072	+	}
1073	+
1074	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1075	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1076	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1077	+	}
1078	+
1079		#endif
877	–	return idat;
1080		}
1081
1082
1083	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
1083	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1084		#ifdef IS_MPI
1085	<	pot_row[atom1] += 0.5 *  *(idat.pot);
1086	<	pot_col[atom2] += 0.5 *  *(idat.pot);
1085	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1086	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1087
1088		atomRowData.force[atom1] += *(idat.f1);
1089		atomColData.force[atom2] -= *(idat.f1);
888	–	#else
889	–	longRangePot_ += *(idat.pot);
890	–
891	–	snap_->atomData.force[atom1] += *(idat.f1);
892	–	snap_->atomData.force[atom2] -= *(idat.f1);
893	–	#endif
1090
1091	<	}
1091	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1092	>	atomRowData.flucQFrc[atom1] += *(idat.dVdFQ1);
1093	>	atomColData.flucQFrc[atom2] += *(idat.dVdFQ2);
1094	>	}
1095
1096	+	if (storageLayout_ & DataStorage::dslElectricField) {
1097	+	atomRowData.electricField[atom1] += *(idat.eField1);
1098	+	atomColData.electricField[atom2] += *(idat.eField2);
1099	+	}
1100
1101	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1101	>	// should particle pot be done here also?
1102	>	#else
1103	>	pairwisePot += *(idat.pot);
1104
1105	<	InteractionData idat;
1106	<	#ifdef IS_MPI
902	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
903	<	ff_->getAtomType(identsCol[atom2]) );
1105	>	snap_->atomData.force[atom1] += *(idat.f1);
1106	>	snap_->atomData.force[atom2] -= *(idat.f1);
1107
1108	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1109	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1110	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1108	>	if (idat.doParticlePot) {
1109	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1110	>	snap_->atomData.particlePot[atom2] -= *(idat.vpair) * *(idat.sw);
1111		}
1112	<	if (storageLayout_ & DataStorage::dslTorque) {
1113	<	idat.t1 = &(atomRowData.torque[atom1]);
1114	<	idat.t2 = &(atomColData.torque[atom2]);
1112	>
1113	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1114	>	snap_->atomData.flucQFrc[atom1] += *(idat.dVdFQ1);
1115	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1116		}
913	–	#else
914	–	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
915	–	ff_->getAtomType(identsLocal[atom2]) );
1117
1118	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1119	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1120	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1118	>	if (storageLayout_ & DataStorage::dslElectricField) {
1119	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1120	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1121		}
1122	<	if (storageLayout_ & DataStorage::dslTorque) {
1123	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1124	<	idat.t2 = &(snap_->atomData.torque[atom2]);
924	<	}
925	<	#endif
1122	>
1123	>	#endif
1124	>
1125		}
1126
1127		/*
#	Line 935 | Line 1134 | namespace OpenMD {
1134
1135		vector<pair<int, int> > neighborList;
1136		groupCutoffs cuts;
1137	+	bool doAllPairs = false;
1138	+
1139		#ifdef IS_MPI
1140		cellListRow_.clear();
1141		cellListCol_.clear();
#	Line 954 | Line 1155 | namespace OpenMD {
1155		nCells_.y() = (int) ( Hy.length() )/ rList_;
1156		nCells_.z() = (int) ( Hz.length() )/ rList_;
1157
1158	+	// handle small boxes where the cell offsets can end up repeating cells
1159	+
1160	+	if (nCells_.x() < 3) doAllPairs = true;
1161	+	if (nCells_.y() < 3) doAllPairs = true;
1162	+	if (nCells_.z() < 3) doAllPairs = true;
1163	+
1164		Mat3x3d invHmat = snap_->getInvHmat();
1165		Vector3d rs, scaled, dr;
1166		Vector3i whichCell;
1167		int cellIndex;
1168	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1169
1170		#ifdef IS_MPI
1171	<	for (int i = 0; i < nGroupsInRow_; i++) {
1172	<	rs = cgRowData.position[i];
1173	<	// scaled positions relative to the box vectors
1174	<	scaled = invHmat * rs;
1175	<	// wrap the vector back into the unit box by subtracting integer box
968	<	// numbers
969	<	for (int j = 0; j < 3; j++)
970	<	scaled[j] -= roundMe(scaled[j]);
971	<
972	<	// find xyz-indices of cell that cutoffGroup is in.
973	<	whichCell.x() = nCells_.x() * scaled.x();
974	<	whichCell.y() = nCells_.y() * scaled.y();
975	<	whichCell.z() = nCells_.z() * scaled.z();
1171	>	cellListRow_.resize(nCtot);
1172	>	cellListCol_.resize(nCtot);
1173	>	#else
1174	>	cellList_.resize(nCtot);
1175	>	#endif
1176
1177	<	// find single index of this cell:
1178	<	cellIndex = Vlinear(whichCell, nCells_);
979	<	// add this cutoff group to the list of groups in this cell;
980	<	cellListRow_[cellIndex].push_back(i);
981	<	}
1177	>	if (!doAllPairs) {
1178	>	#ifdef IS_MPI
1179
1180	<	for (int i = 0; i < nGroupsInCol_; i++) {
1181	<	rs = cgColData.position[i];
1182	<	// scaled positions relative to the box vectors
1183	<	scaled = invHmat * rs;
1184	<	// wrap the vector back into the unit box by subtracting integer box
1185	<	// numbers
1186	<	for (int j = 0; j < 3; j++)
1187	<	scaled[j] -= roundMe(scaled[j]);
1188	<
1189	<	// find xyz-indices of cell that cutoffGroup is in.
1190	<	whichCell.x() = nCells_.x() * scaled.x();
1191	<	whichCell.y() = nCells_.y() * scaled.y();
1192	<	whichCell.z() = nCells_.z() * scaled.z();
1193	<
1194	<	// find single index of this cell:
1195	<	cellIndex = Vlinear(whichCell, nCells_);
1196	<	// add this cutoff group to the list of groups in this cell;
1197	<	cellListCol_[cellIndex].push_back(i);
1198	<	}
1180	>	for (int i = 0; i < nGroupsInRow_; i++) {
1181	>	rs = cgRowData.position[i];
1182	>
1183	>	// scaled positions relative to the box vectors
1184	>	scaled = invHmat * rs;
1185	>
1186	>	// wrap the vector back into the unit box by subtracting integer box
1187	>	// numbers
1188	>	for (int j = 0; j < 3; j++) {
1189	>	scaled[j] -= roundMe(scaled[j]);
1190	>	scaled[j] += 0.5;
1191	>	}
1192	>
1193	>	// find xyz-indices of cell that cutoffGroup is in.
1194	>	whichCell.x() = nCells_.x() * scaled.x();
1195	>	whichCell.y() = nCells_.y() * scaled.y();
1196	>	whichCell.z() = nCells_.z() * scaled.z();
1197	>
1198	>	// find single index of this cell:
1199	>	cellIndex = Vlinear(whichCell, nCells_);
1200	>
1201	>	// add this cutoff group to the list of groups in this cell;
1202	>	cellListRow_[cellIndex].push_back(i);
1203	>	}
1204	>	for (int i = 0; i < nGroupsInCol_; i++) {
1205	>	rs = cgColData.position[i];
1206	>
1207	>	// scaled positions relative to the box vectors
1208	>	scaled = invHmat * rs;
1209	>
1210	>	// wrap the vector back into the unit box by subtracting integer box
1211	>	// numbers
1212	>	for (int j = 0; j < 3; j++) {
1213	>	scaled[j] -= roundMe(scaled[j]);
1214	>	scaled[j] += 0.5;
1215	>	}
1216	>
1217	>	// find xyz-indices of cell that cutoffGroup is in.
1218	>	whichCell.x() = nCells_.x() * scaled.x();
1219	>	whichCell.y() = nCells_.y() * scaled.y();
1220	>	whichCell.z() = nCells_.z() * scaled.z();
1221	>
1222	>	// find single index of this cell:
1223	>	cellIndex = Vlinear(whichCell, nCells_);
1224	>
1225	>	// add this cutoff group to the list of groups in this cell;
1226	>	cellListCol_[cellIndex].push_back(i);
1227	>	}
1228	>
1229		#else
1230	<	for (int i = 0; i < nGroups_; i++) {
1231	<	rs = snap_->cgData.position[i];
1232	<	// scaled positions relative to the box vectors
1233	<	scaled = invHmat * rs;
1234	<	// wrap the vector back into the unit box by subtracting integer box
1235	<	// numbers
1236	<	for (int j = 0; j < 3; j++)
1237	<	scaled[j] -= roundMe(scaled[j]);
1230	>	for (int i = 0; i < nGroups_; i++) {
1231	>	rs = snap_->cgData.position[i];
1232	>
1233	>	// scaled positions relative to the box vectors
1234	>	scaled = invHmat * rs;
1235	>
1236	>	// wrap the vector back into the unit box by subtracting integer box
1237	>	// numbers
1238	>	for (int j = 0; j < 3; j++) {
1239	>	scaled[j] -= roundMe(scaled[j]);
1240	>	scaled[j] += 0.5;
1241	>	}
1242	>
1243	>	// find xyz-indices of cell that cutoffGroup is in.
1244	>	whichCell.x() = nCells_.x() * scaled.x();
1245	>	whichCell.y() = nCells_.y() * scaled.y();
1246	>	whichCell.z() = nCells_.z() * scaled.z();
1247	>
1248	>	// find single index of this cell:
1249	>	cellIndex = Vlinear(whichCell, nCells_);
1250	>
1251	>	// add this cutoff group to the list of groups in this cell;
1252	>	cellList_[cellIndex].push_back(i);
1253	>	}
1254
1012	–	// find xyz-indices of cell that cutoffGroup is in.
1013	–	whichCell.x() = nCells_.x() * scaled.x();
1014	–	whichCell.y() = nCells_.y() * scaled.y();
1015	–	whichCell.z() = nCells_.z() * scaled.z();
1016	–
1017	–	// find single index of this cell:
1018	–	cellIndex = Vlinear(whichCell, nCells_);
1019	–	// add this cutoff group to the list of groups in this cell;
1020	–	cellList_[cellIndex].push_back(i);
1021	–	}
1255		#endif
1256
1257	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1258	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1259	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1260	<	Vector3i m1v(m1x, m1y, m1z);
1261	<	int m1 = Vlinear(m1v, nCells_);
1029	<
1030	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1031	<	os != cellOffsets_.end(); ++os) {
1257	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1258	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1259	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1260	>	Vector3i m1v(m1x, m1y, m1z);
1261	>	int m1 = Vlinear(m1v, nCells_);
1262
1263	<	Vector3i m2v = m1v + (*os);
1264	<
1265	<	if (m2v.x() >= nCells_.x()) {
1266	<	m2v.x() = 0;
1267	<	} else if (m2v.x() < 0) {
1038	<	m2v.x() = nCells_.x() - 1;
1039	<	}
1040	<
1041	<	if (m2v.y() >= nCells_.y()) {
1042	<	m2v.y() = 0;
1043	<	} else if (m2v.y() < 0) {
1044	<	m2v.y() = nCells_.y() - 1;
1045	<	}
1046	<
1047	<	if (m2v.z() >= nCells_.z()) {
1048	<	m2v.z() = 0;
1049	<	} else if (m2v.z() < 0) {
1050	<	m2v.z() = nCells_.z() - 1;
1051	<	}
1052	<
1053	<	int m2 = Vlinear (m2v, nCells_);
1263	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1264	>	os != cellOffsets_.end(); ++os) {
1265	>
1266	>	Vector3i m2v = m1v + (*os);
1267	>
1268
1269	<	#ifdef IS_MPI
1270	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1271	<	j1 != cellListRow_[m1].end(); ++j1) {
1272	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1273	<	j2 != cellListCol_[m2].end(); ++j2) {
1274	<
1275	<	// Always do this if we're in different cells or if
1276	<	// we're in the same cell and the global index of the
1277	<	// j2 cutoff group is less than the j1 cutoff group
1269	>	if (m2v.x() >= nCells_.x()) {
1270	>	m2v.x() = 0;
1271	>	} else if (m2v.x() < 0) {
1272	>	m2v.x() = nCells_.x() - 1;
1273	>	}
1274	>
1275	>	if (m2v.y() >= nCells_.y()) {
1276	>	m2v.y() = 0;
1277	>	} else if (m2v.y() < 0) {
1278	>	m2v.y() = nCells_.y() - 1;
1279	>	}
1280	>
1281	>	if (m2v.z() >= nCells_.z()) {
1282	>	m2v.z() = 0;
1283	>	} else if (m2v.z() < 0) {
1284	>	m2v.z() = nCells_.z() - 1;
1285	>	}
1286
1287	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1287	>	int m2 = Vlinear (m2v, nCells_);
1288	>
1289	>	#ifdef IS_MPI
1290	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1291	>	j1 != cellListRow_[m1].end(); ++j1) {
1292	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1293	>	j2 != cellListCol_[m2].end(); ++j2) {
1294	>
1295	>	// In parallel, we need to visit *all* pairs of row
1296	>	// & column indicies and will divide labor in the
1297	>	// force evaluation later.
1298		dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1299		snap_->wrapVector(dr);
1300		cuts = getGroupCutoffs( (*j1), (*j2) );
1301		if (dr.lengthSquare() < cuts.third) {
1302		neighborList.push_back(make_pair((*j1), (*j2)));
1303	<	}
1303	>	}
1304		}
1305		}
1074	–	}
1306		#else
1307	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1308	<	j1 != cellList_[m1].end(); ++j1) {
1309	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1310	<	j2 != cellList_[m2].end(); ++j2) {
1311	<
1312	<	// Always do this if we're in different cells or if
1313	<	// we're in the same cell and the global index of the
1314	<	// j2 cutoff group is less than the j1 cutoff group
1307	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1308	>	j1 != cellList_[m1].end(); ++j1) {
1309	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1310	>	j2 != cellList_[m2].end(); ++j2) {
1311	>
1312	>	// Always do this if we're in different cells or if
1313	>	// we're in the same cell and the global index of
1314	>	// the j2 cutoff group is greater than or equal to
1315	>	// the j1 cutoff group.  Note that Rappaport's code
1316	>	// has a "less than" conditional here, but that
1317	>	// deals with atom-by-atom computation.  OpenMD
1318	>	// allows atoms within a single cutoff group to
1319	>	// interact with each other.
1320
1321	<	if (m2 != m1 || (*j2) < (*j1)) {
1322	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1323	<	snap_->wrapVector(dr);
1324	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1325	<	if (dr.lengthSquare() < cuts.third) {
1326	<	neighborList.push_back(make_pair((*j1), (*j2)));
1321	>
1322	>
1323	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1324	>
1325	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1326	>	snap_->wrapVector(dr);
1327	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1328	>	if (dr.lengthSquare() < cuts.third) {
1329	>	neighborList.push_back(make_pair((*j1), (*j2)));
1330	>	}
1331		}
1332		}
1333		}
1094	–	}
1334		#endif
1335	+	}
1336		}
1337		}
1338		}
1339	+	} else {
1340	+	// branch to do all cutoff group pairs
1341	+	#ifdef IS_MPI
1342	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1343	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1344	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1345	+	snap_->wrapVector(dr);
1346	+	cuts = getGroupCutoffs( j1, j2 );
1347	+	if (dr.lengthSquare() < cuts.third) {
1348	+	neighborList.push_back(make_pair(j1, j2));
1349	+	}
1350	+	}
1351	+	}
1352	+	#else
1353	+	// include all groups here.
1354	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1355	+	// include self group interactions j2 == j1
1356	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1357	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1358	+	snap_->wrapVector(dr);
1359	+	cuts = getGroupCutoffs( j1, j2 );
1360	+	if (dr.lengthSquare() < cuts.third) {
1361	+	neighborList.push_back(make_pair(j1, j2));
1362	+	}
1363	+	}
1364	+	}
1365	+	#endif
1366		}
1367	<
1367	>
1368		// save the local cutoff group positions for the check that is
1369		// done on each loop:
1370		saved_CG_positions_.clear();
1371		for (int i = 0; i < nGroups_; i++)
1372		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1373	<
1373	>
1374		return neighborList;
1375		}
1376		} //end namespace OpenMD

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