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

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1586 by gezelter, Tue Jun 21 06:34:35 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 2069 by gezelter, Thu Mar 5 16:30:23 2015 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
#	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	+	// Row and colum scans must visit all surrounding cells
54	+	cellOffsets_.clear();
55	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
56	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
57	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
58	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
65	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
66	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
67	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
74	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
75	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
76	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
82	+	}
83	+
84	+
85		/**
86		* distributeInitialData is essentially a copy of the older fortran
87		* SimulationSetup
88		*/
54	–
89		void ForceMatrixDecomposition::distributeInitialData() {
90		snap_ = sman_->getCurrentSnapshot();
91		storageLayout_ = sman_->getStorageLayout();
92		ff_ = info_->getForceField();
93		nLocal_ = snap_->getNumberOfAtoms();
94	<
94	>
95		nGroups_ = info_->getNLocalCutoffGroups();
96		// gather the information for atomtype IDs (atids):
97		idents = info_->getIdentArray();
98	+	regions = info_->getRegions();
99		AtomLocalToGlobal = info_->getGlobalAtomIndices();
100		cgLocalToGlobal = info_->getGlobalGroupIndices();
101		vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
102
103		massFactors = info_->getMassFactors();
104
105	<	PairList excludes = info_->getExcludedInteractions();
106	<	PairList oneTwo = info_->getOneTwoInteractions();
107	<	PairList oneThree = info_->getOneThreeInteractions();
108	<	PairList oneFour = info_->getOneFourInteractions();
109	<
105	>	PairList* excludes = info_->getExcludedInteractions();
106	>	PairList* oneTwo = info_->getOneTwoInteractions();
107	>	PairList* oneThree = info_->getOneThreeInteractions();
108	>	PairList* oneFour = info_->getOneFourInteractions();
109	>
110	>	if (needVelocities_)
111	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
112	>	DataStorage::dslVelocity);
113	>	else
114	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
115	>
116		#ifdef IS_MPI
117
118	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
119	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
79	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
80	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
81	<	AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
118	>	MPI_Comm row = rowComm.getComm();
119	>	MPI_Comm col = colComm.getComm();
120
121	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
122	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
123	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
124	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
125	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
121	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
122	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
123	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
124	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
125	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
126
127	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
128	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
129	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
130	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
127	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
128	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
129	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
130	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
131	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
132
133	<	nAtomsInRow_ = AtomCommIntRow->getSize();
134	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
135	<	nGroupsInRow_ = cgCommIntRow->getSize();
136	<	nGroupsInCol_ = cgCommIntColumn->getSize();
133	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
134	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
135	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
136	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
137
138	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
139	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
140	+	nGroupsInRow_ = cgPlanIntRow->getSize();
141	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
142	+
143		// Modify the data storage objects with the correct layouts and sizes:
144		atomRowData.resize(nAtomsInRow_);
145		atomRowData.setStorageLayout(storageLayout_);
#	Line 104 | Line 148 | namespace OpenMD {
148		cgRowData.resize(nGroupsInRow_);
149		cgRowData.setStorageLayout(DataStorage::dslPosition);
150		cgColData.resize(nGroupsInCol_);
151	<	cgColData.setStorageLayout(DataStorage::dslPosition);
152	<
151	>	if (needVelocities_)
152	>	// we only need column velocities if we need them.
153	>	cgColData.setStorageLayout(DataStorage::dslPosition |
154	>	DataStorage::dslVelocity);
155	>	else
156	>	cgColData.setStorageLayout(DataStorage::dslPosition);
157	>
158		identsRow.resize(nAtomsInRow_);
159		identsCol.resize(nAtomsInCol_);
160
161	<	AtomCommIntRow->gather(idents, identsRow);
162	<	AtomCommIntColumn->gather(idents, identsCol);
161	>	AtomPlanIntRow->gather(idents, identsRow);
162	>	AtomPlanIntColumn->gather(idents, identsCol);
163	>
164	>	regionsRow.resize(nAtomsInRow_);
165	>	regionsCol.resize(nAtomsInCol_);
166
167	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
168	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
167	>	AtomPlanIntRow->gather(regions, regionsRow);
168	>	AtomPlanIntColumn->gather(regions, regionsCol);
169
170	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
171	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
170	>	// allocate memory for the parallel objects
171	>	atypesRow.resize(nAtomsInRow_);
172	>	atypesCol.resize(nAtomsInCol_);
173
174	<	AtomCommRealRow->gather(massFactors, massFactorsRow);
175	<	AtomCommRealColumn->gather(massFactors, massFactorsCol);
174	>	for (int i = 0; i < nAtomsInRow_; i++)
175	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
176	>	for (int i = 0; i < nAtomsInCol_; i++)
177	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
178
179	+	pot_row.resize(nAtomsInRow_);
180	+	pot_col.resize(nAtomsInCol_);
181	+
182	+	expot_row.resize(nAtomsInRow_);
183	+	expot_col.resize(nAtomsInCol_);
184	+
185	+	AtomRowToGlobal.resize(nAtomsInRow_);
186	+	AtomColToGlobal.resize(nAtomsInCol_);
187	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
188	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
189	+
190	+	cgRowToGlobal.resize(nGroupsInRow_);
191	+	cgColToGlobal.resize(nGroupsInCol_);
192	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
193	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
194	+
195	+	massFactorsRow.resize(nAtomsInRow_);
196	+	massFactorsCol.resize(nAtomsInCol_);
197	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
198	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
199	+
200		groupListRow_.clear();
201		groupListRow_.resize(nGroupsInRow_);
202		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 143 | Line 219 | namespace OpenMD {
219		}
220		}
221
222	<	skipsForAtom.clear();
223	<	skipsForAtom.resize(nAtomsInRow_);
222	>	excludesForAtom.clear();
223	>	excludesForAtom.resize(nAtomsInRow_);
224		toposForAtom.clear();
225		toposForAtom.resize(nAtomsInRow_);
226		topoDist.clear();
#	Line 155 | Line 231 | namespace OpenMD {
231		for (int j = 0; j < nAtomsInCol_; j++) {
232		int jglob = AtomColToGlobal[j];
233
234	<	if (excludes.hasPair(iglob, jglob))
235	<	skipsForAtom[i].push_back(j);
234	>	if (excludes->hasPair(iglob, jglob))
235	>	excludesForAtom[i].push_back(j);
236
237	<	if (oneTwo.hasPair(iglob, jglob)) {
237	>	if (oneTwo->hasPair(iglob, jglob)) {
238		toposForAtom[i].push_back(j);
239		topoDist[i].push_back(1);
240		} else {
241	<	if (oneThree.hasPair(iglob, jglob)) {
241	>	if (oneThree->hasPair(iglob, jglob)) {
242		toposForAtom[i].push_back(j);
243		topoDist[i].push_back(2);
244		} else {
245	<	if (oneFour.hasPair(iglob, jglob)) {
245	>	if (oneFour->hasPair(iglob, jglob)) {
246		toposForAtom[i].push_back(j);
247		topoDist[i].push_back(3);
248		}
#	Line 175 | Line 251 | namespace OpenMD {
251		}
252		}
253
254	<	#endif
255	<
256	<	groupList_.clear();
181	<	groupList_.resize(nGroups_);
182	<	for (int i = 0; i < nGroups_; i++) {
183	<	int gid = cgLocalToGlobal[i];
184	<	for (int j = 0; j < nLocal_; j++) {
185	<	int aid = AtomLocalToGlobal[j];
186	<	if (globalGroupMembership[aid] == gid) {
187	<	groupList_[i].push_back(j);
188	<	}
189	<	}
190	<	}
191	<
192	<	skipsForAtom.clear();
193	<	skipsForAtom.resize(nLocal_);
254	>	#else
255	>	excludesForAtom.clear();
256	>	excludesForAtom.resize(nLocal_);
257		toposForAtom.clear();
258		toposForAtom.resize(nLocal_);
259		topoDist.clear();
#	Line 202 | Line 265 | namespace OpenMD {
265		for (int j = 0; j < nLocal_; j++) {
266		int jglob = AtomLocalToGlobal[j];
267
268	<	if (excludes.hasPair(iglob, jglob))
269	<	skipsForAtom[i].push_back(j);
268	>	if (excludes->hasPair(iglob, jglob))
269	>	excludesForAtom[i].push_back(j);
270
271	<	if (oneTwo.hasPair(iglob, jglob)) {
271	>	if (oneTwo->hasPair(iglob, jglob)) {
272		toposForAtom[i].push_back(j);
273		topoDist[i].push_back(1);
274		} else {
275	<	if (oneThree.hasPair(iglob, jglob)) {
275	>	if (oneThree->hasPair(iglob, jglob)) {
276		toposForAtom[i].push_back(j);
277		topoDist[i].push_back(2);
278		} else {
279	<	if (oneFour.hasPair(iglob, jglob)) {
279	>	if (oneFour->hasPair(iglob, jglob)) {
280		toposForAtom[i].push_back(j);
281		topoDist[i].push_back(3);
282		}
#	Line 221 | Line 284 | namespace OpenMD {
284		}
285		}
286		}
287	<
225	<	createGtypeCutoffMap();
226	<	}
227	<
228	<	void ForceMatrixDecomposition::createGtypeCutoffMap() {
229	<
230	<	RealType tol = 1e-6;
231	<	RealType rc;
232	<	int atid;
233	<	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
234	<	vector<RealType> atypeCutoff;
235	<	atypeCutoff.resize( atypes.size() );
236	<
237	<	for (set<AtomType*>::iterator at = atypes.begin();
238	<	at != atypes.end(); ++at){
239	<	atid = (*at)->getIdent();
287	>	#endif
288
289	<	if (userChoseCutoff_)
290	<	atypeCutoff[atid] = userCutoff_;
243	<	else
244	<	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
245	<	}
289	>	// allocate memory for the parallel objects
290	>	atypesLocal.resize(nLocal_);
291
292	<	vector<RealType> gTypeCutoffs;
292	>	for (int i = 0; i < nLocal_; i++)
293	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
294
295	<	// first we do a single loop over the cutoff groups to find the
296	<	// largest cutoff for any atypes present in this group.
297	<	#ifdef IS_MPI
298	<	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
299	<	groupRowToGtype.resize(nGroupsInRow_);
300	<	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
301	<	vector<int> atomListRow = getAtomsInGroupRow(cg1);
302	<	for (vector<int>::iterator ia = atomListRow.begin();
257	<	ia != atomListRow.end(); ++ia) {
258	<	int atom1 = (*ia);
259	<	atid = identsRow[atom1];
260	<	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
261	<	groupCutoffRow[cg1] = atypeCutoff[atid];
295	>	groupList_.clear();
296	>	groupList_.resize(nGroups_);
297	>	for (int i = 0; i < nGroups_; i++) {
298	>	int gid = cgLocalToGlobal[i];
299	>	for (int j = 0; j < nLocal_; j++) {
300	>	int aid = AtomLocalToGlobal[j];
301	>	if (globalGroupMembership[aid] == gid) {
302	>	groupList_[i].push_back(j);
303		}
263	–	}
264	–
265	–	bool gTypeFound = false;
266	–	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
267	–	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
268	–	groupRowToGtype[cg1] = gt;
269	–	gTypeFound = true;
270	–	}
271	–	}
272	–	if (!gTypeFound) {
273	–	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
274	–	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
275	–	}
276	–
277	–	}
278	–	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
279	–	groupColToGtype.resize(nGroupsInCol_);
280	–	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
281	–	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
282	–	for (vector<int>::iterator jb = atomListCol.begin();
283	–	jb != atomListCol.end(); ++jb) {
284	–	int atom2 = (*jb);
285	–	atid = identsCol[atom2];
286	–	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
287	–	groupCutoffCol[cg2] = atypeCutoff[atid];
288	–	}
289	–	}
290	–	bool gTypeFound = false;
291	–	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
292	–	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
293	–	groupColToGtype[cg2] = gt;
294	–	gTypeFound = true;
295	–	}
296	–	}
297	–	if (!gTypeFound) {
298	–	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
299	–	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
300	–	}
301	–	}
302	–	#else
303	–
304	–	vector<RealType> groupCutoff(nGroups_, 0.0);
305	–	groupToGtype.resize(nGroups_);
306	–
307	–	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
308	–
309	–	groupCutoff[cg1] = 0.0;
310	–	vector<int> atomList = getAtomsInGroupRow(cg1);
311	–
312	–	for (vector<int>::iterator ia = atomList.begin();
313	–	ia != atomList.end(); ++ia) {
314	–	int atom1 = (*ia);
315	–	atid = idents[atom1];
316	–	if (atypeCutoff[atid] > groupCutoff[cg1]) {
317	–	groupCutoff[cg1] = atypeCutoff[atid];
318	–	}
319	–	}
320	–
321	–	bool gTypeFound = false;
322	–	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
323	–	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
324	–	groupToGtype[cg1] = gt;
325	–	gTypeFound = true;
326	–	}
327	–	}
328	–	if (!gTypeFound) {
329	–	gTypeCutoffs.push_back( groupCutoff[cg1] );
330	–	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
304		}
305	<	}
333	<	#endif
334	<
335	<	// Now we find the maximum group cutoff value present in the simulation
336	<
337	<	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
338	<
339	<	#ifdef IS_MPI
340	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
341	<	#endif
342	<
343	<	RealType tradRcut = groupMax;
344	<
345	<	for (int i = 0; i < gTypeCutoffs.size();  i++) {
346	<	for (int j = 0; j < gTypeCutoffs.size();  j++) {
347	<	RealType thisRcut;
348	<	switch(cutoffPolicy_) {
349	<	case TRADITIONAL:
350	<	thisRcut = tradRcut;
351	<	break;
352	<	case MIX:
353	<	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
354	<	break;
355	<	case MAX:
356	<	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
357	<	break;
358	<	default:
359	<	sprintf(painCave.errMsg,
360	<	"ForceMatrixDecomposition::createGtypeCutoffMap "
361	<	"hit an unknown cutoff policy!\n");
362	<	painCave.severity = OPENMD_ERROR;
363	<	painCave.isFatal = 1;
364	<	simError();
365	<	break;
366	<	}
367	<
368	<	pair<int,int> key = make_pair(i,j);
369	<	gTypeCutoffMap[key].first = thisRcut;
370	<
371	<	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
372	<
373	<	gTypeCutoffMap[key].second = thisRcut*thisRcut;
374	<
375	<	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
376	<
377	<	// sanity check
378	<
379	<	if (userChoseCutoff_) {
380	<	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
381	<	sprintf(painCave.errMsg,
382	<	"ForceMatrixDecomposition::createGtypeCutoffMap "
383	<	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
384	<	painCave.severity = OPENMD_ERROR;
385	<	painCave.isFatal = 1;
386	<	simError();
387	<	}
388	<	}
389	<	}
390	<	}
305	>	}
306		}
307	<
393	<
394	<	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
395	<	int i, j;
396	<	#ifdef IS_MPI
397	<	i = groupRowToGtype[cg1];
398	<	j = groupColToGtype[cg2];
399	<	#else
400	<	i = groupToGtype[cg1];
401	<	j = groupToGtype[cg2];
402	<	#endif
403	<	return gTypeCutoffMap[make_pair(i,j)];
404	<	}
405	<
307	>
308		int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
309	<	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
309	>	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
310		if (toposForAtom[atom1][j] == atom2)
311		return topoDist[atom1][j];
312	<	}
312	>	}
313		return 0;
314		}
315
316		void ForceMatrixDecomposition::zeroWorkArrays() {
317		pairwisePot = 0.0;
318		embeddingPot = 0.0;
319	+	excludedPot = 0.0;
320	+	excludedSelfPot = 0.0;
321
322		#ifdef IS_MPI
323		if (storageLayout_ & DataStorage::dslForce) {
#	Line 432 | Line 336 | namespace OpenMD {
336		fill(pot_col.begin(), pot_col.end(),
337		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
338
339	+	fill(expot_row.begin(), expot_row.end(),
340	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
341	+
342	+	fill(expot_col.begin(), expot_col.end(),
343	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
344	+
345		if (storageLayout_ & DataStorage::dslParticlePot) {
346	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
347	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
346	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
347	>	0.0);
348	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
349	>	0.0);
350		}
351
352		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 443 | Line 355 | namespace OpenMD {
355		}
356
357		if (storageLayout_ & DataStorage::dslFunctional) {
358	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
359	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
358	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
359	>	0.0);
360	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
361	>	0.0);
362		}
363
364		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 455 | Line 369 | namespace OpenMD {
369		}
370
371		if (storageLayout_ & DataStorage::dslSkippedCharge) {
372	<	fill(atomRowData.skippedCharge.begin(), atomRowData.skippedCharge.end(), 0.0);
373	<	fill(atomColData.skippedCharge.begin(), atomColData.skippedCharge.end(), 0.0);
372	>	fill(atomRowData.skippedCharge.begin(),
373	>	atomRowData.skippedCharge.end(), 0.0);
374	>	fill(atomColData.skippedCharge.begin(),
375	>	atomColData.skippedCharge.end(), 0.0);
376		}
377
378	<	#else
379	<
378	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
379	>	fill(atomRowData.flucQFrc.begin(),
380	>	atomRowData.flucQFrc.end(), 0.0);
381	>	fill(atomColData.flucQFrc.begin(),
382	>	atomColData.flucQFrc.end(), 0.0);
383	>	}
384	>
385	>	if (storageLayout_ & DataStorage::dslElectricField) {
386	>	fill(atomRowData.electricField.begin(),
387	>	atomRowData.electricField.end(), V3Zero);
388	>	fill(atomColData.electricField.begin(),
389	>	atomColData.electricField.end(), V3Zero);
390	>	}
391	>
392	>	if (storageLayout_ & DataStorage::dslSitePotential) {
393	>	fill(atomRowData.sitePotential.begin(),
394	>	atomRowData.sitePotential.end(), 0.0);
395	>	fill(atomColData.sitePotential.begin(),
396	>	atomColData.sitePotential.end(), 0.0);
397	>	}
398	>
399	>	#endif
400	>	// even in parallel, we need to zero out the local arrays:
401	>
402		if (storageLayout_ & DataStorage::dslParticlePot) {
403		fill(snap_->atomData.particlePot.begin(),
404		snap_->atomData.particlePot.end(), 0.0);
#	Line 470 | Line 408 | namespace OpenMD {
408		fill(snap_->atomData.density.begin(),
409		snap_->atomData.density.end(), 0.0);
410		}
411	+
412		if (storageLayout_ & DataStorage::dslFunctional) {
413		fill(snap_->atomData.functional.begin(),
414		snap_->atomData.functional.end(), 0.0);
415		}
416	+
417		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
418		fill(snap_->atomData.functionalDerivative.begin(),
419		snap_->atomData.functionalDerivative.end(), 0.0);
420		}
421	+
422		if (storageLayout_ & DataStorage::dslSkippedCharge) {
423		fill(snap_->atomData.skippedCharge.begin(),
424		snap_->atomData.skippedCharge.end(), 0.0);
425		}
426	<	#endif
427	<
426	>
427	>	if (storageLayout_ & DataStorage::dslElectricField) {
428	>	fill(snap_->atomData.electricField.begin(),
429	>	snap_->atomData.electricField.end(), V3Zero);
430	>	}
431	>	if (storageLayout_ & DataStorage::dslSitePotential) {
432	>	fill(snap_->atomData.sitePotential.begin(),
433	>	snap_->atomData.sitePotential.end(), 0.0);
434	>	}
435		}
436
437
438		void ForceMatrixDecomposition::distributeData()  {
439	+
440	+	#ifdef IS_MPI
441	+
442		snap_ = sman_->getCurrentSnapshot();
443		storageLayout_ = sman_->getStorageLayout();
493	–	#ifdef IS_MPI
444
445	+	bool needsCG = true;
446	+	if(info_->getNCutoffGroups() != info_->getNAtoms())
447	+	needsCG = false;
448	+
449		// gather up the atomic positions
450	<	AtomCommVectorRow->gather(snap_->atomData.position,
450	>	AtomPlanVectorRow->gather(snap_->atomData.position,
451		atomRowData.position);
452	<	AtomCommVectorColumn->gather(snap_->atomData.position,
452	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
453		atomColData.position);
454
455		// gather up the cutoff group positions
456	<	cgCommVectorRow->gather(snap_->cgData.position,
457	<	cgRowData.position);
458	<	cgCommVectorColumn->gather(snap_->cgData.position,
459	<	cgColData.position);
456	>
457	>	if (needsCG) {
458	>	cgPlanVectorRow->gather(snap_->cgData.position,
459	>	cgRowData.position);
460	>
461	>	cgPlanVectorColumn->gather(snap_->cgData.position,
462	>	cgColData.position);
463	>	}
464	>
465	>
466	>	if (needVelocities_) {
467	>	// gather up the atomic velocities
468	>	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
469	>	atomColData.velocity);
470	>
471	>	if (needsCG) {
472	>	cgPlanVectorColumn->gather(snap_->cgData.velocity,
473	>	cgColData.velocity);
474	>	}
475	>	}
476	>
477
478		// if needed, gather the atomic rotation matrices
479		if (storageLayout_ & DataStorage::dslAmat) {
480	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
480	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
481		atomRowData.aMat);
482	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
482	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
483		atomColData.aMat);
484		}
485	<
486	<	// if needed, gather the atomic eletrostatic frames
487	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
488	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
489	<	atomRowData.electroFrame);
490	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
491	<	atomColData.electroFrame);
485	>
486	>	// if needed, gather the atomic eletrostatic information
487	>	if (storageLayout_ & DataStorage::dslDipole) {
488	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
489	>	atomRowData.dipole);
490	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
491	>	atomColData.dipole);
492		}
493	+
494	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
495	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
496	+	atomRowData.quadrupole);
497	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
498	+	atomColData.quadrupole);
499	+	}
500	+
501	+	// if needed, gather the atomic fluctuating charge values
502	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
503	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
504	+	atomRowData.flucQPos);
505	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
506	+	atomColData.flucQPos);
507	+	}
508	+
509		#endif
510		}
511
#	Line 526 | Line 513 | namespace OpenMD {
513		* data structures.
514		*/
515		void ForceMatrixDecomposition::collectIntermediateData() {
516	+	#ifdef IS_MPI
517	+
518		snap_ = sman_->getCurrentSnapshot();
519		storageLayout_ = sman_->getStorageLayout();
520	<	#ifdef IS_MPI
532	<
520	>
521		if (storageLayout_ & DataStorage::dslDensity) {
522
523	<	AtomCommRealRow->scatter(atomRowData.density,
523	>	AtomPlanRealRow->scatter(atomRowData.density,
524		snap_->atomData.density);
525
526		int n = snap_->atomData.density.size();
527		vector<RealType> rho_tmp(n, 0.0);
528	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
528	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
529		for (int i = 0; i < n; i++)
530		snap_->atomData.density[i] += rho_tmp[i];
531		}
532	+
533	+	// this isn't necessary if we don't have polarizable atoms, but
534	+	// we'll leave it here for now.
535	+	if (storageLayout_ & DataStorage::dslElectricField) {
536	+
537	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
538	+	snap_->atomData.electricField);
539	+
540	+	int n = snap_->atomData.electricField.size();
541	+	vector<Vector3d> field_tmp(n, V3Zero);
542	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
543	+	field_tmp);
544	+	for (int i = 0; i < n; i++)
545	+	snap_->atomData.electricField[i] += field_tmp[i];
546	+	}
547		#endif
548		}
549
#	Line 549 | Line 552 | namespace OpenMD {
552		* row and column-indexed data structures
553		*/
554		void ForceMatrixDecomposition::distributeIntermediateData() {
555	+	#ifdef IS_MPI
556		snap_ = sman_->getCurrentSnapshot();
557		storageLayout_ = sman_->getStorageLayout();
558	<	#ifdef IS_MPI
558	>
559		if (storageLayout_ & DataStorage::dslFunctional) {
560	<	AtomCommRealRow->gather(snap_->atomData.functional,
560	>	AtomPlanRealRow->gather(snap_->atomData.functional,
561		atomRowData.functional);
562	<	AtomCommRealColumn->gather(snap_->atomData.functional,
562	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
563		atomColData.functional);
564		}
565
566		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
567	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
567	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
568		atomRowData.functionalDerivative);
569	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
569	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
570		atomColData.functionalDerivative);
571		}
572		#endif
#	Line 570 | Line 574 | namespace OpenMD {
574
575
576		void ForceMatrixDecomposition::collectData() {
577	+	#ifdef IS_MPI
578		snap_ = sman_->getCurrentSnapshot();
579		storageLayout_ = sman_->getStorageLayout();
580	<	#ifdef IS_MPI
580	>
581		int n = snap_->atomData.force.size();
582		vector<Vector3d> frc_tmp(n, V3Zero);
583
584	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
584	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
585		for (int i = 0; i < n; i++) {
586		snap_->atomData.force[i] += frc_tmp[i];
587		frc_tmp[i] = 0.0;
588		}
589
590	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
591	<	for (int i = 0; i < n; i++)
590	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
591	>	for (int i = 0; i < n; i++) {
592		snap_->atomData.force[i] += frc_tmp[i];
593	<
594	<
593	>	}
594	>
595		if (storageLayout_ & DataStorage::dslTorque) {
596
597	<	int nt = snap_->atomData.force.size();
597	>	int nt = snap_->atomData.torque.size();
598		vector<Vector3d> trq_tmp(nt, V3Zero);
599
600	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
601	<	for (int i = 0; i < n; i++) {
600	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
601	>	for (int i = 0; i < nt; i++) {
602		snap_->atomData.torque[i] += trq_tmp[i];
603		trq_tmp[i] = 0.0;
604		}
605
606	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
607	<	for (int i = 0; i < n; i++)
606	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
607	>	for (int i = 0; i < nt; i++)
608		snap_->atomData.torque[i] += trq_tmp[i];
609		}
610	+
611	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
612	+
613	+	int ns = snap_->atomData.skippedCharge.size();
614	+	vector<RealType> skch_tmp(ns, 0.0);
615	+
616	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
617	+	for (int i = 0; i < ns; i++) {
618	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
619	+	skch_tmp[i] = 0.0;
620	+	}
621	+
622	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
623	+	for (int i = 0; i < ns; i++)
624	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
625	+
626	+	}
627
628	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
629	+
630	+	int nq = snap_->atomData.flucQFrc.size();
631	+	vector<RealType> fqfrc_tmp(nq, 0.0);
632	+
633	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
634	+	for (int i = 0; i < nq; i++) {
635	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
636	+	fqfrc_tmp[i] = 0.0;
637	+	}
638	+
639	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
640	+	for (int i = 0; i < nq; i++)
641	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
642	+
643	+	}
644	+
645	+	if (storageLayout_ & DataStorage::dslElectricField) {
646	+
647	+	int nef = snap_->atomData.electricField.size();
648	+	vector<Vector3d> efield_tmp(nef, V3Zero);
649	+
650	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
651	+	for (int i = 0; i < nef; i++) {
652	+	snap_->atomData.electricField[i] += efield_tmp[i];
653	+	efield_tmp[i] = 0.0;
654	+	}
655	+
656	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
657	+	for (int i = 0; i < nef; i++)
658	+	snap_->atomData.electricField[i] += efield_tmp[i];
659	+	}
660	+
661	+	if (storageLayout_ & DataStorage::dslSitePotential) {
662	+
663	+	int nsp = snap_->atomData.sitePotential.size();
664	+	vector<RealType> sp_tmp(nsp, 0.0);
665	+
666	+	AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
667	+	for (int i = 0; i < nsp; i++) {
668	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
669	+	sp_tmp[i] = 0.0;
670	+	}
671	+
672	+	AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
673	+	for (int i = 0; i < nsp; i++)
674	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
675	+	}
676	+
677		nLocal_ = snap_->getNumberOfAtoms();
678
679		vector<potVec> pot_temp(nLocal_,
680		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
681	+	vector<potVec> expot_temp(nLocal_,
682	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
683
684		// scatter/gather pot_row into the members of my column
685
686	<	AtomCommPotRow->scatter(pot_row, pot_temp);
686	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
687	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
688
689	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
689	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
690		pairwisePot += pot_temp[ii];
691	<
691	>
692	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
693	>	excludedPot += expot_temp[ii];
694	>
695	>	if (storageLayout_ & DataStorage::dslParticlePot) {
696	>	// This is the pairwise contribution to the particle pot.  The
697	>	// embedding contribution is added in each of the low level
698	>	// non-bonded routines.  In single processor, this is done in
699	>	// unpackInteractionData, not in collectData.
700	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
701	>	for (int i = 0; i < nLocal_; i++) {
702	>	// factor of two is because the total potential terms are divided
703	>	// by 2 in parallel due to row/ column scatter
704	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
705	>	}
706	>	}
707	>	}
708	>
709		fill(pot_temp.begin(), pot_temp.end(),
710		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
711	+	fill(expot_temp.begin(), expot_temp.end(),
712	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
713
714	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
714	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
715	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
716
717		for (int ii = 0;  ii < pot_temp.size(); ii++ )
718		pairwisePot += pot_temp[ii];
719	+
720	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
721	+	excludedPot += expot_temp[ii];
722	+
723	+	if (storageLayout_ & DataStorage::dslParticlePot) {
724	+	// This is the pairwise contribution to the particle pot.  The
725	+	// embedding contribution is added in each of the low level
726	+	// non-bonded routines.  In single processor, this is done in
727	+	// unpackInteractionData, not in collectData.
728	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
729	+	for (int i = 0; i < nLocal_; i++) {
730	+	// factor of two is because the total potential terms are divided
731	+	// by 2 in parallel due to row/ column scatter
732	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
733	+	}
734	+	}
735	+	}
736	+
737	+	if (storageLayout_ & DataStorage::dslParticlePot) {
738	+	int npp = snap_->atomData.particlePot.size();
739	+	vector<RealType> ppot_temp(npp, 0.0);
740	+
741	+	// This is the direct or embedding contribution to the particle
742	+	// pot.
743	+
744	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
745	+	for (int i = 0; i < npp; i++) {
746	+	snap_->atomData.particlePot[i] += ppot_temp[i];
747	+	}
748	+
749	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
750	+
751	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
752	+	for (int i = 0; i < npp; i++) {
753	+	snap_->atomData.particlePot[i] += ppot_temp[i];
754	+	}
755	+	}
756	+
757	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
758	+	RealType ploc1 = pairwisePot[ii];
759	+	RealType ploc2 = 0.0;
760	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
761	+	pairwisePot[ii] = ploc2;
762	+	}
763	+
764	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
765	+	RealType ploc1 = excludedPot[ii];
766	+	RealType ploc2 = 0.0;
767	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
768	+	excludedPot[ii] = ploc2;
769	+	}
770	+
771	+	// Here be dragons.
772	+	MPI_Comm col = colComm.getComm();
773	+
774	+	MPI_Allreduce(MPI_IN_PLACE,
775	+	&snap_->frameData.conductiveHeatFlux[0], 3,
776	+	MPI_REALTYPE, MPI_SUM, col);
777	+
778	+
779		#endif
780
781		}
782
783	<	int ForceMatrixDecomposition::getNAtomsInRow() {
783	>	/**
784	>	* Collects information obtained during the post-pair (and embedding
785	>	* functional) loops onto local data structures.
786	>	*/
787	>	void ForceMatrixDecomposition::collectSelfData() {
788	>
789		#ifdef IS_MPI
790	+	snap_ = sman_->getCurrentSnapshot();
791	+	storageLayout_ = sman_->getStorageLayout();
792	+
793	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
794	+	RealType ploc1 = embeddingPot[ii];
795	+	RealType ploc2 = 0.0;
796	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
797	+	embeddingPot[ii] = ploc2;
798	+	}
799	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
800	+	RealType ploc1 = excludedSelfPot[ii];
801	+	RealType ploc2 = 0.0;
802	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
803	+	excludedSelfPot[ii] = ploc2;
804	+	}
805	+	#endif
806	+
807	+	}
808	+
809	+	int& ForceMatrixDecomposition::getNAtomsInRow() {
810	+	#ifdef IS_MPI
811		return nAtomsInRow_;
812		#else
813		return nLocal_;
#	Line 637 | Line 817 | namespace OpenMD {
817		/**
818		* returns the list of atoms belonging to this group.
819		*/
820	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
820	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
821		#ifdef IS_MPI
822		return groupListRow_[cg1];
823		#else
#	Line 645 | Line 825 | namespace OpenMD {
825		#endif
826		}
827
828	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
828	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
829		#ifdef IS_MPI
830		return groupListCol_[cg2];
831		#else
#	Line 653 | Line 833 | namespace OpenMD {
833		#endif
834		}
835
836	<	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
836	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1,
837	>	int cg2){
838	>
839		Vector3d d;
658	–
840		#ifdef IS_MPI
841		d = cgColData.position[cg2] - cgRowData.position[cg1];
842		#else
843		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
844		#endif
845
846	<	snap_->wrapVector(d);
846	>	if (usePeriodicBoundaryConditions_) {
847	>	snap_->wrapVector(d);
848	>	}
849		return d;
850		}
851
852	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
853	+	#ifdef IS_MPI
854	+	return cgColData.velocity[cg2];
855	+	#else
856	+	return snap_->cgData.velocity[cg2];
857	+	#endif
858	+	}
859
860	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
860	>	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
861	>	#ifdef IS_MPI
862	>	return atomColData.velocity[atom2];
863	>	#else
864	>	return snap_->atomData.velocity[atom2];
865	>	#endif
866	>	}
867
868	+
869	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1,
870	+	int cg1) {
871		Vector3d d;
872
873		#ifdef IS_MPI
#	Line 676 | Line 875 | namespace OpenMD {
875		#else
876		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
877		#endif
878	<
879	<	snap_->wrapVector(d);
878	>	if (usePeriodicBoundaryConditions_) {
879	>	snap_->wrapVector(d);
880	>	}
881		return d;
882		}
883
884	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
884	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2,
885	>	int cg2) {
886		Vector3d d;
887
888		#ifdef IS_MPI
#	Line 689 | Line 890 | namespace OpenMD {
890		#else
891		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
892		#endif
893	<
894	<	snap_->wrapVector(d);
893	>	if (usePeriodicBoundaryConditions_) {
894	>	snap_->wrapVector(d);
895	>	}
896		return d;
897		}
898
899	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
899	>	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
900		#ifdef IS_MPI
901		return massFactorsRow[atom1];
902		#else
#	Line 702 | Line 904 | namespace OpenMD {
904		#endif
905		}
906
907	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
907	>	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
908		#ifdef IS_MPI
909		return massFactorsCol[atom2];
910		#else
#	Line 711 | Line 913 | namespace OpenMD {
913
914		}
915
916	<	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
916	>	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1,
917	>	int atom2){
918		Vector3d d;
919
920		#ifdef IS_MPI
#	Line 719 | Line 922 | namespace OpenMD {
922		#else
923		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
924		#endif
925	<
926	<	snap_->wrapVector(d);
925	>	if (usePeriodicBoundaryConditions_) {
926	>	snap_->wrapVector(d);
927	>	}
928		return d;
929		}
930
931	<	vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
932	<	return skipsForAtom[atom1];
931	>	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
932	>	return excludesForAtom[atom1];
933		}
934
935		/**
936	<	* There are a number of reasons to skip a pair or a
733	<	* particle. Mostly we do this to exclude atoms who are involved in
734	<	* short range interactions (bonds, bends, torsions), but we also
735	<	* need to exclude some overcounted interactions that result from
936	>	* We need to exclude some overcounted interactions that result from
937		* the parallel decomposition.
938		*/
939	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
939	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2,
940	>	int cg1, int cg2) {
941		int unique_id_1, unique_id_2;
942	<
942	>
943		#ifdef IS_MPI
944		// in MPI, we have to look up the unique IDs for each atom
945		unique_id_1 = AtomRowToGlobal[atom1];
946		unique_id_2 = AtomColToGlobal[atom2];
947	+	// group1 = cgRowToGlobal[cg1];
948	+	// group2 = cgColToGlobal[cg2];
949	+	#else
950	+	unique_id_1 = AtomLocalToGlobal[atom1];
951	+	unique_id_2 = AtomLocalToGlobal[atom2];
952	+	int group1 = cgLocalToGlobal[cg1];
953	+	int group2 = cgLocalToGlobal[cg2];
954	+	#endif
955
746	–	// this situation should only arise in MPI simulations
956		if (unique_id_1 == unique_id_2) return true;
957	<
957	>
958	>	#ifdef IS_MPI
959		// this prevents us from doing the pair on multiple processors
960		if (unique_id_1 < unique_id_2) {
961		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
962		} else {
963	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
963	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
964		}
965	<	#else
966	<	// in the normal loop, the atom numbers are unique
967	<	unique_id_1 = atom1;
968	<	unique_id_2 = atom2;
965	>	#endif
966	>
967	>	#ifndef IS_MPI
968	>	if (group1 == group2) {
969	>	if (unique_id_1 < unique_id_2) return true;
970	>	}
971		#endif
972
973	<	for (vector<int>::iterator i = skipsForAtom[atom1].begin();
974	<	i != skipsForAtom[atom1].end(); ++i) {
975	<	if ( (*i) == unique_id_2 ) return true;
973	>	return false;
974	>	}
975	>
976	>	/**
977	>	* We need to handle the interactions for atoms who are involved in
978	>	* the same rigid body as well as some short range interactions
979	>	* (bonds, bends, torsions) differently from other interactions.
980	>	* We'll still visit the pairwise routines, but with a flag that
981	>	* tells those routines to exclude the pair from direct long range
982	>	* interactions.  Some indirect interactions (notably reaction
983	>	* field) must still be handled for these pairs.
984	>	*/
985	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
986	>
987	>	// excludesForAtom was constructed to use row/column indices in the MPI
988	>	// version, and to use local IDs in the non-MPI version:
989	>
990	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
991	>	i != excludesForAtom[atom1].end(); ++i) {
992	>	if ( (*i) == atom2 ) return true;
993		}
994
995		return false;
#	Line 785 | Line 1014 | namespace OpenMD {
1014
1015		// filling interaction blocks with pointers
1016		void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1017	<	int atom1, int atom2) {
1017	>	int atom1, int atom2,
1018	>	bool newAtom1) {
1019	>
1020	>	idat.excluded = excludeAtomPair(atom1, atom2);
1021	>
1022	>	if (newAtom1) {
1023	>
1024		#ifdef IS_MPI
1025	<
1026	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1027	<	ff_->getAtomType(identsCol[atom2]) );
1028	<
1025	>	idat.atid1 = identsRow[atom1];
1026	>	idat.atid2 = identsCol[atom2];
1027	>
1028	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1029	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1030	>	} else {
1031	>	idat.sameRegion = false;
1032	>	}
1033	>
1034	>	if (storageLayout_ & DataStorage::dslAmat) {
1035	>	idat.A1 = &(atomRowData.aMat[atom1]);
1036	>	idat.A2 = &(atomColData.aMat[atom2]);
1037	>	}
1038	>
1039	>	if (storageLayout_ & DataStorage::dslTorque) {
1040	>	idat.t1 = &(atomRowData.torque[atom1]);
1041	>	idat.t2 = &(atomColData.torque[atom2]);
1042	>	}
1043	>
1044	>	if (storageLayout_ & DataStorage::dslDipole) {
1045	>	idat.dipole1 = &(atomRowData.dipole[atom1]);
1046	>	idat.dipole2 = &(atomColData.dipole[atom2]);
1047	>	}
1048	>
1049	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1050	>	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1051	>	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1052	>	}
1053	>
1054	>	if (storageLayout_ & DataStorage::dslDensity) {
1055	>	idat.rho1 = &(atomRowData.density[atom1]);
1056	>	idat.rho2 = &(atomColData.density[atom2]);
1057	>	}
1058	>
1059	>	if (storageLayout_ & DataStorage::dslFunctional) {
1060	>	idat.frho1 = &(atomRowData.functional[atom1]);
1061	>	idat.frho2 = &(atomColData.functional[atom2]);
1062	>	}
1063	>
1064	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1065	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1066	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1067	>	}
1068	>
1069	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1070	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1071	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1072	>	}
1073	>
1074	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1075	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1076	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1077	>	}
1078	>
1079	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1080	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1081	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1082	>	}
1083	>
1084	>	#else
1085	>
1086	>	idat.atid1 = idents[atom1];
1087	>	idat.atid2 = idents[atom2];
1088	>
1089	>	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1090	>	idat.sameRegion = (regions[atom1] == regions[atom2]);
1091	>	} else {
1092	>	idat.sameRegion = false;
1093	>	}
1094	>
1095	>	if (storageLayout_ & DataStorage::dslAmat) {
1096	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1097	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1098	>	}
1099	>
1100	>	if (storageLayout_ & DataStorage::dslTorque) {
1101	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1102	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1103	>	}
1104	>
1105	>	if (storageLayout_ & DataStorage::dslDipole) {
1106	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1107	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1108	>	}
1109	>
1110	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1111	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1112	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1113	>	}
1114	>
1115	>	if (storageLayout_ & DataStorage::dslDensity) {
1116	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1117	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1118	>	}
1119	>
1120	>	if (storageLayout_ & DataStorage::dslFunctional) {
1121	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1122	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1123	>	}
1124	>
1125	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1126	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1127	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1128	>	}
1129	>
1130	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1131	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1132	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1133	>	}
1134	>
1135	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1136	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1137	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1138	>	}
1139	>
1140	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1141	>	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1142	>	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1143	>	}
1144	>	#endif
1145	>
1146	>	} else {
1147	>	// atom1 is not new, so don't bother updating properties of that atom:
1148	>	#ifdef IS_MPI
1149	>	idat.atid2 = identsCol[atom2];
1150	>
1151	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1152	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1153	>	} else {
1154	>	idat.sameRegion = false;
1155	>	}
1156	>
1157		if (storageLayout_ & DataStorage::dslAmat) {
795	–	idat.A1 = &(atomRowData.aMat[atom1]);
1158		idat.A2 = &(atomColData.aMat[atom2]);
1159		}
1160
799	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
800	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
801	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
802	–	}
803	–
1161		if (storageLayout_ & DataStorage::dslTorque) {
805	–	idat.t1 = &(atomRowData.torque[atom1]);
1162		idat.t2 = &(atomColData.torque[atom2]);
1163		}
1164
1165	+	if (storageLayout_ & DataStorage::dslDipole) {
1166	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1167	+	}
1168	+
1169	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1170	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1171	+	}
1172	+
1173		if (storageLayout_ & DataStorage::dslDensity) {
810	–	idat.rho1 = &(atomRowData.density[atom1]);
1174		idat.rho2 = &(atomColData.density[atom2]);
1175		}
1176
1177		if (storageLayout_ & DataStorage::dslFunctional) {
815	–	idat.frho1 = &(atomRowData.functional[atom1]);
1178		idat.frho2 = &(atomColData.functional[atom2]);
1179		}
1180
1181		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
820	–	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1182		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1183		}
1184
1185		if (storageLayout_ & DataStorage::dslParticlePot) {
825	–	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1186		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1187		}
1188
1189	<	#else
1189	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1190	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1191	>	}
1192
1193	<	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1194	<	ff_->getAtomType(idents[atom2]) );
1193	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1194	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1195	>	}
1196
1197	+	#else
1198	+	idat.atid2 = idents[atom2];
1199	+
1200	+	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1201	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1202	+	} else {
1203	+	idat.sameRegion = false;
1204	+	}
1205	+
1206		if (storageLayout_ & DataStorage::dslAmat) {
835	–	idat.A1 = &(snap_->atomData.aMat[atom1]);
1207		idat.A2 = &(snap_->atomData.aMat[atom2]);
1208		}
1209
839	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
840	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
841	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
842	–	}
843	–
1210		if (storageLayout_ & DataStorage::dslTorque) {
845	–	idat.t1 = &(snap_->atomData.torque[atom1]);
1211		idat.t2 = &(snap_->atomData.torque[atom2]);
1212		}
1213
1214	+	if (storageLayout_ & DataStorage::dslDipole) {
1215	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1216	+	}
1217	+
1218	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1219	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1220	+	}
1221	+
1222		if (storageLayout_ & DataStorage::dslDensity) {
850	–	idat.rho1 = &(snap_->atomData.density[atom1]);
1223		idat.rho2 = &(snap_->atomData.density[atom2]);
1224		}
1225
1226		if (storageLayout_ & DataStorage::dslFunctional) {
855	–	idat.frho1 = &(snap_->atomData.functional[atom1]);
1227		idat.frho2 = &(snap_->atomData.functional[atom2]);
1228		}
1229
1230		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
860	–	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1231		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1232		}
1233
1234		if (storageLayout_ & DataStorage::dslParticlePot) {
865	–	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1235		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1236		}
1237
1238	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1239	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1240	+	}
1241	+
1242	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1243	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1244	+	}
1245	+
1246		#endif
1247	+	}
1248		}
871	–
1249
1250	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1250	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat,
1251	>	int atom1, int atom2) {
1252		#ifdef IS_MPI
1253	<	pot_row[atom1] += 0.5 *  *(idat.pot);
1254	<	pot_col[atom2] += 0.5 *  *(idat.pot);
1253	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1254	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1255	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1256	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1257
1258		atomRowData.force[atom1] += *(idat.f1);
1259		atomColData.force[atom2] -= *(idat.f1);
880	–	#else
881	–	pairwisePot += *(idat.pot);
1260
1261	<	snap_->atomData.force[atom1] += *(idat.f1);
1262	<	snap_->atomData.force[atom2] -= *(idat.f1);
1263	<	#endif
886	<
887	<	}
888	<
889	<
890	<	void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
891	<	int atom1, int atom2) {
892	<	#ifdef IS_MPI
893	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
894	<	ff_->getAtomType(identsCol[atom2]) );
895	<
896	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
897	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
898	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1261	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1262	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1263	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1264		}
1265
1266	<	if (storageLayout_ & DataStorage::dslTorque) {
1267	<	idat.t1 = &(atomRowData.torque[atom1]);
1268	<	idat.t2 = &(atomColData.torque[atom2]);
1266	>	if (storageLayout_ & DataStorage::dslElectricField) {
1267	>	atomRowData.electricField[atom1] += *(idat.eField1);
1268	>	atomColData.electricField[atom2] += *(idat.eField2);
1269		}
1270
1271	<	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1272	<	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1273	<	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1271	>	if (storageLayout_ & DataStorage::dslSitePotential) {
1272	>	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1273	>	atomColData.sitePotential[atom2] += *(idat.sPot2);
1274		}
1275	+
1276		#else
1277	<	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1278	<	ff_->getAtomType(idents[atom2]) );
1277	>	pairwisePot += *(idat.pot);
1278	>	excludedPot += *(idat.excludedPot);
1279
1280	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1281	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1282	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1280	>	snap_->atomData.force[atom1] += *(idat.f1);
1281	>	snap_->atomData.force[atom2] -= *(idat.f1);
1282	>
1283	>	if (idat.doParticlePot) {
1284	>	// This is the pairwise contribution to the particle pot.  The
1285	>	// embedding contribution is added in each of the low level
1286	>	// non-bonded routines.  In parallel, this calculation is done
1287	>	// in collectData, not in unpackInteractionData.
1288	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1289	>	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1290		}
1291	+
1292	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1293	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1294	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1295	+	}
1296
1297	<	if (storageLayout_ & DataStorage::dslTorque) {
1298	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1299	<	idat.t2 = &(snap_->atomData.torque[atom2]);
1297	>	if (storageLayout_ & DataStorage::dslElectricField) {
1298	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1299	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1300		}
1301
1302	<	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1303	<	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1304	<	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1302	>	if (storageLayout_ & DataStorage::dslSitePotential) {
1303	>	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1304	>	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1305		}
928	–	#endif
929	–	}
1306
931	–
932	–	void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {
933	–	#ifdef IS_MPI
934	–	pot_row[atom1] += 0.5 *  *(idat.pot);
935	–	pot_col[atom2] += 0.5 *  *(idat.pot);
936	–	#else
937	–	pairwisePot += *(idat.pot);
1307		#endif
1308	<
1308	>
1309		}
1310
942	–
1311		/*
1312		* buildNeighborList
1313		*
1314	<	* first element of pair is row-indexed CutoffGroup
1315	<	* second element of pair is column-indexed CutoffGroup
1314	>	* Constructs the Verlet neighbor list for a force-matrix
1315	>	* decomposition.  In this case, each processor is responsible for
1316	>	* row-site interactions with column-sites.
1317	>	*
1318	>	* neighborList is returned as a packed array of neighboring
1319	>	* column-ordered CutoffGroups.  The starting position in
1320	>	* neighborList for each row-ordered CutoffGroup is given by the
1321	>	* returned vector point.
1322		*/
1323	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1324	<
1325	<	vector<pair<int, int> > neighborList;
1326	<	groupCutoffs cuts;
1323	>	void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
1324	>	vector<int>& point) {
1325	>	neighborList.clear();
1326	>	point.clear();
1327	>	int len = 0;
1328	>
1329	>	bool doAllPairs = false;
1330	>
1331	>	Snapshot* snap_ = sman_->getCurrentSnapshot();
1332	>	Mat3x3d box;
1333	>	Mat3x3d invBox;
1334	>
1335	>	Vector3d rs, scaled, dr;
1336	>	Vector3i whichCell;
1337	>	int cellIndex;
1338	>
1339		#ifdef IS_MPI
1340		cellListRow_.clear();
1341		cellListCol_.clear();
1342	+	point.resize(nGroupsInRow_+1);
1343		#else
1344		cellList_.clear();
1345	+	point.resize(nGroups_+1);
1346		#endif
1347	+
1348	+	if (!usePeriodicBoundaryConditions_) {
1349	+	box = snap_->getBoundingBox();
1350	+	invBox = snap_->getInvBoundingBox();
1351	+	} else {
1352	+	box = snap_->getHmat();
1353	+	invBox = snap_->getInvHmat();
1354	+	}
1355	+
1356	+	Vector3d A = box.getColumn(0);
1357	+	Vector3d B = box.getColumn(1);
1358	+	Vector3d C = box.getColumn(2);
1359
1360	<	RealType rList_ = (largestRcut_ + skinThickness_);
1361	<	RealType rl2 = rList_ * rList_;
1362	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
1363	<	Mat3x3d Hmat = snap_->getHmat();
964	<	Vector3d Hx = Hmat.getColumn(0);
965	<	Vector3d Hy = Hmat.getColumn(1);
966	<	Vector3d Hz = Hmat.getColumn(2);
967	<
968	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
969	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
970	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
1360	>	// Required for triclinic cells
1361	>	Vector3d AxB = cross(A, B);
1362	>	Vector3d BxC = cross(B, C);
1363	>	Vector3d CxA = cross(C, A);
1364
1365	<	Mat3x3d invHmat = snap_->getInvHmat();
1366	<	Vector3d rs, scaled, dr;
1367	<	Vector3i whichCell;
1368	<	int cellIndex;
976	<	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1365	>	// unit vectors perpendicular to the faces of the triclinic cell:
1366	>	AxB.normalize();
1367	>	BxC.normalize();
1368	>	CxA.normalize();
1369
1370	+	// A set of perpendicular lengths in triclinic cells:
1371	+	RealType Wa = abs(dot(A, BxC));
1372	+	RealType Wb = abs(dot(B, CxA));
1373	+	RealType Wc = abs(dot(C, AxB));
1374	+
1375	+	nCells_.x() = int( Wa / rList_ );
1376	+	nCells_.y() = int( Wb / rList_ );
1377	+	nCells_.z() = int( Wc / rList_ );
1378	+
1379	+	// handle small boxes where the cell offsets can end up repeating cells
1380	+	if (nCells_.x() < 3) doAllPairs = true;
1381	+	if (nCells_.y() < 3) doAllPairs = true;
1382	+	if (nCells_.z() < 3) doAllPairs = true;
1383	+
1384	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1385	+
1386		#ifdef IS_MPI
1387		cellListRow_.resize(nCtot);
1388		cellListCol_.resize(nCtot);
1389		#else
1390		cellList_.resize(nCtot);
1391		#endif
1392	<
1392	>
1393	>	if (!doAllPairs) {
1394	>
1395		#ifdef IS_MPI
1396	<	for (int i = 0; i < nGroupsInRow_; i++) {
1397	<	rs = cgRowData.position[i];
1398	<
1399	<	// scaled positions relative to the box vectors
1400	<	scaled = invHmat * rs;
1401	<
1402	<	// wrap the vector back into the unit box by subtracting integer box
1403	<	// numbers
1404	<	for (int j = 0; j < 3; j++) {
1405	<	scaled[j] -= roundMe(scaled[j]);
1406	<	scaled[j] += 0.5;
1396	>
1397	>	for (int i = 0; i < nGroupsInRow_; i++) {
1398	>	rs = cgRowData.position[i];
1399	>
1400	>	// scaled positions relative to the box vectors
1401	>	scaled = invBox * rs;
1402	>
1403	>	// wrap the vector back into the unit box by subtracting integer box
1404	>	// numbers
1405	>	for (int j = 0; j < 3; j++) {
1406	>	scaled[j] -= roundMe(scaled[j]);
1407	>	scaled[j] += 0.5;
1408	>	// Handle the special case when an object is exactly on the
1409	>	// boundary (a scaled coordinate of 1.0 is the same as
1410	>	// scaled coordinate of 0.0)
1411	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1412	>	}
1413	>
1414	>	// find xyz-indices of cell that cutoffGroup is in.
1415	>	whichCell.x() = nCells_.x() * scaled.x();
1416	>	whichCell.y() = nCells_.y() * scaled.y();
1417	>	whichCell.z() = nCells_.z() * scaled.z();
1418	>
1419	>	// find single index of this cell:
1420	>	cellIndex = Vlinear(whichCell, nCells_);
1421	>
1422	>	// add this cutoff group to the list of groups in this cell;
1423	>	cellListRow_[cellIndex].push_back(i);
1424		}
1425	<
1426	<	// find xyz-indices of cell that cutoffGroup is in.
1427	<	whichCell.x() = nCells_.x() * scaled.x();
1428	<	whichCell.y() = nCells_.y() * scaled.y();
1429	<	whichCell.z() = nCells_.z() * scaled.z();
1430	<
1431	<	// find single index of this cell:
1432	<	cellIndex = Vlinear(whichCell, nCells_);
1433	<
1434	<	// add this cutoff group to the list of groups in this cell;
1435	<	cellListRow_[cellIndex].push_back(i);
1436	<	}
1437	<
1438	<	for (int i = 0; i < nGroupsInCol_; i++) {
1439	<	rs = cgColData.position[i];
1440	<
1441	<	// scaled positions relative to the box vectors
1442	<	scaled = invHmat * rs;
1443	<
1444	<	// wrap the vector back into the unit box by subtracting integer box
1445	<	// numbers
1446	<	for (int j = 0; j < 3; j++) {
1447	<	scaled[j] -= roundMe(scaled[j]);
1448	<	scaled[j] += 0.5;
1425	>	for (int i = 0; i < nGroupsInCol_; i++) {
1426	>	rs = cgColData.position[i];
1427	>
1428	>	// scaled positions relative to the box vectors
1429	>	scaled = invBox * rs;
1430	>
1431	>	// wrap the vector back into the unit box by subtracting integer box
1432	>	// numbers
1433	>	for (int j = 0; j < 3; j++) {
1434	>	scaled[j] -= roundMe(scaled[j]);
1435	>	scaled[j] += 0.5;
1436	>	// Handle the special case when an object is exactly on the
1437	>	// boundary (a scaled coordinate of 1.0 is the same as
1438	>	// scaled coordinate of 0.0)
1439	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1440	>	}
1441	>
1442	>	// find xyz-indices of cell that cutoffGroup is in.
1443	>	whichCell.x() = nCells_.x() * scaled.x();
1444	>	whichCell.y() = nCells_.y() * scaled.y();
1445	>	whichCell.z() = nCells_.z() * scaled.z();
1446	>
1447	>	// find single index of this cell:
1448	>	cellIndex = Vlinear(whichCell, nCells_);
1449	>
1450	>	// add this cutoff group to the list of groups in this cell;
1451	>	cellListCol_[cellIndex].push_back(i);
1452		}
1453	<
1024	<	// find xyz-indices of cell that cutoffGroup is in.
1025	<	whichCell.x() = nCells_.x() * scaled.x();
1026	<	whichCell.y() = nCells_.y() * scaled.y();
1027	<	whichCell.z() = nCells_.z() * scaled.z();
1028	<
1029	<	// find single index of this cell:
1030	<	cellIndex = Vlinear(whichCell, nCells_);
1031	<
1032	<	// add this cutoff group to the list of groups in this cell;
1033	<	cellListCol_[cellIndex].push_back(i);
1034	<	}
1453	>
1454		#else
1455	<	for (int i = 0; i < nGroups_; i++) {
1456	<	rs = snap_->cgData.position[i];
1457	<
1458	<	// scaled positions relative to the box vectors
1459	<	scaled = invHmat * rs;
1460	<
1461	<	// wrap the vector back into the unit box by subtracting integer box
1462	<	// numbers
1463	<	for (int j = 0; j < 3; j++) {
1464	<	scaled[j] -= roundMe(scaled[j]);
1465	<	scaled[j] += 0.5;
1455	>	for (int i = 0; i < nGroups_; i++) {
1456	>	rs = snap_->cgData.position[i];
1457	>
1458	>	// scaled positions relative to the box vectors
1459	>	scaled = invBox * rs;
1460	>
1461	>	// wrap the vector back into the unit box by subtracting integer box
1462	>	// numbers
1463	>	for (int j = 0; j < 3; j++) {
1464	>	scaled[j] -= roundMe(scaled[j]);
1465	>	scaled[j] += 0.5;
1466	>	// Handle the special case when an object is exactly on the
1467	>	// boundary (a scaled coordinate of 1.0 is the same as
1468	>	// scaled coordinate of 0.0)
1469	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1470	>	}
1471	>
1472	>	// find xyz-indices of cell that cutoffGroup is in.
1473	>	whichCell.x() = int(nCells_.x() * scaled.x());
1474	>	whichCell.y() = int(nCells_.y() * scaled.y());
1475	>	whichCell.z() = int(nCells_.z() * scaled.z());
1476	>
1477	>	// find single index of this cell:
1478	>	cellIndex = Vlinear(whichCell, nCells_);
1479	>
1480	>	// add this cutoff group to the list of groups in this cell;
1481	>	cellList_[cellIndex].push_back(i);
1482		}
1483
1484	<	// find xyz-indices of cell that cutoffGroup is in.
1050	<	whichCell.x() = nCells_.x() * scaled.x();
1051	<	whichCell.y() = nCells_.y() * scaled.y();
1052	<	whichCell.z() = nCells_.z() * scaled.z();
1484	>	#endif
1485
1486	<	// find single index of this cell:
1487	<	cellIndex = Vlinear(whichCell, nCells_);
1486	>	#ifdef IS_MPI
1487	>	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1488	>	rs = cgRowData.position[j1];
1489	>	#else
1490
1491	<	// add this cutoff group to the list of groups in this cell;
1492	<	cellList_[cellIndex].push_back(i);
1059	<	}
1491	>	for (int j1 = 0; j1 < nGroups_; j1++) {
1492	>	rs = snap_->cgData.position[j1];
1493		#endif
1494	+	point[j1] = len;
1495	+
1496	+	// scaled positions relative to the box vectors
1497	+	scaled = invBox * rs;
1498	+
1499	+	// wrap the vector back into the unit box by subtracting integer box
1500	+	// numbers
1501	+	for (int j = 0; j < 3; j++) {
1502	+	scaled[j] -= roundMe(scaled[j]);
1503	+	scaled[j] += 0.5;
1504	+	// Handle the special case when an object is exactly on the
1505	+	// boundary (a scaled coordinate of 1.0 is the same as
1506	+	// scaled coordinate of 0.0)
1507	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1508	+	}
1509	+
1510	+	// find xyz-indices of cell that cutoffGroup is in.
1511	+	whichCell.x() = nCells_.x() * scaled.x();
1512	+	whichCell.y() = nCells_.y() * scaled.y();
1513	+	whichCell.z() = nCells_.z() * scaled.z();
1514	+
1515	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1516	+	os != cellOffsets_.end(); ++os) {
1517	+
1518	+	Vector3i m2v = whichCell + (*os);
1519
1520	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1521	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1522	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1523	<	Vector3i m1v(m1x, m1y, m1z);
1524	<	int m1 = Vlinear(m1v, nCells_);
1525	<
1526	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1527	<	os != cellOffsets_.end(); ++os) {
1520	>	if (m2v.x() >= nCells_.x()) {
1521	>	m2v.x() = 0;
1522	>	} else if (m2v.x() < 0) {
1523	>	m2v.x() = nCells_.x() - 1;
1524	>	}
1525	>
1526	>	if (m2v.y() >= nCells_.y()) {
1527	>	m2v.y() = 0;
1528	>	} else if (m2v.y() < 0) {
1529	>	m2v.y() = nCells_.y() - 1;
1530	>	}
1531	>
1532	>	if (m2v.z() >= nCells_.z()) {
1533	>	m2v.z() = 0;
1534	>	} else if (m2v.z() < 0) {
1535	>	m2v.z() = nCells_.z() - 1;
1536	>	}
1537	>	int m2 = Vlinear (m2v, nCells_);
1538	>	#ifdef IS_MPI
1539	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1540	>	j2 != cellListCol_[m2].end(); ++j2) {
1541
1542	<	Vector3i m2v = m1v + (*os);
1543	<
1544	<	if (m2v.x() >= nCells_.x()) {
1545	<	m2v.x() = 0;
1546	<	} else if (m2v.x() < 0) {
1547	<	m2v.x() = nCells_.x() - 1;
1542	>	// In parallel, we need to visit *all* pairs of row
1543	>	// & column indicies and will divide labor in the
1544	>	// force evaluation later.
1545	>	dr = cgColData.position[(*j2)] - rs;
1546	>	if (usePeriodicBoundaryConditions_) {
1547	>	snap_->wrapVector(dr);
1548		}
1549	+	if (dr.lengthSquare() < rListSq_) {
1550	+	neighborList.push_back( (*j2) );
1551	+	++len;
1552	+	}
1553	+	}
1554	+	#else
1555	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1556	+	j2 != cellList_[m2].end(); ++j2) {
1557	+
1558	+	// Always do this if we're in different cells or if
1559	+	// we're in the same cell and the global index of
1560	+	// the j2 cutoff group is greater than or equal to
1561	+	// the j1 cutoff group.  Note that Rappaport's code
1562	+	// has a "less than" conditional here, but that
1563	+	// deals with atom-by-atom computation.  OpenMD
1564	+	// allows atoms within a single cutoff group to
1565	+	// interact with each other.
1566
1567	<	if (m2v.y() >= nCells_.y()) {
1568	<	m2v.y() = 0;
1569	<	} else if (m2v.y() < 0) {
1570	<	m2v.y() = nCells_.y() - 1;
1571	<	}
1084	<
1085	<	if (m2v.z() >= nCells_.z()) {
1086	<	m2v.z() = 0;
1087	<	} else if (m2v.z() < 0) {
1088	<	m2v.z() = nCells_.z() - 1;
1089	<	}
1090	<
1091	<	int m2 = Vlinear (m2v, nCells_);
1092	<
1093	<	#ifdef IS_MPI
1094	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1095	<	j1 != cellListRow_[m1].end(); ++j1) {
1096	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1097	<	j2 != cellListCol_[m2].end(); ++j2) {
1098	<
1099	<	// Always do this if we're in different cells or if
1100	<	// we're in the same cell and the global index of the
1101	<	// j2 cutoff group is less than the j1 cutoff group
1102	<
1103	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1104	<	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1105	<	snap_->wrapVector(dr);
1106	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1107	<	if (dr.lengthSquare() < cuts.third) {
1108	<	neighborList.push_back(make_pair((*j1), (*j2)));
1109	<	}
1110	<	}
1567	>	if ( (*j2) >= j1 ) {
1568	>
1569	>	dr = snap_->cgData.position[(*j2)] - rs;
1570	>	if (usePeriodicBoundaryConditions_) {
1571	>	snap_->wrapVector(dr);
1572		}
1573	<	}
1574	<	#else
1575	<
1115	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1116	<	j1 != cellList_[m1].end(); ++j1) {
1117	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1118	<	j2 != cellList_[m2].end(); ++j2) {
1119	<
1120	<	// Always do this if we're in different cells or if
1121	<	// we're in the same cell and the global index of the
1122	<	// j2 cutoff group is less than the j1 cutoff group
1123	<
1124	<	if (m2 != m1 || (*j2) < (*j1)) {
1125	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1126	<	snap_->wrapVector(dr);
1127	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1128	<	if (dr.lengthSquare() < cuts.third) {
1129	<	neighborList.push_back(make_pair((*j1), (*j2)));
1130	<	}
1131	<	}
1573	>	if ( dr.lengthSquare() < rListSq_) {
1574	>	neighborList.push_back( (*j2) );
1575	>	++len;
1576		}
1577		}
1578	+	}
1579		#endif
1580	+	}
1581	+	}
1582	+	} else {
1583	+	// branch to do all cutoff group pairs
1584	+	#ifdef IS_MPI
1585	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1586	+	point[j1] = len;
1587	+	rs = cgRowData.position[j1];
1588	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1589	+	dr = cgColData.position[j2] - rs;
1590	+	if (usePeriodicBoundaryConditions_) {
1591	+	snap_->wrapVector(dr);
1592		}
1593	+	if (dr.lengthSquare() < rListSq_) {
1594	+	neighborList.push_back( j2 );
1595	+	++len;
1596	+	}
1597		}
1598	+	}
1599	+	#else
1600	+	// include all groups here.
1601	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1602	+	point[j1] = len;
1603	+	rs = snap_->cgData.position[j1];
1604	+	// include self group interactions j2 == j1
1605	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1606	+	dr = snap_->cgData.position[j2] - rs;
1607	+	if (usePeriodicBoundaryConditions_) {
1608	+	snap_->wrapVector(dr);
1609	+	}
1610	+	if (dr.lengthSquare() < rListSq_) {
1611	+	neighborList.push_back( j2 );
1612	+	++len;
1613	+	}
1614	+	}
1615		}
1616	+	#endif
1617		}
1618	<
1618	>
1619	>	#ifdef IS_MPI
1620	>	point[nGroupsInRow_] = len;
1621	>	#else
1622	>	point[nGroups_] = len;
1623	>	#endif
1624	>
1625		// save the local cutoff group positions for the check that is
1626		// done on each loop:
1627		saved_CG_positions_.clear();
1628	+	saved_CG_positions_.reserve(nGroups_);
1629		for (int i = 0; i < nGroups_; i++)
1630		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1145	–
1146	–	return neighborList;
1631		}
1632		} //end namespace OpenMD

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