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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1571 by gezelter, Fri May 27 16:45:44 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	<	nGroups_ = snap_->getNumberOfCutoffGroups();
99	<
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();
72	–	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
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_);
78	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
79	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
115	>	MPI::Intracomm row = rowComm.getComm();
116	>	MPI::Intracomm col = colComm.getComm();
117
118	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
119	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
120	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
121	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
118	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
119	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
120	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
121	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
122	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
123
124	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
125	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
126	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
127	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
124	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
125	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
126	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
127	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
128	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
129
130	<	nAtomsInRow_ = AtomCommIntRow->getSize();
131	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
132	<	nGroupsInRow_ = cgCommIntRow->getSize();
133	<	nGroupsInCol_ = cgCommIntColumn->getSize();
130	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
131	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
132	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
133	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
134
135	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
136	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
137	+	nGroupsInRow_ = cgPlanIntRow->getSize();
138	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
139	+
140		// Modify the data storage objects with the correct layouts and sizes:
141		atomRowData.resize(nAtomsInRow_);
142		atomRowData.setStorageLayout(storageLayout_);
#	Line 102 | Line 146 | namespace OpenMD {
146		cgRowData.setStorageLayout(DataStorage::dslPosition);
147		cgColData.resize(nGroupsInCol_);
148		cgColData.setStorageLayout(DataStorage::dslPosition);
149	+
150	+	identsRow.resize(nAtomsInRow_);
151	+	identsCol.resize(nAtomsInCol_);
152
153	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
154	<	vector<RealType> (nAtomsInRow_, 0.0));
108	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
109	<	vector<RealType> (nAtomsInCol_, 0.0));
153	>	AtomPlanIntRow->gather(idents, identsRow);
154	>	AtomPlanIntColumn->gather(idents, identsCol);
155
156	<	identsRow.reserve(nAtomsInRow_);
157	<	identsCol.reserve(nAtomsInCol_);
158	<
114	<	AtomCommIntRow->gather(identsLocal, identsRow);
115	<	AtomCommIntColumn->gather(identsLocal, identsCol);
116	<
117	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
118	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
119	<
120	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
121	<	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_.reserve(nGroupsInRow_);
184	>	groupListRow_.resize(nGroupsInRow_);
185		for (int i = 0; i < nGroupsInRow_; i++) {
186		int gid = cgRowToGlobal[i];
187		for (int j = 0; j < nAtomsInRow_; j++) {
#	Line 135 | Line 192 | namespace OpenMD {
192		}
193
194		groupListCol_.clear();
195	<	groupListCol_.reserve(nGroupsInCol_);
195	>	groupListCol_.resize(nGroupsInCol_);
196		for (int i = 0; i < nGroupsInCol_; i++) {
197		int gid = cgColToGlobal[i];
198		for (int j = 0; j < nAtomsInCol_; j++) {
#	Line 145 | Line 202 | namespace OpenMD {
202		}
203		}
204
205	<	skipsForRowAtom.clear();
206	<	skipsForRowAtom.reserve(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.reserve(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		}
171	–	if (oneThree.hasPair(iglob, jglob)) {
172	–	toposForRowAtom[i].push_back(j);
173	–	topoDistRow[i][nTopos] = 2;
174	–	nTopos++;
175	–	}
176	–	if (oneFour.hasPair(iglob, jglob)) {
177	–	toposForRowAtom[i].push_back(j);
178	–	topoDistRow[i][nTopos] = 3;
179	–	nTopos++;
180	–	}
268		}
269		}
183	–
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_.reserve(nGroups_);
279	>	groupList_.resize(nGroups_);
280		for (int i = 0; i < nGroups_; i++) {
281		int gid = cgLocalToGlobal[i];
282		for (int j = 0; j < nLocal_; j++) {
283		int aid = AtomLocalToGlobal[j];
284	<	if (globalGroupMembership[aid] == gid)
284	>	if (globalGroupMembership[aid] == gid) {
285		groupList_[i].push_back(j);
286	+	}
287		}
288		}
289
197	–	skipsForLocalAtom.clear();
198	–	skipsForLocalAtom.reserve(nLocal_);
290
291	<	for (int i = 0; i < nLocal_; i++) {
201	<	int iglob = AtomLocalToGlobal[i];
202	<	for (int j = 0; j < nLocal_; j++) {
203	<	int jglob = AtomLocalToGlobal[j];
204	<	if (excludes.hasPair(iglob, jglob))
205	<	skipsForLocalAtom[i].push_back(j);
206	<	}
207	<	}
291	>	createGtypeCutoffMap();
292
293	<	toposForLocalAtom.clear();
294	<	toposForLocalAtom.reserve(nLocal_);
295	<	for (int i = 0; i < nLocal_; i++) {
296	<	int iglob = AtomLocalToGlobal[i];
297	<	int nTopos = 0;
298	<	for (int j = 0; j < nLocal_; j++) {
299	<	int jglob = AtomLocalToGlobal[j];
300	<	if (oneTwo.hasPair(iglob, jglob)) {
301	<	toposForLocalAtom[i].push_back(j);
302	<	topoDistLocal[i][nTopos] = 1;
303	<	nTopos++;
293	>	}
294	>
295	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
296	>
297	>	RealType tol = 1e-6;
298	>	largestRcut_ = 0.0;
299	>	RealType rc;
300	>	int atid;
301	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
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	>	if (userChoseCutoff_)
309	>	atypeCutoff[atid] = userCutoff_;
310	>	else
311	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312	>	}
313	>
314	>	vector<RealType> gTypeCutoffs;
315	>	// first we do a single loop over the cutoff groups to find the
316	>	// largest cutoff for any atypes present in this group.
317	>	#ifdef IS_MPI
318	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
319	>	groupRowToGtype.resize(nGroupsInRow_);
320	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
321	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
322	>	for (vector<int>::iterator ia = atomListRow.begin();
323	>	ia != atomListRow.end(); ++ia) {
324	>	int atom1 = (*ia);
325	>	atid = identsRow[atom1];
326	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
327	>	groupCutoffRow[cg1] = atypeCutoff[atid];
328		}
329	<	if (oneThree.hasPair(iglob, jglob)) {
330	<	toposForLocalAtom[i].push_back(j);
331	<	topoDistLocal[i][nTopos] = 2;
332	<	nTopos++;
333	<	}
334	<	if (oneFour.hasPair(iglob, jglob)) {
335	<	toposForLocalAtom[i].push_back(j);
336	<	topoDistLocal[i][nTopos] = 3;
337	<	nTopos++;
329	>	}
330	>
331	>	bool gTypeFound = false;
332	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
333	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
334	>	groupRowToGtype[cg1] = gt;
335	>	gTypeFound = true;
336	>	}
337	>	}
338	>	if (!gTypeFound) {
339	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
340	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
341	>	}
342	>
343	>	}
344	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
345	>	groupColToGtype.resize(nGroupsInCol_);
346	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
347	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
348	>	for (vector<int>::iterator jb = atomListCol.begin();
349	>	jb != atomListCol.end(); ++jb) {
350	>	int atom2 = (*jb);
351	>	atid = identsCol[atom2];
352	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
353	>	groupCutoffCol[cg2] = atypeCutoff[atid];
354		}
355	+	}
356	+	bool gTypeFound = false;
357	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
358	+	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
359	+	groupColToGtype[cg2] = gt;
360	+	gTypeFound = true;
361	+	}
362	+	}
363	+	if (!gTypeFound) {
364	+	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
365	+	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
366	+	}
367	+	}
368	+	#else
369	+
370	+	vector<RealType> groupCutoff(nGroups_, 0.0);
371	+	groupToGtype.resize(nGroups_);
372	+	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
373	+	groupCutoff[cg1] = 0.0;
374	+	vector<int> atomList = getAtomsInGroupRow(cg1);
375	+	for (vector<int>::iterator ia = atomList.begin();
376	+	ia != atomList.end(); ++ia) {
377	+	int atom1 = (*ia);
378	+	atid = idents[atom1];
379	+	if (atypeCutoff[atid] > groupCutoff[cg1])
380	+	groupCutoff[cg1] = atypeCutoff[atid];
381	+	}
382	+
383	+	bool gTypeFound = false;
384	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385	+	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
386	+	groupToGtype[cg1] = gt;
387	+	gTypeFound = true;
388	+	}
389	+	}
390	+	if (!gTypeFound) {
391	+	gTypeCutoffs.push_back( groupCutoff[cg1] );
392	+	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393		}
394		}
395	+	#endif
396	+
397	+	// Now we find the maximum group cutoff value present in the simulation
398	+
399	+	RealType groupMax = *max_element(gTypeCutoffs.begin(),
400	+	gTypeCutoffs.end());
401	+
402	+	#ifdef IS_MPI
403	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
404	+	MPI::MAX);
405	+	#endif
406	+
407	+	RealType tradRcut = groupMax;
408	+
409	+	for (int i = 0; i < gTypeCutoffs.size();  i++) {
410	+	for (int j = 0; j < gTypeCutoffs.size();  j++) {
411	+	RealType thisRcut;
412	+	switch(cutoffPolicy_) {
413	+	case TRADITIONAL:
414	+	thisRcut = tradRcut;
415	+	break;
416	+	case MIX:
417	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
418	+	break;
419	+	case MAX:
420	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
421	+	break;
422	+	default:
423	+	sprintf(painCave.errMsg,
424	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
425	+	"hit an unknown cutoff policy!\n");
426	+	painCave.severity = OPENMD_ERROR;
427	+	painCave.isFatal = 1;
428	+	simError();
429	+	break;
430	+	}
431	+
432	+	pair<int,int> key = make_pair(i,j);
433	+	gTypeCutoffMap[key].first = thisRcut;
434	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
435	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
436	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
437	+	// sanity check
438	+
439	+	if (userChoseCutoff_) {
440	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
441	+	sprintf(painCave.errMsg,
442	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
443	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
444	+	painCave.severity = OPENMD_ERROR;
445	+	painCave.isFatal = 1;
446	+	simError();
447	+	}
448	+	}
449	+	}
450	+	}
451		}
452	<
452	>
453	>
454	>	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
455	>	int i, j;
456	>	#ifdef IS_MPI
457	>	i = groupRowToGtype[cg1];
458	>	j = groupColToGtype[cg2];
459	>	#else
460	>	i = groupToGtype[cg1];
461	>	j = groupToGtype[cg2];
462	>	#endif
463	>	return gTypeCutoffMap[make_pair(i,j)];
464	>	}
465	>
466	>	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
467	>	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
468	>	if (toposForAtom[atom1][j] == atom2)
469	>	return topoDist[atom1][j];
470	>	}
471	>	return 0;
472	>	}
473	>
474	>	void ForceMatrixDecomposition::zeroWorkArrays() {
475	>	pairwisePot = 0.0;
476	>	embeddingPot = 0.0;
477	>
478	>	#ifdef IS_MPI
479	>	if (storageLayout_ & DataStorage::dslForce) {
480	>	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
481	>	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
482	>	}
483	>
484	>	if (storageLayout_ & DataStorage::dslTorque) {
485	>	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
486	>	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
487	>	}
488	>
489	>	fill(pot_row.begin(), pot_row.end(),
490	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
491	>
492	>	fill(pot_col.begin(), pot_col.end(),
493	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
494	>
495	>	if (storageLayout_ & DataStorage::dslParticlePot) {
496	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
497	>	0.0);
498	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
499	>	0.0);
500	>	}
501	>
502	>	if (storageLayout_ & DataStorage::dslDensity) {
503	>	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
504	>	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
505	>	}
506	>
507	>	if (storageLayout_ & DataStorage::dslFunctional) {
508	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
509	>	0.0);
510	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
511	>	0.0);
512	>	}
513	>
514	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
515	>	fill(atomRowData.functionalDerivative.begin(),
516	>	atomRowData.functionalDerivative.end(), 0.0);
517	>	fill(atomColData.functionalDerivative.begin(),
518	>	atomColData.functionalDerivative.end(), 0.0);
519	>	}
520	>
521	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
522	>	fill(atomRowData.skippedCharge.begin(),
523	>	atomRowData.skippedCharge.end(), 0.0);
524	>	fill(atomColData.skippedCharge.begin(),
525	>	atomColData.skippedCharge.end(), 0.0);
526	>	}
527	>
528	>	if (storageLayout_ & DataStorage::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);
555	>	}
556	>
557	>	if (storageLayout_ & DataStorage::dslDensity) {
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	>
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	>
584		void ForceMatrixDecomposition::distributeData()  {
585		snap_ = sman_->getCurrentSnapshot();
586		storageLayout_ = sman_->getStorageLayout();
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
631	+	/* collects information obtained during the pre-pair loop onto local
632	+	* data structures.
633	+	*/
634		void ForceMatrixDecomposition::collectIntermediateData() {
635		snap_ = sman_->getCurrentSnapshot();
636		storageLayout_ = sman_->getStorageLayout();
#	Line 274 | 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	<	std::vector<RealType> rho_tmp(n, 0.0);
646	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
645	>	vector<RealType> rho_tmp(n, 0.0);
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	<
664	>
665	>	/*
666	>	* redistributes information obtained during the pre-pair loop out to
667	>	* row and column-indexed data structures
668	>	*/
669		void ForceMatrixDecomposition::distributeIntermediateData() {
670		snap_ = sman_->getCurrentSnapshot();
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 314 | 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<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
761	<	vector<RealType> (nLocal_, 0.0));
760	>	vector<potVec> pot_temp(nLocal_,
761	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
762	>
763	>	// scatter/gather pot_row into the members of my column
764	>
765	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
766	>
767	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
768	>	pairwisePot += pot_temp[ii];
769
770	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
771	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
772	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
773	<	pot_local[i] += pot_temp[i][ii];
774	<	}
770	>	fill(pot_temp.begin(), pot_temp.end(),
771	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
772	>
773	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
774	>
775	>	for (int ii = 0;  ii < pot_temp.size(); 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 427 | 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 435 | 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 453 | Line 891 | namespace OpenMD {
891		return d;
892		}
893
894	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
895	<	#ifdef IS_MPI
458	<	return skipsForRowAtom[atom1];
459	<	#else
460	<	return skipsForLocalAtom[atom1];
461	<	#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 particle mostly
900	<	* we do this to exclude atoms who are involved in short range
467	<	* interactions (bonds, bends, torsions), but we also need to
468	<	* exclude some overcounted interactions that result from the
469	<	* parallel decomposition.
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
479	–	// 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		}
488	–	#else
489	–	// in the normal loop, the atom numbers are unique
490	–	unique_id_1 = atom1;
491	–	unique_id_2 = atom2;
923		#endif
924
925	<	#ifdef IS_MPI
495	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
496	<	i != skipsForRowAtom[atom1].end(); ++i) {
497	<	if ( (*i) == unique_id_2 ) return true;
498	<	}
499	<	#else
500	<	for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
501	<	i != skipsForLocalAtom[atom1].end(); ++i) {
502	<	if ( (*i) == unique_id_2 ) return true;
503	<	}
504	<	#endif
925	>	return false;
926		}
927
928	<	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
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	<	#ifdef IS_MPI
943	<	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
944	<	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
942	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
943	>	i != excludesForAtom[atom1].end(); ++i) {
944	>	if ( (*i) == atom2 ) return true;
945		}
513	–	#else
514	–	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
515	–	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
516	–	}
517	–	#endif
946
947	<	// zero is default for unconnected (i.e. normal) pair interactions
520	<	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 537 | 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
545	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
546	–	ff_->getAtomType(identsCol[atom2]) );
547	–
978		if (storageLayout_ & DataStorage::dslAmat) {
979		idat.A1 = &(atomRowData.aMat[atom1]);
980		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 565 | Line 995 | namespace OpenMD {
995		idat.rho2 = &(atomColData.density[atom2]);
996		}
997
998	+	if (storageLayout_ & DataStorage::dslFunctional) {
999	+	idat.frho1 = &(atomRowData.functional[atom1]);
1000	+	idat.frho2 = &(atomColData.functional[atom2]);
1001	+	}
1002	+
1003		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1004		idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1005		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1006		}
1007
1008	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1009	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
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 590 | 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		}
1053
1054	+	if (storageLayout_ & DataStorage::dslFunctional) {
1055	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1056	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1057	+	}
1058	+
1059		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1060		idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1061		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1062		}
1063	+
1064	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1065	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
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
603	–	return idat;
1080		}
1081
1082	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1083	<
608	<	InteractionData idat;
1082	>
1083	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1084		#ifdef IS_MPI
1085	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1086	<	ff_->getAtomType(identsCol[atom2]) );
1085	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1086	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1087
1088	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1089	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1090	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1088	>	atomRowData.force[atom1] += *(idat.f1);
1089	>	atomColData.force[atom2] -= *(idat.f1);
1090	>
1091	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1092	>	atomRowData.flucQFrc[atom1] += *(idat.dVdFQ1);
1093	>	atomColData.flucQFrc[atom2] += *(idat.dVdFQ2);
1094		}
1095	<	if (storageLayout_ & DataStorage::dslTorque) {
1096	<	idat.t1 = &(atomRowData.torque[atom1]);
1097	<	idat.t2 = &(atomColData.torque[atom2]);
1095	>
1096	>	if (storageLayout_ & DataStorage::dslElectricField) {
1097	>	atomRowData.electricField[atom1] += *(idat.eField1);
1098	>	atomColData.electricField[atom2] += *(idat.eField2);
1099		}
1100	<	if (storageLayout_ & DataStorage::dslForce) {
1101	<	idat.t1 = &(atomRowData.force[atom1]);
623	<	idat.t2 = &(atomColData.force[atom2]);
624	<	}
1100	>
1101	>	// should particle pot be done here also?
1102		#else
1103	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
627	<	ff_->getAtomType(identsLocal[atom2]) );
1103	>	pairwisePot += *(idat.pot);
1104
1105	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1106	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1107	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1105	>	snap_->atomData.force[atom1] += *(idat.f1);
1106	>	snap_->atomData.force[atom2] -= *(idat.f1);
1107	>
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 = &(snap_->atomData.torque[atom1]);
1114	<	idat.t2 = &(snap_->atomData.torque[atom2]);
1112	>
1113	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1114	>	snap_->atomData.flucQFrc[atom1] += *(idat.dVdFQ1);
1115	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1116		}
1117	<	if (storageLayout_ & DataStorage::dslForce) {
1118	<	idat.t1 = &(snap_->atomData.force[atom1]);
1119	<	idat.t2 = &(snap_->atomData.force[atom2]);
1117	>
1118	>	if (storageLayout_ & DataStorage::dslElectricField) {
1119	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1120	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1121		}
1122	<	#endif
1122	>
1123	>	#endif
1124	>
1125		}
1126
1127		/*
#	Line 650 | Line 1133 | namespace OpenMD {
1133		vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
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 657 | Line 1143 | namespace OpenMD {
1143		cellList_.clear();
1144		#endif
1145
1146	<	// dangerous to not do error checking.
661	<	RealType rCut_;
662	<
663	<	RealType rList_ = (rCut_ + skinThickness_);
1146	>	RealType rList_ = (largestRcut_ + skinThickness_);
1147		RealType rl2 = rList_ * rList_;
1148		Snapshot* snap_ = sman_->getCurrentSnapshot();
1149		Mat3x3d Hmat = snap_->getHmat();
#	Line 672 | 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
686	<	// numbers
687	<	for (int j = 0; j < 3; j++)
688	<	scaled[j] -= roundMe(scaled[j]);
689	<
690	<	// find xyz-indices of cell that cutoffGroup is in.
691	<	whichCell.x() = nCells_.x() * scaled.x();
692	<	whichCell.y() = nCells_.y() * scaled.y();
693	<	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_);
697	<	// add this cutoff group to the list of groups in this cell;
698	<	cellListRow_[cellIndex].push_back(i);
699	<	}
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
730	–	// find xyz-indices of cell that cutoffGroup is in.
731	–	whichCell.x() = nCells_.x() * scaled.x();
732	–	whichCell.y() = nCells_.y() * scaled.y();
733	–	whichCell.z() = nCells_.z() * scaled.z();
734	–
735	–	// find single index of this cell:
736	–	cellIndex = Vlinear(whichCell, nCells_);
737	–	// add this cutoff group to the list of groups in this cell;
738	–	cellList_[cellIndex].push_back(i);
739	–	}
1255		#endif
1256
1257	<
1258	<
1259	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1260	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1261	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
747	<	Vector3i m1v(m1x, m1y, m1z);
748	<	int m1 = Vlinear(m1v, nCells_);
749	<
750	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
751	<	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) {
758	<	m2v.x() = nCells_.x() - 1;
759	<	}
760	<
761	<	if (m2v.y() >= nCells_.y()) {
762	<	m2v.y() = 0;
763	<	} else if (m2v.y() < 0) {
764	<	m2v.y() = nCells_.y() - 1;
765	<	}
766	<
767	<	if (m2v.z() >= nCells_.z()) {
768	<	m2v.z() = 0;
769	<	} else if (m2v.z() < 0) {
770	<	m2v.z() = nCells_.z() - 1;
771	<	}
772	<
773	<	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	<	if (dr.lengthSquare() < rl2) {
1300	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1301	>	if (dr.lengthSquare() < cuts.third) {
1302		neighborList.push_back(make_pair((*j1), (*j2)));
1303	<	}
1303	>	}
1304		}
1305		}
793	–	}
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	<	if (dr.lengthSquare() < rl2) {
1325	<	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		}
812	–	}
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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