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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1562 by gezelter, Thu May 12 17:00:14 2011 UTC vs.
Revision 1756 by gezelter, Mon Jun 18 18:23:20 2012 UTC

#	Line 36 | Line 36
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
44		#include "nonbonded/NonBondedInteraction.hpp"
45		#include "brains/SnapshotManager.hpp"
46	+	#include "brains/PairList.hpp"
47
48		using namespace std;
49		namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	+
53	+	// In a parallel computation, row and colum scans must visit all
54	+	// surrounding cells (not just the 14 upper triangular blocks that
55	+	// are used when the processor can see all pairs)
56	+	#ifdef IS_MPI
57	+	cellOffsets_.clear();
58	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
66	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	+	#endif
86	+	}
87	+
88	+
89		/**
90		* distributeInitialData is essentially a copy of the older fortran
91		* SimulationSetup
92		*/
53	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96	<	#ifdef IS_MPI
97	<	int nLocal = snap_->getNumberOfAtoms();
98	<	int nGroups = snap_->getNumberOfCutoffGroups();
96	>	ff_ = info_->getForceField();
97	>	nLocal_ = snap_->getNumberOfAtoms();
98	>
99	>	nGroups_ = info_->getNLocalCutoffGroups();
100	>	// gather the information for atomtype IDs (atids):
101	>	idents = info_->getIdentArray();
102	>	AtomLocalToGlobal = info_->getGlobalAtomIndices();
103	>	cgLocalToGlobal = info_->getGlobalGroupIndices();
104	>	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
105	>
106	>	massFactors = info_->getMassFactors();
107	>
108	>	PairList* excludes = info_->getExcludedInteractions();
109	>	PairList* oneTwo = info_->getOneTwoInteractions();
110	>	PairList* oneThree = info_->getOneThreeInteractions();
111	>	PairList* oneFour = info_->getOneFourInteractions();
112
113	<	AtomCommIntRow = new Communicator<Row,int>(nLocal);
114	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
115	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
116	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
113	>	if (needVelocities_)
114	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
115	>	DataStorage::dslVelocity);
116	>	else
117	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118	>
119	>	#ifdef IS_MPI
120	>
121	>	MPI::Intracomm row = rowComm.getComm();
122	>	MPI::Intracomm col = colComm.getComm();
123
124	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal);
125	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
126	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
127	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
124	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
125	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
126	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
127	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
128	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
129
130	<	cgCommIntRow = new Communicator<Row,int>(nGroups);
131	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
132	<	cgCommIntColumn = new Communicator<Column,int>(nGroups);
133	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
130	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
131	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
132	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
133	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
134	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
135
136	<	int nAtomsInRow = AtomCommIntRow->getSize();
137	<	int nAtomsInCol = AtomCommIntColumn->getSize();
138	<	int nGroupsInRow = cgCommIntRow->getSize();
139	<	int nGroupsInCol = cgCommIntColumn->getSize();
136	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
137	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
138	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
139	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
140
141	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
142	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
143	+	nGroupsInRow_ = cgPlanIntRow->getSize();
144	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
145	+
146		// Modify the data storage objects with the correct layouts and sizes:
147	<	atomRowData.resize(nAtomsInRow);
147	>	atomRowData.resize(nAtomsInRow_);
148		atomRowData.setStorageLayout(storageLayout_);
149	<	atomColData.resize(nAtomsInCol);
149	>	atomColData.resize(nAtomsInCol_);
150		atomColData.setStorageLayout(storageLayout_);
151	<	cgRowData.resize(nGroupsInRow);
151	>	cgRowData.resize(nGroupsInRow_);
152		cgRowData.setStorageLayout(DataStorage::dslPosition);
153	<	cgColData.resize(nGroupsInCol);
154	<	cgColData.setStorageLayout(DataStorage::dslPosition);
153	>	cgColData.resize(nGroupsInCol_);
154	>	if (needVelocities_)
155	>	// we only need column velocities if we need them.
156	>	cgColData.setStorageLayout(DataStorage::dslPosition |
157	>	DataStorage::dslVelocity);
158	>	else
159	>	cgColData.setStorageLayout(DataStorage::dslPosition);
160	>
161	>	identsRow.resize(nAtomsInRow_);
162	>	identsCol.resize(nAtomsInCol_);
163
164	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
165	<	vector<RealType> (nAtomsInRow, 0.0));
166	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
167	<	vector<RealType> (nAtomsInCol, 0.0));
164	>	AtomPlanIntRow->gather(idents, identsRow);
165	>	AtomPlanIntColumn->gather(idents, identsCol);
166	>
167	>	// allocate memory for the parallel objects
168	>	atypesRow.resize(nAtomsInRow_);
169	>	atypesCol.resize(nAtomsInCol_);
170
171	+	for (int i = 0; i < nAtomsInRow_; i++)
172	+	atypesRow[i] = ff_->getAtomType(identsRow[i]);
173	+	for (int i = 0; i < nAtomsInCol_; i++)
174	+	atypesCol[i] = ff_->getAtomType(identsCol[i]);
175
176	<	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
176	>	pot_row.resize(nAtomsInRow_);
177	>	pot_col.resize(nAtomsInCol_);
178	>
179	>	AtomRowToGlobal.resize(nAtomsInRow_);
180	>	AtomColToGlobal.resize(nAtomsInCol_);
181	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
182	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
183	>
184	>	cgRowToGlobal.resize(nGroupsInRow_);
185	>	cgColToGlobal.resize(nGroupsInCol_);
186	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
187	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
188	>
189	>	massFactorsRow.resize(nAtomsInRow_);
190	>	massFactorsCol.resize(nAtomsInCol_);
191	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
192	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
193	>
194	>	groupListRow_.clear();
195	>	groupListRow_.resize(nGroupsInRow_);
196	>	for (int i = 0; i < nGroupsInRow_; i++) {
197	>	int gid = cgRowToGlobal[i];
198	>	for (int j = 0; j < nAtomsInRow_; j++) {
199	>	int aid = AtomRowToGlobal[j];
200	>	if (globalGroupMembership[aid] == gid)
201	>	groupListRow_[i].push_back(j);
202	>	}
203	>	}
204	>
205	>	groupListCol_.clear();
206	>	groupListCol_.resize(nGroupsInCol_);
207	>	for (int i = 0; i < nGroupsInCol_; i++) {
208	>	int gid = cgColToGlobal[i];
209	>	for (int j = 0; j < nAtomsInCol_; j++) {
210	>	int aid = AtomColToGlobal[j];
211	>	if (globalGroupMembership[aid] == gid)
212	>	groupListCol_[i].push_back(j);
213	>	}
214	>	}
215	>
216	>	excludesForAtom.clear();
217	>	excludesForAtom.resize(nAtomsInRow_);
218	>	toposForAtom.clear();
219	>	toposForAtom.resize(nAtomsInRow_);
220	>	topoDist.clear();
221	>	topoDist.resize(nAtomsInRow_);
222	>	for (int i = 0; i < nAtomsInRow_; i++) {
223	>	int iglob = AtomRowToGlobal[i];
224	>
225	>	for (int j = 0; j < nAtomsInCol_; j++) {
226	>	int jglob = AtomColToGlobal[j];
227	>
228	>	if (excludes->hasPair(iglob, jglob))
229	>	excludesForAtom[i].push_back(j);
230	>
231	>	if (oneTwo->hasPair(iglob, jglob)) {
232	>	toposForAtom[i].push_back(j);
233	>	topoDist[i].push_back(1);
234	>	} else {
235	>	if (oneThree->hasPair(iglob, jglob)) {
236	>	toposForAtom[i].push_back(j);
237	>	topoDist[i].push_back(2);
238	>	} else {
239	>	if (oneFour->hasPair(iglob, jglob)) {
240	>	toposForAtom[i].push_back(j);
241	>	topoDist[i].push_back(3);
242	>	}
243	>	}
244	>	}
245	>	}
246	>	}
247	>
248	>	#else
249	>	excludesForAtom.clear();
250	>	excludesForAtom.resize(nLocal_);
251	>	toposForAtom.clear();
252	>	toposForAtom.resize(nLocal_);
253	>	topoDist.clear();
254	>	topoDist.resize(nLocal_);
255	>
256	>	for (int i = 0; i < nLocal_; i++) {
257	>	int iglob = AtomLocalToGlobal[i];
258	>
259	>	for (int j = 0; j < nLocal_; j++) {
260	>	int jglob = AtomLocalToGlobal[j];
261	>
262	>	if (excludes->hasPair(iglob, jglob))
263	>	excludesForAtom[i].push_back(j);
264	>
265	>	if (oneTwo->hasPair(iglob, jglob)) {
266	>	toposForAtom[i].push_back(j);
267	>	topoDist[i].push_back(1);
268	>	} else {
269	>	if (oneThree->hasPair(iglob, jglob)) {
270	>	toposForAtom[i].push_back(j);
271	>	topoDist[i].push_back(2);
272	>	} else {
273	>	if (oneFour->hasPair(iglob, jglob)) {
274	>	toposForAtom[i].push_back(j);
275	>	topoDist[i].push_back(3);
276	>	}
277	>	}
278	>	}
279	>	}
280	>	}
281	>	#endif
282	>
283	>	// allocate memory for the parallel objects
284	>	atypesLocal.resize(nLocal_);
285	>
286	>	for (int i = 0; i < nLocal_; i++)
287	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
288	>
289	>	groupList_.clear();
290	>	groupList_.resize(nGroups_);
291	>	for (int i = 0; i < nGroups_; i++) {
292	>	int gid = cgLocalToGlobal[i];
293	>	for (int j = 0; j < nLocal_; j++) {
294	>	int aid = AtomLocalToGlobal[j];
295	>	if (globalGroupMembership[aid] == gid) {
296	>	groupList_[i].push_back(j);
297	>	}
298	>	}
299	>	}
300	>
301	>
302	>	createGtypeCutoffMap();
303	>
304	>	}
305	>
306	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
307
308	<	// gather the information for atomtype IDs (atids):
309	<	vector<int> identsLocal = info_->getIdentArray();
310	<	identsRow.reserve(nAtomsInRow);
311	<	identsCol.reserve(nAtomsInCol);
308	>	RealType tol = 1e-6;
309	>	largestRcut_ = 0.0;
310	>	RealType rc;
311	>	int atid;
312	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
313
314	<	AtomCommIntRow->gather(identsLocal, identsRow);
315	<	AtomCommIntColumn->gather(identsLocal, identsCol);
314	>	map<int, RealType> atypeCutoff;
315	>
316	>	for (set<AtomType*>::iterator at = atypes.begin();
317	>	at != atypes.end(); ++at){
318	>	atid = (*at)->getIdent();
319	>	if (userChoseCutoff_)
320	>	atypeCutoff[atid] = userCutoff_;
321	>	else
322	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
323	>	}
324
325	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
326	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
327	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
328	<
329	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
330	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
331	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
325	>	vector<RealType> gTypeCutoffs;
326	>	// first we do a single loop over the cutoff groups to find the
327	>	// largest cutoff for any atypes present in this group.
328	>	#ifdef IS_MPI
329	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
330	>	groupRowToGtype.resize(nGroupsInRow_);
331	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
332	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
333	>	for (vector<int>::iterator ia = atomListRow.begin();
334	>	ia != atomListRow.end(); ++ia) {
335	>	int atom1 = (*ia);
336	>	atid = identsRow[atom1];
337	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
338	>	groupCutoffRow[cg1] = atypeCutoff[atid];
339	>	}
340	>	}
341
342	<	// still need:
343	<	// topoDist
344	<	// exclude
342	>	bool gTypeFound = false;
343	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
344	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
345	>	groupRowToGtype[cg1] = gt;
346	>	gTypeFound = true;
347	>	}
348	>	}
349	>	if (!gTypeFound) {
350	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
351	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
352	>	}
353	>
354	>	}
355	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
356	>	groupColToGtype.resize(nGroupsInCol_);
357	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
358	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
359	>	for (vector<int>::iterator jb = atomListCol.begin();
360	>	jb != atomListCol.end(); ++jb) {
361	>	int atom2 = (*jb);
362	>	atid = identsCol[atom2];
363	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
364	>	groupCutoffCol[cg2] = atypeCutoff[atid];
365	>	}
366	>	}
367	>	bool gTypeFound = false;
368	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
369	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
370	>	groupColToGtype[cg2] = gt;
371	>	gTypeFound = true;
372	>	}
373	>	}
374	>	if (!gTypeFound) {
375	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
376	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
377	>	}
378	>	}
379	>	#else
380	>
381	>	vector<RealType> groupCutoff(nGroups_, 0.0);
382	>	groupToGtype.resize(nGroups_);
383	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
384	>	groupCutoff[cg1] = 0.0;
385	>	vector<int> atomList = getAtomsInGroupRow(cg1);
386	>	for (vector<int>::iterator ia = atomList.begin();
387	>	ia != atomList.end(); ++ia) {
388	>	int atom1 = (*ia);
389	>	atid = idents[atom1];
390	>	if (atypeCutoff[atid] > groupCutoff[cg1])
391	>	groupCutoff[cg1] = atypeCutoff[atid];
392	>	}
393	>
394	>	bool gTypeFound = false;
395	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
396	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
397	>	groupToGtype[cg1] = gt;
398	>	gTypeFound = true;
399	>	}
400	>	}
401	>	if (!gTypeFound) {
402	>	gTypeCutoffs.push_back( groupCutoff[cg1] );
403	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
404	>	}
405	>	}
406		#endif
407	+
408	+	// Now we find the maximum group cutoff value present in the simulation
409	+
410	+	RealType groupMax = *max_element(gTypeCutoffs.begin(),
411	+	gTypeCutoffs.end());
412	+
413	+	#ifdef IS_MPI
414	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
415	+	MPI::MAX);
416	+	#endif
417	+
418	+	RealType tradRcut = groupMax;
419	+
420	+	for (int i = 0; i < gTypeCutoffs.size();  i++) {
421	+	for (int j = 0; j < gTypeCutoffs.size();  j++) {
422	+	RealType thisRcut;
423	+	switch(cutoffPolicy_) {
424	+	case TRADITIONAL:
425	+	thisRcut = tradRcut;
426	+	break;
427	+	case MIX:
428	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
429	+	break;
430	+	case MAX:
431	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
432	+	break;
433	+	default:
434	+	sprintf(painCave.errMsg,
435	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
436	+	"hit an unknown cutoff policy!\n");
437	+	painCave.severity = OPENMD_ERROR;
438	+	painCave.isFatal = 1;
439	+	simError();
440	+	break;
441	+	}
442	+
443	+	pair<int,int> key = make_pair(i,j);
444	+	gTypeCutoffMap[key].first = thisRcut;
445	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
446	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
447	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
448	+	// sanity check
449	+
450	+	if (userChoseCutoff_) {
451	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
452	+	sprintf(painCave.errMsg,
453	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
454	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
455	+	painCave.severity = OPENMD_ERROR;
456	+	painCave.isFatal = 1;
457	+	simError();
458	+	}
459	+	}
460	+	}
461	+	}
462		}
463	+
464	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
465	+	int i, j;
466	+	#ifdef IS_MPI
467	+	i = groupRowToGtype[cg1];
468	+	j = groupColToGtype[cg2];
469	+	#else
470	+	i = groupToGtype[cg1];
471	+	j = groupToGtype[cg2];
472	+	#endif
473	+	return gTypeCutoffMap[make_pair(i,j)];
474	+	}
475	+
476	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
477	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
478	+	if (toposForAtom[atom1][j] == atom2)
479	+	return topoDist[atom1][j];
480	+	}
481	+	return 0;
482	+	}
483	+
484	+	void ForceMatrixDecomposition::zeroWorkArrays() {
485	+	pairwisePot = 0.0;
486	+	embeddingPot = 0.0;
487	+
488	+	#ifdef IS_MPI
489	+	if (storageLayout_ & DataStorage::dslForce) {
490	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
491	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
492	+	}
493	+
494	+	if (storageLayout_ & DataStorage::dslTorque) {
495	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
496	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
497	+	}
498
499	+	fill(pot_row.begin(), pot_row.end(),
500	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
501
502	+	fill(pot_col.begin(), pot_col.end(),
503	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
504
505	+	if (storageLayout_ & DataStorage::dslParticlePot) {
506	+	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
507	+	0.0);
508	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
509	+	0.0);
510	+	}
511	+
512	+	if (storageLayout_ & DataStorage::dslDensity) {
513	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
514	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
515	+	}
516	+
517	+	if (storageLayout_ & DataStorage::dslFunctional) {
518	+	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
519	+	0.0);
520	+	fill(atomColData.functional.begin(), atomColData.functional.end(),
521	+	0.0);
522	+	}
523	+
524	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
525	+	fill(atomRowData.functionalDerivative.begin(),
526	+	atomRowData.functionalDerivative.end(), 0.0);
527	+	fill(atomColData.functionalDerivative.begin(),
528	+	atomColData.functionalDerivative.end(), 0.0);
529	+	}
530	+
531	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
532	+	fill(atomRowData.skippedCharge.begin(),
533	+	atomRowData.skippedCharge.end(), 0.0);
534	+	fill(atomColData.skippedCharge.begin(),
535	+	atomColData.skippedCharge.end(), 0.0);
536	+	}
537	+
538	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
539	+	fill(atomRowData.flucQFrc.begin(),
540	+	atomRowData.flucQFrc.end(), 0.0);
541	+	fill(atomColData.flucQFrc.begin(),
542	+	atomColData.flucQFrc.end(), 0.0);
543	+	}
544	+
545	+	if (storageLayout_ & DataStorage::dslElectricField) {
546	+	fill(atomRowData.electricField.begin(),
547	+	atomRowData.electricField.end(), V3Zero);
548	+	fill(atomColData.electricField.begin(),
549	+	atomColData.electricField.end(), V3Zero);
550	+	}
551	+
552	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
553	+	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
554	+	0.0);
555	+	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
556	+	0.0);
557	+	}
558	+
559	+	#endif
560	+	// even in parallel, we need to zero out the local arrays:
561	+
562	+	if (storageLayout_ & DataStorage::dslParticlePot) {
563	+	fill(snap_->atomData.particlePot.begin(),
564	+	snap_->atomData.particlePot.end(), 0.0);
565	+	}
566	+
567	+	if (storageLayout_ & DataStorage::dslDensity) {
568	+	fill(snap_->atomData.density.begin(),
569	+	snap_->atomData.density.end(), 0.0);
570	+	}
571	+
572	+	if (storageLayout_ & DataStorage::dslFunctional) {
573	+	fill(snap_->atomData.functional.begin(),
574	+	snap_->atomData.functional.end(), 0.0);
575	+	}
576	+
577	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
578	+	fill(snap_->atomData.functionalDerivative.begin(),
579	+	snap_->atomData.functionalDerivative.end(), 0.0);
580	+	}
581	+
582	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
583	+	fill(snap_->atomData.skippedCharge.begin(),
584	+	snap_->atomData.skippedCharge.end(), 0.0);
585	+	}
586	+
587	+	if (storageLayout_ & DataStorage::dslElectricField) {
588	+	fill(snap_->atomData.electricField.begin(),
589	+	snap_->atomData.electricField.end(), V3Zero);
590	+	}
591	+	}
592	+
593	+
594		void ForceMatrixDecomposition::distributeData()  {
595		snap_ = sman_->getCurrentSnapshot();
596		storageLayout_ = sman_->getStorageLayout();
597		#ifdef IS_MPI
598
599		// gather up the atomic positions
600	<	AtomCommVectorRow->gather(snap_->atomData.position,
600	>	AtomPlanVectorRow->gather(snap_->atomData.position,
601		atomRowData.position);
602	<	AtomCommVectorColumn->gather(snap_->atomData.position,
602	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
603		atomColData.position);
604
605		// gather up the cutoff group positions
606	<	cgCommVectorRow->gather(snap_->cgData.position,
606	>
607	>	cgPlanVectorRow->gather(snap_->cgData.position,
608		cgRowData.position);
609	<	cgCommVectorColumn->gather(snap_->cgData.position,
609	>
610	>	cgPlanVectorColumn->gather(snap_->cgData.position,
611		cgColData.position);
612	+
613	+
614	+
615	+	if (needVelocities_) {
616	+	// gather up the atomic velocities
617	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
618	+	atomColData.velocity);
619	+
620	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
621	+	cgColData.velocity);
622	+	}
623	+
624
625		// if needed, gather the atomic rotation matrices
626		if (storageLayout_ & DataStorage::dslAmat) {
627	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
627	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
628		atomRowData.aMat);
629	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
629	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
630		atomColData.aMat);
631		}
632
633		// if needed, gather the atomic eletrostatic frames
634		if (storageLayout_ & DataStorage::dslElectroFrame) {
635	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
635	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
636		atomRowData.electroFrame);
637	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
637	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
638		atomColData.electroFrame);
639		}
640	+
641	+	// if needed, gather the atomic fluctuating charge values
642	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
643	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
644	+	atomRowData.flucQPos);
645	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
646	+	atomColData.flucQPos);
647	+	}
648	+
649		#endif
650		}
651
652	+	/* collects information obtained during the pre-pair loop onto local
653	+	* data structures.
654	+	*/
655		void ForceMatrixDecomposition::collectIntermediateData() {
656		snap_ = sman_->getCurrentSnapshot();
657		storageLayout_ = sman_->getStorageLayout();
#	Line 162 | Line 659 | namespace OpenMD {
659
660		if (storageLayout_ & DataStorage::dslDensity) {
661
662	<	AtomCommRealRow->scatter(atomRowData.density,
662	>	AtomPlanRealRow->scatter(atomRowData.density,
663		snap_->atomData.density);
664
665		int n = snap_->atomData.density.size();
666	<	std::vector<RealType> rho_tmp(n, 0.0);
667	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
666	>	vector<RealType> rho_tmp(n, 0.0);
667	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
668		for (int i = 0; i < n; i++)
669		snap_->atomData.density[i] += rho_tmp[i];
670		}
671	+
672	+	if (storageLayout_ & DataStorage::dslElectricField) {
673	+
674	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
675	+	snap_->atomData.electricField);
676	+
677	+	int n = snap_->atomData.electricField.size();
678	+	vector<Vector3d> field_tmp(n, V3Zero);
679	+	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
680	+	for (int i = 0; i < n; i++)
681	+	snap_->atomData.electricField[i] += field_tmp[i];
682	+	}
683		#endif
684		}
685	<
685	>
686	>	/*
687	>	* redistributes information obtained during the pre-pair loop out to
688	>	* row and column-indexed data structures
689	>	*/
690		void ForceMatrixDecomposition::distributeIntermediateData() {
691		snap_ = sman_->getCurrentSnapshot();
692		storageLayout_ = sman_->getStorageLayout();
693		#ifdef IS_MPI
694		if (storageLayout_ & DataStorage::dslFunctional) {
695	<	AtomCommRealRow->gather(snap_->atomData.functional,
695	>	AtomPlanRealRow->gather(snap_->atomData.functional,
696		atomRowData.functional);
697	<	AtomCommRealColumn->gather(snap_->atomData.functional,
697	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
698		atomColData.functional);
699		}
700
701		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
702	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
702	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
703		atomRowData.functionalDerivative);
704	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
704	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
705		atomColData.functionalDerivative);
706		}
707		#endif
#	Line 202 | Line 715 | namespace OpenMD {
715		int n = snap_->atomData.force.size();
716		vector<Vector3d> frc_tmp(n, V3Zero);
717
718	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
718	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
719		for (int i = 0; i < n; i++) {
720		snap_->atomData.force[i] += frc_tmp[i];
721		frc_tmp[i] = 0.0;
722		}
723
724	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
725	<	for (int i = 0; i < n; i++)
724	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
725	>	for (int i = 0; i < n; i++) {
726		snap_->atomData.force[i] += frc_tmp[i];
727	<
728	<
727	>	}
728	>
729		if (storageLayout_ & DataStorage::dslTorque) {
730
731	<	int nt = snap_->atomData.force.size();
731	>	int nt = snap_->atomData.torque.size();
732		vector<Vector3d> trq_tmp(nt, V3Zero);
733
734	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
735	<	for (int i = 0; i < n; i++) {
734	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
735	>	for (int i = 0; i < nt; i++) {
736		snap_->atomData.torque[i] += trq_tmp[i];
737		trq_tmp[i] = 0.0;
738		}
739
740	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
741	<	for (int i = 0; i < n; i++)
740	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
741	>	for (int i = 0; i < nt; i++)
742		snap_->atomData.torque[i] += trq_tmp[i];
743		}
231	–
232	–	int nLocal = snap_->getNumberOfAtoms();
744
745	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
746	<	vector<RealType> (nLocal, 0.0));
747	<
748	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
749	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
750	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
751	<	pot_local[i] += pot_temp[i][ii];
745	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
746	>
747	>	int ns = snap_->atomData.skippedCharge.size();
748	>	vector<RealType> skch_tmp(ns, 0.0);
749	>
750	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
751	>	for (int i = 0; i < ns; i++) {
752	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
753	>	skch_tmp[i] = 0.0;
754		}
755	+
756	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
757	+	for (int i = 0; i < ns; i++)
758	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
759	+
760		}
761	+
762	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
763	+
764	+	int nq = snap_->atomData.flucQFrc.size();
765	+	vector<RealType> fqfrc_tmp(nq, 0.0);
766	+
767	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
768	+	for (int i = 0; i < nq; i++) {
769	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
770	+	fqfrc_tmp[i] = 0.0;
771	+	}
772	+
773	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
774	+	for (int i = 0; i < nq; i++)
775	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
776	+
777	+	}
778	+
779	+	nLocal_ = snap_->getNumberOfAtoms();
780	+
781	+	vector<potVec> pot_temp(nLocal_,
782	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
783	+
784	+	// scatter/gather pot_row into the members of my column
785	+
786	+	AtomPlanPotRow->scatter(pot_row, pot_temp);
787	+
788	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
789	+	pairwisePot += pot_temp[ii];
790	+
791	+	if (storageLayout_ & DataStorage::dslParticlePot) {
792	+	// This is the pairwise contribution to the particle pot.  The
793	+	// embedding contribution is added in each of the low level
794	+	// non-bonded routines.  In single processor, this is done in
795	+	// unpackInteractionData, not in collectData.
796	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
797	+	for (int i = 0; i < nLocal_; i++) {
798	+	// factor of two is because the total potential terms are divided
799	+	// by 2 in parallel due to row/ column scatter
800	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
801	+	}
802	+	}
803	+	}
804	+
805	+	fill(pot_temp.begin(), pot_temp.end(),
806	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
807	+
808	+	AtomPlanPotColumn->scatter(pot_col, pot_temp);
809	+
810	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
811	+	pairwisePot += pot_temp[ii];
812	+
813	+	if (storageLayout_ & DataStorage::dslParticlePot) {
814	+	// This is the pairwise contribution to the particle pot.  The
815	+	// embedding contribution is added in each of the low level
816	+	// non-bonded routines.  In single processor, this is done in
817	+	// unpackInteractionData, not in collectData.
818	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
819	+	for (int i = 0; i < nLocal_; i++) {
820	+	// factor of two is because the total potential terms are divided
821	+	// by 2 in parallel due to row/ column scatter
822	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
823	+	}
824	+	}
825	+	}
826	+
827	+	if (storageLayout_ & DataStorage::dslParticlePot) {
828	+	int npp = snap_->atomData.particlePot.size();
829	+	vector<RealType> ppot_temp(npp, 0.0);
830	+
831	+	// This is the direct or embedding contribution to the particle
832	+	// pot.
833	+
834	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
835	+	for (int i = 0; i < npp; i++) {
836	+	snap_->atomData.particlePot[i] += ppot_temp[i];
837	+	}
838	+
839	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
840	+
841	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
842	+	for (int i = 0; i < npp; i++) {
843	+	snap_->atomData.particlePot[i] += ppot_temp[i];
844	+	}
845	+	}
846	+
847	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
848	+	RealType ploc1 = pairwisePot[ii];
849	+	RealType ploc2 = 0.0;
850	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
851	+	pairwisePot[ii] = ploc2;
852	+	}
853	+
854	+	// Here be dragons.
855	+	MPI::Intracomm col = colComm.getComm();
856	+
857	+	col.Allreduce(MPI::IN_PLACE,
858	+	&snap_->frameData.conductiveHeatFlux[0], 3,
859	+	MPI::REALTYPE, MPI::SUM);
860	+
861	+
862		#endif
863	+
864		}
865
866	+	/**
867	+	* Collects information obtained during the post-pair (and embedding
868	+	* functional) loops onto local data structures.
869	+	*/
870	+	void ForceMatrixDecomposition::collectSelfData() {
871	+	snap_ = sman_->getCurrentSnapshot();
872	+	storageLayout_ = sman_->getStorageLayout();
873	+
874	+	#ifdef IS_MPI
875	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
876	+	RealType ploc1 = embeddingPot[ii];
877	+	RealType ploc2 = 0.0;
878	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
879	+	embeddingPot[ii] = ploc2;
880	+	}
881	+	#endif
882	+
883	+	}
884	+
885	+
886	+
887	+	int ForceMatrixDecomposition::getNAtomsInRow() {
888	+	#ifdef IS_MPI
889	+	return nAtomsInRow_;
890	+	#else
891	+	return nLocal_;
892	+	#endif
893	+	}
894	+
895	+	/**
896	+	* returns the list of atoms belonging to this group.
897	+	*/
898	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
899	+	#ifdef IS_MPI
900	+	return groupListRow_[cg1];
901	+	#else
902	+	return groupList_[cg1];
903	+	#endif
904	+	}
905	+
906	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
907	+	#ifdef IS_MPI
908	+	return groupListCol_[cg2];
909	+	#else
910	+	return groupList_[cg2];
911	+	#endif
912	+	}
913
914		Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
915		Vector3d d;
#	Line 257 | Line 924 | namespace OpenMD {
924		return d;
925		}
926
927	+	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
928	+	#ifdef IS_MPI
929	+	return cgColData.velocity[cg2];
930	+	#else
931	+	return snap_->cgData.velocity[cg2];
932	+	#endif
933	+	}
934
935	+	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
936	+	#ifdef IS_MPI
937	+	return atomColData.velocity[atom2];
938	+	#else
939	+	return snap_->atomData.velocity[atom2];
940	+	#endif
941	+	}
942	+
943	+
944		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
945
946		Vector3d d;
#	Line 284 | Line 967 | namespace OpenMD {
967		snap_->wrapVector(d);
968		return d;
969		}
970	+
971	+	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
972	+	#ifdef IS_MPI
973	+	return massFactorsRow[atom1];
974	+	#else
975	+	return massFactors[atom1];
976	+	#endif
977	+	}
978	+
979	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
980	+	#ifdef IS_MPI
981	+	return massFactorsCol[atom2];
982	+	#else
983	+	return massFactors[atom2];
984	+	#endif
985	+
986	+	}
987
988		Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
989		Vector3d d;
#	Line 298 | Line 998 | namespace OpenMD {
998		return d;
999		}
1000
1001	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1002	+	return excludesForAtom[atom1];
1003	+	}
1004	+
1005	+	/**
1006	+	* We need to exclude some overcounted interactions that result from
1007	+	* the parallel decomposition.
1008	+	*/
1009	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1010	+	int unique_id_1, unique_id_2, group1, group2;
1011	+
1012	+	#ifdef IS_MPI
1013	+	// in MPI, we have to look up the unique IDs for each atom
1014	+	unique_id_1 = AtomRowToGlobal[atom1];
1015	+	unique_id_2 = AtomColToGlobal[atom2];
1016	+	group1 = cgRowToGlobal[cg1];
1017	+	group2 = cgColToGlobal[cg2];
1018	+	#else
1019	+	unique_id_1 = AtomLocalToGlobal[atom1];
1020	+	unique_id_2 = AtomLocalToGlobal[atom2];
1021	+	group1 = cgLocalToGlobal[cg1];
1022	+	group2 = cgLocalToGlobal[cg2];
1023	+	#endif
1024	+
1025	+	if (unique_id_1 == unique_id_2) return true;
1026	+
1027	+	#ifdef IS_MPI
1028	+	// this prevents us from doing the pair on multiple processors
1029	+	if (unique_id_1 < unique_id_2) {
1030	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1031	+	} else {
1032	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1033	+	}
1034	+	#endif
1035	+
1036	+	#ifndef IS_MPI
1037	+	if (group1 == group2) {
1038	+	if (unique_id_1 < unique_id_2) return true;
1039	+	}
1040	+	#endif
1041	+
1042	+	return false;
1043	+	}
1044	+
1045	+	/**
1046	+	* We need to handle the interactions for atoms who are involved in
1047	+	* the same rigid body as well as some short range interactions
1048	+	* (bonds, bends, torsions) differently from other interactions.
1049	+	* We'll still visit the pairwise routines, but with a flag that
1050	+	* tells those routines to exclude the pair from direct long range
1051	+	* interactions.  Some indirect interactions (notably reaction
1052	+	* field) must still be handled for these pairs.
1053	+	*/
1054	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1055	+
1056	+	// excludesForAtom was constructed to use row/column indices in the MPI
1057	+	// version, and to use local IDs in the non-MPI version:
1058	+
1059	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1060	+	i != excludesForAtom[atom1].end(); ++i) {
1061	+	if ( (*i) == atom2 ) return true;
1062	+	}
1063	+
1064	+	return false;
1065	+	}
1066	+
1067	+
1068		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1069		#ifdef IS_MPI
1070		atomRowData.force[atom1] += fg;
#	Line 312 | Line 1079 | namespace OpenMD {
1079		#else
1080		snap_->atomData.force[atom2] += fg;
1081		#endif
315	–
1082		}
1083
1084		// filling interaction blocks with pointers
1085	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1085	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1086	>	int atom1, int atom2) {
1087
1088	<	InteractionData idat;
1088	>	idat.excluded = excludeAtomPair(atom1, atom2);
1089	>
1090		#ifdef IS_MPI
1091	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1092	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1093	+	//                         ff_->getAtomType(identsCol[atom2]) );
1094	+
1095		if (storageLayout_ & DataStorage::dslAmat) {
1096		idat.A1 = &(atomRowData.aMat[atom1]);
1097		idat.A2 = &(atomColData.aMat[atom2]);
1098		}
1099	<
1099	>
1100		if (storageLayout_ & DataStorage::dslElectroFrame) {
1101		idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1102		idat.eFrame2 = &(atomColData.electroFrame[atom2]);
#	Line 340 | Line 1112 | namespace OpenMD {
1112		idat.rho2 = &(atomColData.density[atom2]);
1113		}
1114
1115	+	if (storageLayout_ & DataStorage::dslFunctional) {
1116	+	idat.frho1 = &(atomRowData.functional[atom1]);
1117	+	idat.frho2 = &(atomColData.functional[atom2]);
1118	+	}
1119	+
1120		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1121		idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1122		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1123		}
1124	+
1125	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1126	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1127	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1128	+	}
1129	+
1130	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1131	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1132	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1133	+	}
1134	+
1135	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1136	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1137	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1138	+	}
1139	+
1140		#else
1141	+
1142	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1143	+
1144		if (storageLayout_ & DataStorage::dslAmat) {
1145		idat.A1 = &(snap_->atomData.aMat[atom1]);
1146		idat.A2 = &(snap_->atomData.aMat[atom2]);
#	Line 360 | Line 1156 | namespace OpenMD {
1156		idat.t2 = &(snap_->atomData.torque[atom2]);
1157		}
1158
1159	<	if (storageLayout_ & DataStorage::dslDensity) {
1159	>	if (storageLayout_ & DataStorage::dslDensity) {
1160		idat.rho1 = &(snap_->atomData.density[atom1]);
1161		idat.rho2 = &(snap_->atomData.density[atom2]);
1162		}
1163
1164	+	if (storageLayout_ & DataStorage::dslFunctional) {
1165	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1166	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1167	+	}
1168	+
1169		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1170		idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1171		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1172		}
1173	+
1174	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1175	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1176	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1177	+	}
1178	+
1179	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1180	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1181	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1182	+	}
1183	+
1184	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1185	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1186	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1187	+	}
1188	+
1189		#endif
373	–
1190		}
1191	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1192	<	InteractionData idat;
1193	<	skippedCharge1
378	<	skippedCharge2
379	<	rij
380	<	d
381	<	electroMult
382	<	sw
383	<	f
1191	>
1192	>
1193	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1194		#ifdef IS_MPI
1195	+	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1196	+	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1197
1198	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1199	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1200	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1198	>	atomRowData.force[atom1] += *(idat.f1);
1199	>	atomColData.force[atom2] -= *(idat.f1);
1200	>
1201	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1202	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1203	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1204		}
1205	<	if (storageLayout_ & DataStorage::dslTorque) {
1206	<	idat.t1 = &(atomRowData.torque[atom1]);
1207	<	idat.t2 = &(atomColData.torque[atom2]);
1205	>
1206	>	if (storageLayout_ & DataStorage::dslElectricField) {
1207	>	atomRowData.electricField[atom1] += *(idat.eField1);
1208	>	atomColData.electricField[atom2] += *(idat.eField2);
1209		}
1210
1211	+	#else
1212	+	pairwisePot += *(idat.pot);
1213	+
1214	+	snap_->atomData.force[atom1] += *(idat.f1);
1215	+	snap_->atomData.force[atom2] -= *(idat.f1);
1216	+
1217	+	if (idat.doParticlePot) {
1218	+	// This is the pairwise contribution to the particle pot.  The
1219	+	// embedding contribution is added in each of the low level
1220	+	// non-bonded routines.  In parallel, this calculation is done
1221	+	// in collectData, not in unpackInteractionData.
1222	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1223	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1224	+	}
1225
1226	<	}
1227	<	SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
1228	<	}
1226	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1227	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1228	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1229	>	}
1230
1231	+	if (storageLayout_ & DataStorage::dslElectricField) {
1232	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1233	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1234	+	}
1235
1236	+	#endif
1237	+
1238	+	}
1239	+
1240		/*
1241		* buildNeighborList
1242		*
1243		* first element of pair is row-indexed CutoffGroup
1244		* second element of pair is column-indexed CutoffGroup
1245		*/
1246	<	vector<pair<int, int> >  buildNeighborList() {
1247	<	Vector3d dr, invWid, rs, shift;
1248	<	Vector3i cc, m1v, m2s;
1249	<	RealType rrNebr;
1250	<	int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset;
1246	>	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1247	>
1248	>	vector<pair<int, int> > neighborList;
1249	>	groupCutoffs cuts;
1250	>	bool doAllPairs = false;
1251
1252	+	#ifdef IS_MPI
1253	+	cellListRow_.clear();
1254	+	cellListCol_.clear();
1255	+	#else
1256	+	cellList_.clear();
1257	+	#endif
1258
1259	<	vector<pair<int, int> > neighborList;
1260	<	Vector3i nCells;
1261	<	Vector3d invWid, r;
417	<
418	<	rList_ = (rCut_ + skinThickness_);
419	<	rl2 = rList_ * rList_;
420	<
421	<	snap_ = sman_->getCurrentSnapshot();
1259	>	RealType rList_ = (largestRcut_ + skinThickness_);
1260	>	RealType rl2 = rList_ * rList_;
1261	>	Snapshot* snap_ = sman_->getCurrentSnapshot();
1262		Mat3x3d Hmat = snap_->getHmat();
1263		Vector3d Hx = Hmat.getColumn(0);
1264		Vector3d Hy = Hmat.getColumn(1);
1265		Vector3d Hz = Hmat.getColumn(2);
1266
1267	<	nCells.x() = (int) ( Hx.length() )/ rList_;
1268	<	nCells.y() = (int) ( Hy.length() )/ rList_;
1269	<	nCells.z() = (int) ( Hz.length() )/ rList_;
1267	>	nCells_.x() = (int) ( Hx.length() )/ rList_;
1268	>	nCells_.y() = (int) ( Hy.length() )/ rList_;
1269	>	nCells_.z() = (int) ( Hz.length() )/ rList_;
1270
1271	<	for (i = 0; i < nGroupsInRow; i++) {
432	<	rs = cgRowData.position[i];
433	<	snap_->scaleVector(rs);
434	<	}
1271	>	// handle small boxes where the cell offsets can end up repeating cells
1272
1273	+	if (nCells_.x() < 3) doAllPairs = true;
1274	+	if (nCells_.y() < 3) doAllPairs = true;
1275	+	if (nCells_.z() < 3) doAllPairs = true;
1276
1277	<	VDiv (invWid, cells, region);
1278	<	for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1;
1279	<	for (n = 0; n < nMol; n ++) {
1280	<	VSAdd (rs, mol[n].r, 0.5, region);
1281	<	VMul (cc, rs, invWid);
442	<	c = VLinear (cc, cells) + nMol;
443	<	cellList[n] = cellList[c];
444	<	cellList[c] = n;
445	<	}
446	<	nebrTabLen = 0;
447	<	for (m1z = 0; m1z < cells.z(); m1z++) {
448	<	for (m1y = 0; m1y < cells.y(); m1y++) {
449	<	for (m1x = 0; m1x < cells.x(); m1x++) {
450	<	Vector3i m1v(m1x, m1y, m1z);
451	<	m1 = VLinear(m1v, cells) + nMol;
452	<	for (offset = 0; offset < nOffset_; offset++) {
453	<	m2v = m1v + cellOffsets_[offset];
454	<	shift = V3Zero();
1277	>	Mat3x3d invHmat = snap_->getInvHmat();
1278	>	Vector3d rs, scaled, dr;
1279	>	Vector3i whichCell;
1280	>	int cellIndex;
1281	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1282
1283	<	if (m2v.x() >= cells.x) {
1284	<	m2v.x() = 0;
1285	<	shift.x() = region.x();
1286	<	} else if (m2v.x() < 0) {
1287	<	m2v.x() = cells.x() - 1;
1288	<	shift.x() = - region.x();
462	<	}
1283	>	#ifdef IS_MPI
1284	>	cellListRow_.resize(nCtot);
1285	>	cellListCol_.resize(nCtot);
1286	>	#else
1287	>	cellList_.resize(nCtot);
1288	>	#endif
1289
1290	<	if (m2v.y() >= cells.y()) {
1291	<	m2v.y() = 0;
466	<	shift.y() = region.y();
467	<	} else if (m2v.y() < 0) {
468	<	m2v.y() = cells.y() - 1;
469	<	shift.y() = - region.y();
470	<	}
1290	>	if (!doAllPairs) {
1291	>	#ifdef IS_MPI
1292
1293	<	m2 = VLinear (m2v, cells) + nMol;
1294	<	for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) {
1295	<	for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) {
1296	<	if (m1 != m2 || j2 < j1) {
1297	<	dr = mol[j1].r - mol[j2].r;
1298	<	VSub (dr, mol[j1].r, mol[j2].r);
1299	<	VVSub (dr, shift);
1300	<	if (VLenSq (dr) < rrNebr) {
1301	<	neighborList.push_back(make_pair(j1, j2));
1293	>	for (int i = 0; i < nGroupsInRow_; i++) {
1294	>	rs = cgRowData.position[i];
1295	>
1296	>	// scaled positions relative to the box vectors
1297	>	scaled = invHmat * rs;
1298	>
1299	>	// wrap the vector back into the unit box by subtracting integer box
1300	>	// numbers
1301	>	for (int j = 0; j < 3; j++) {
1302	>	scaled[j] -= roundMe(scaled[j]);
1303	>	scaled[j] += 0.5;
1304	>	}
1305	>
1306	>	// find xyz-indices of cell that cutoffGroup is in.
1307	>	whichCell.x() = nCells_.x() * scaled.x();
1308	>	whichCell.y() = nCells_.y() * scaled.y();
1309	>	whichCell.z() = nCells_.z() * scaled.z();
1310	>
1311	>	// find single index of this cell:
1312	>	cellIndex = Vlinear(whichCell, nCells_);
1313	>
1314	>	// add this cutoff group to the list of groups in this cell;
1315	>	cellListRow_[cellIndex].push_back(i);
1316	>	}
1317	>	for (int i = 0; i < nGroupsInCol_; i++) {
1318	>	rs = cgColData.position[i];
1319	>
1320	>	// scaled positions relative to the box vectors
1321	>	scaled = invHmat * rs;
1322	>
1323	>	// wrap the vector back into the unit box by subtracting integer box
1324	>	// numbers
1325	>	for (int j = 0; j < 3; j++) {
1326	>	scaled[j] -= roundMe(scaled[j]);
1327	>	scaled[j] += 0.5;
1328	>	}
1329	>
1330	>	// find xyz-indices of cell that cutoffGroup is in.
1331	>	whichCell.x() = nCells_.x() * scaled.x();
1332	>	whichCell.y() = nCells_.y() * scaled.y();
1333	>	whichCell.z() = nCells_.z() * scaled.z();
1334	>
1335	>	// find single index of this cell:
1336	>	cellIndex = Vlinear(whichCell, nCells_);
1337	>
1338	>	// add this cutoff group to the list of groups in this cell;
1339	>	cellListCol_[cellIndex].push_back(i);
1340	>	}
1341	>
1342	>	#else
1343	>	for (int i = 0; i < nGroups_; i++) {
1344	>	rs = snap_->cgData.position[i];
1345	>
1346	>	// scaled positions relative to the box vectors
1347	>	scaled = invHmat * rs;
1348	>
1349	>	// wrap the vector back into the unit box by subtracting integer box
1350	>	// numbers
1351	>	for (int j = 0; j < 3; j++) {
1352	>	scaled[j] -= roundMe(scaled[j]);
1353	>	scaled[j] += 0.5;
1354	>	}
1355	>
1356	>	// find xyz-indices of cell that cutoffGroup is in.
1357	>	whichCell.x() = nCells_.x() * scaled.x();
1358	>	whichCell.y() = nCells_.y() * scaled.y();
1359	>	whichCell.z() = nCells_.z() * scaled.z();
1360	>
1361	>	// find single index of this cell:
1362	>	cellIndex = Vlinear(whichCell, nCells_);
1363	>
1364	>	// add this cutoff group to the list of groups in this cell;
1365	>	cellList_[cellIndex].push_back(i);
1366	>	}
1367	>
1368	>	#endif
1369	>
1370	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1371	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1372	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1373	>	Vector3i m1v(m1x, m1y, m1z);
1374	>	int m1 = Vlinear(m1v, nCells_);
1375	>
1376	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1377	>	os != cellOffsets_.end(); ++os) {
1378	>
1379	>	Vector3i m2v = m1v + (*os);
1380	>
1381	>
1382	>	if (m2v.x() >= nCells_.x()) {
1383	>	m2v.x() = 0;
1384	>	} else if (m2v.x() < 0) {
1385	>	m2v.x() = nCells_.x() - 1;
1386	>	}
1387	>
1388	>	if (m2v.y() >= nCells_.y()) {
1389	>	m2v.y() = 0;
1390	>	} else if (m2v.y() < 0) {
1391	>	m2v.y() = nCells_.y() - 1;
1392	>	}
1393	>
1394	>	if (m2v.z() >= nCells_.z()) {
1395	>	m2v.z() = 0;
1396	>	} else if (m2v.z() < 0) {
1397	>	m2v.z() = nCells_.z() - 1;
1398	>	}
1399	>
1400	>	int m2 = Vlinear (m2v, nCells_);
1401	>
1402	>	#ifdef IS_MPI
1403	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1404	>	j1 != cellListRow_[m1].end(); ++j1) {
1405	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1406	>	j2 != cellListCol_[m2].end(); ++j2) {
1407	>
1408	>	// In parallel, we need to visit *all* pairs of row
1409	>	// & column indicies and will divide labor in the
1410	>	// force evaluation later.
1411	>	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1412	>	snap_->wrapVector(dr);
1413	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1414	>	if (dr.lengthSquare() < cuts.third) {
1415	>	neighborList.push_back(make_pair((*j1), (*j2)));
1416	>	}
1417	>	}
1418	>	}
1419	>	#else
1420	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1421	>	j1 != cellList_[m1].end(); ++j1) {
1422	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1423	>	j2 != cellList_[m2].end(); ++j2) {
1424	>
1425	>	// Always do this if we're in different cells or if
1426	>	// we're in the same cell and the global index of
1427	>	// the j2 cutoff group is greater than or equal to
1428	>	// the j1 cutoff group.  Note that Rappaport's code
1429	>	// has a "less than" conditional here, but that
1430	>	// deals with atom-by-atom computation.  OpenMD
1431	>	// allows atoms within a single cutoff group to
1432	>	// interact with each other.
1433	>
1434	>
1435	>
1436	>	if (m2 != m1 || (*j2) >= (*j1) ) {
1437	>
1438	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1439	>	snap_->wrapVector(dr);
1440	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1441	>	if (dr.lengthSquare() < cuts.third) {
1442	>	neighborList.push_back(make_pair((*j1), (*j2)));
1443	>	}
1444		}
1445		}
1446		}
1447	+	#endif
1448		}
1449		}
1450		}
1451		}
1452	+	} else {
1453	+	// branch to do all cutoff group pairs
1454	+	#ifdef IS_MPI
1455	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1456	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1457	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1458	+	snap_->wrapVector(dr);
1459	+	cuts = getGroupCutoffs( j1, j2 );
1460	+	if (dr.lengthSquare() < cuts.third) {
1461	+	neighborList.push_back(make_pair(j1, j2));
1462	+	}
1463	+	}
1464	+	}
1465	+	#else
1466	+	// include all groups here.
1467	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1468	+	// include self group interactions j2 == j1
1469	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1470	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1471	+	snap_->wrapVector(dr);
1472	+	cuts = getGroupCutoffs( j1, j2 );
1473	+	if (dr.lengthSquare() < cuts.third) {
1474	+	neighborList.push_back(make_pair(j1, j2));
1475	+	}
1476	+	}
1477	+	}
1478	+	#endif
1479		}
1480	+
1481	+	// save the local cutoff group positions for the check that is
1482	+	// done on each loop:
1483	+	saved_CG_positions_.clear();
1484	+	for (int i = 0; i < nGroups_; i++)
1485	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1486	+
1487	+	return neighborList;
1488		}
490	–
491	–
1489		} //end namespace OpenMD

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