ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/branches/devel_omp/src/parallel/ForceMatrixDecomposition.cpp

Comparing:
branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1541 by gezelter, Fri Feb 4 20:04:56 2011 UTC vs.
branches/devel_omp/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1595 by chuckv, Tue Jul 19 18:50:04 2011 UTC

#	Line 38 | Line 38
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39		* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41	<	#include "parallel/ForceDecomposition.hpp"
42	<	#include "parallel/Communicator.hpp"
41	>	#include "parallel/ForceMatrixDecomposition.hpp"
42		#include "math/SquareMatrix3.hpp"
43	+	#include "nonbonded/NonBondedInteraction.hpp"
44	+	#include "brains/SnapshotManager.hpp"
45	+	#include "brains/PairList.hpp"
46
47		using namespace std;
48		namespace OpenMD {
49
50	<	void ForceDecomposition::distributeInitialData() {
50	>	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
51	>
52	>	// In a parallel computation, row and colum scans must visit all
53	>	// surrounding cells (not just the 14 upper triangular blocks that
54	>	// are used when the processor can see all pairs)
55		#ifdef IS_MPI
56	<	Snapshot* snap = sman_->getCurrentSnapshot();
57	<	int nAtoms = snap->getNumberOfAtoms();
58	<	int nGroups = snap->getNumberOfCutoffGroups();
56	>	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
57	>	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
58	>	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
59	>	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
60	>	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
61	>	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
62	>	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
63	>	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
64	>	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
65	>	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
66	>	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	>	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
68	>	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
69	>	#endif
70	>	}
71
54	–	AtomCommRealI = new Communicator<Row,RealType>(nAtoms);
55	–	AtomCommVectorI = new Communicator<Row,Vector3d>(nAtoms);
56	–	AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nAtoms);
72
73	<	AtomCommRealJ = new Communicator<Column,RealType>(nAtoms);
74	<	AtomCommVectorJ = new Communicator<Column,Vector3d>(nAtoms);
75	<	AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nAtoms);
73	>	/**
74	>	* distributeInitialData is essentially a copy of the older fortran
75	>	* SimulationSetup
76	>	*/
77	>	void ForceMatrixDecomposition::distributeInitialData() {
78	>	snap_ = sman_->getCurrentSnapshot();
79	>	storageLayout_ = sman_->getStorageLayout();
80	>	ff_ = info_->getForceField();
81	>	nLocal_ = snap_->getNumberOfAtoms();
82	>
83	>	nGroups_ = info_->getNLocalCutoffGroups();
84	>	// gather the information for atomtype IDs (atids):
85	>	idents = info_->getIdentArray();
86	>	AtomLocalToGlobal = info_->getGlobalAtomIndices();
87	>	cgLocalToGlobal = info_->getGlobalGroupIndices();
88	>	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
89
90	<	cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
63	<	cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
90	>	massFactors = info_->getMassFactors();
91
92	<	int nInRow = AtomCommRealI.getSize();
93	<	int nInCol = AtomCommRealJ.getSize();
92	>	PairList* excludes = info_->getExcludedInteractions();
93	>	PairList* oneTwo = info_->getOneTwoInteractions();
94	>	PairList* oneThree = info_->getOneThreeInteractions();
95	>	PairList* oneFour = info_->getOneFourInteractions();
96
97	<	vector<vector<RealType> > pot_row(LR_POT_TYPES,
98	<	vector<RealType> (nInRow, 0.0));
99	<	vector<vector<RealType> > pot_col(LR_POT_TYPES,
100	<	vector<RealType> (nInCol, 0.0));
97	>	#ifdef IS_MPI
98	>
99	>	MPI::Intracomm row = rowComm.getComm();
100	>	MPI::Intracomm col = colComm.getComm();
101
102	<	vector<vector<RealType> > pot_local(LR_POT_TYPES,
103	<	vector<RealType> (nAtoms, 0.0));
102	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
103	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
104	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
105	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
106	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
107
108	+	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
109	+	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
110	+	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
111	+	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
112	+	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
113	+
114	+	cgPlanIntRow = new Plan<int>(row, nGroups_);
115	+	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
116	+	cgPlanIntColumn = new Plan<int>(col, nGroups_);
117	+	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
118	+
119	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
120	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
121	+	nGroupsInRow_ = cgPlanIntRow->getSize();
122	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
123	+
124	+	// Modify the data storage objects with the correct layouts and sizes:
125	+	atomRowData.resize(nAtomsInRow_);
126	+	atomRowData.setStorageLayout(storageLayout_);
127	+	atomColData.resize(nAtomsInCol_);
128	+	atomColData.setStorageLayout(storageLayout_);
129	+	cgRowData.resize(nGroupsInRow_);
130	+	cgRowData.setStorageLayout(DataStorage::dslPosition);
131	+	cgColData.resize(nGroupsInCol_);
132	+	cgColData.setStorageLayout(DataStorage::dslPosition);
133	+
134	+	identsRow.resize(nAtomsInRow_);
135	+	identsCol.resize(nAtomsInCol_);
136	+
137	+	AtomPlanIntRow->gather(idents, identsRow);
138	+	AtomPlanIntColumn->gather(idents, identsCol);
139	+
140	+	// allocate memory for the parallel objects
141	+	atypesRow.resize(nAtomsInRow_);
142	+	atypesCol.resize(nAtomsInCol_);
143	+
144	+	for (int i = 0; i < nAtomsInRow_; i++)
145	+	atypesRow[i] = ff_->getAtomType(identsRow[i]);
146	+	for (int i = 0; i < nAtomsInCol_; i++)
147	+	atypesCol[i] = ff_->getAtomType(identsCol[i]);
148	+
149	+	pot_row.resize(nAtomsInRow_);
150	+	pot_col.resize(nAtomsInCol_);
151	+
152	+	AtomRowToGlobal.resize(nAtomsInRow_);
153	+	AtomColToGlobal.resize(nAtomsInCol_);
154	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156	+
157	+	cerr << "Atoms in Local:\n";
158	+	for (int i = 0; i < AtomLocalToGlobal.size(); i++) {
159	+	cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
160	+	}
161	+	cerr << "Atoms in Row:\n";
162	+	for (int i = 0; i < AtomRowToGlobal.size(); i++) {
163	+	cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
164	+	}
165	+	cerr << "Atoms in Col:\n";
166	+	for (int i = 0; i < AtomColToGlobal.size(); i++) {
167	+	cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
168	+	}
169	+
170	+	cgRowToGlobal.resize(nGroupsInRow_);
171	+	cgColToGlobal.resize(nGroupsInCol_);
172	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
173	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
174	+
175	+	cerr << "Gruops in Local:\n";
176	+	for (int i = 0; i < cgLocalToGlobal.size(); i++) {
177	+	cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
178	+	}
179	+	cerr << "Groups in Row:\n";
180	+	for (int i = 0; i < cgRowToGlobal.size(); i++) {
181	+	cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
182	+	}
183	+	cerr << "Groups in Col:\n";
184	+	for (int i = 0; i < cgColToGlobal.size(); i++) {
185	+	cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
186	+	}
187	+
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		#endif
249	+
250	+	// allocate memory for the parallel objects
251	+	atypesLocal.resize(nLocal_);
252	+
253	+	for (int i = 0; i < nLocal_; i++)
254	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
255	+
256	+	groupList_.clear();
257	+	groupList_.resize(nGroups_);
258	+	for (int i = 0; i < nGroups_; i++) {
259	+	int gid = cgLocalToGlobal[i];
260	+	for (int j = 0; j < nLocal_; j++) {
261	+	int aid = AtomLocalToGlobal[j];
262	+	if (globalGroupMembership[aid] == gid) {
263	+	groupList_[i].push_back(j);
264	+	}
265	+	}
266	+	}
267	+
268	+	excludesForAtom.clear();
269	+	excludesForAtom.resize(nLocal_);
270	+	toposForAtom.clear();
271	+	toposForAtom.resize(nLocal_);
272	+	topoDist.clear();
273	+	topoDist.resize(nLocal_);
274	+
275	+	for (int i = 0; i < nLocal_; i++) {
276	+	int iglob = AtomLocalToGlobal[i];
277	+
278	+	for (int j = 0; j < nLocal_; j++) {
279	+	int jglob = AtomLocalToGlobal[j];
280	+
281	+	if (excludes->hasPair(iglob, jglob))
282	+	excludesForAtom[i].push_back(j);
283	+
284	+	if (oneTwo->hasPair(iglob, jglob)) {
285	+	toposForAtom[i].push_back(j);
286	+	topoDist[i].push_back(1);
287	+	} else {
288	+	if (oneThree->hasPair(iglob, jglob)) {
289	+	toposForAtom[i].push_back(j);
290	+	topoDist[i].push_back(2);
291	+	} else {
292	+	if (oneFour->hasPair(iglob, jglob)) {
293	+	toposForAtom[i].push_back(j);
294	+	topoDist[i].push_back(3);
295	+	}
296	+	}
297	+	}
298	+	}
299	+	}
300	+
301	+	createGtypeCutoffMap();
302	+
303		}
304	+
305	+	void ForceMatrixDecomposition::createGtypeCutoffMap() {
306
307	+	RealType tol = 1e-6;
308	+	largestRcut_ = 0.0;
309	+	RealType rc;
310	+	int atid;
311	+	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
312	+
313	+	map<int, RealType> atypeCutoff;
314	+
315	+	for (set<AtomType*>::iterator at = atypes.begin();
316	+	at != atypes.end(); ++at){
317	+	atid = (*at)->getIdent();
318	+	if (userChoseCutoff_)
319	+	atypeCutoff[atid] = userCutoff_;
320	+	else
321	+	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
322	+	}
323	+
324	+	vector<RealType> gTypeCutoffs;
325	+	// first we do a single loop over the cutoff groups to find the
326	+	// largest cutoff for any atypes present in this group.
327	+	#ifdef IS_MPI
328	+	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
329	+	groupRowToGtype.resize(nGroupsInRow_);
330	+	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
331	+	vector<int> atomListRow = getAtomsInGroupRow(cg1);
332	+	for (vector<int>::iterator ia = atomListRow.begin();
333	+	ia != atomListRow.end(); ++ia) {
334	+	int atom1 = (*ia);
335	+	atid = identsRow[atom1];
336	+	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
337	+	groupCutoffRow[cg1] = atypeCutoff[atid];
338	+	}
339	+	}
340
341	+	bool gTypeFound = false;
342	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
343	+	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
344	+	groupRowToGtype[cg1] = gt;
345	+	gTypeFound = true;
346	+	}
347	+	}
348	+	if (!gTypeFound) {
349	+	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
350	+	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
351	+	}
352	+
353	+	}
354	+	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
355	+	groupColToGtype.resize(nGroupsInCol_);
356	+	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
357	+	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
358	+	for (vector<int>::iterator jb = atomListCol.begin();
359	+	jb != atomListCol.end(); ++jb) {
360	+	int atom2 = (*jb);
361	+	atid = identsCol[atom2];
362	+	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
363	+	groupCutoffCol[cg2] = atypeCutoff[atid];
364	+	}
365	+	}
366	+	bool gTypeFound = false;
367	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
368	+	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
369	+	groupColToGtype[cg2] = gt;
370	+	gTypeFound = true;
371	+	}
372	+	}
373	+	if (!gTypeFound) {
374	+	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
375	+	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
376	+	}
377	+	}
378	+	#else
379
380	<	void ForceDecomposition::distributeData()  {
380	>	vector<RealType> groupCutoff(nGroups_, 0.0);
381	>	groupToGtype.resize(nGroups_);
382	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
383	>	groupCutoff[cg1] = 0.0;
384	>	vector<int> atomList = getAtomsInGroupRow(cg1);
385	>	for (vector<int>::iterator ia = atomList.begin();
386	>	ia != atomList.end(); ++ia) {
387	>	int atom1 = (*ia);
388	>	atid = idents[atom1];
389	>	if (atypeCutoff[atid] > groupCutoff[cg1])
390	>	groupCutoff[cg1] = atypeCutoff[atid];
391	>	}
392	>
393	>	bool gTypeFound = false;
394	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
395	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
396	>	groupToGtype[cg1] = gt;
397	>	gTypeFound = true;
398	>	}
399	>	}
400	>	if (!gTypeFound) {
401	>	gTypeCutoffs.push_back( groupCutoff[cg1] );
402	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
403	>	}
404	>	}
405	>	#endif
406	>
407	>	// Now we find the maximum group cutoff value present in the simulation
408	>
409	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
410	>	gTypeCutoffs.end());
411	>
412		#ifdef IS_MPI
413	<	Snapshot* snap = sman_->getCurrentSnapshot();
413	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
414	>	MPI::MAX);
415	>	#endif
416
417	+	RealType tradRcut = groupMax;
418	+
419	+	for (int i = 0; i < gTypeCutoffs.size();  i++) {
420	+	for (int j = 0; j < gTypeCutoffs.size();  j++) {
421	+	RealType thisRcut;
422	+	switch(cutoffPolicy_) {
423	+	case TRADITIONAL:
424	+	thisRcut = tradRcut;
425	+	break;
426	+	case MIX:
427	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
428	+	break;
429	+	case MAX:
430	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
431	+	break;
432	+	default:
433	+	sprintf(painCave.errMsg,
434	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
435	+	"hit an unknown cutoff policy!\n");
436	+	painCave.severity = OPENMD_ERROR;
437	+	painCave.isFatal = 1;
438	+	simError();
439	+	break;
440	+	}
441	+
442	+	pair<int,int> key = make_pair(i,j);
443	+	gTypeCutoffMap[key].first = thisRcut;
444	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
445	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
446	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
447	+	// sanity check
448	+
449	+	if (userChoseCutoff_) {
450	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
451	+	sprintf(painCave.errMsg,
452	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
453	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
454	+	painCave.severity = OPENMD_ERROR;
455	+	painCave.isFatal = 1;
456	+	simError();
457	+	}
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	+	#endif
539	+	// even in parallel, we need to zero out the local arrays:
540	+
541	+	if (storageLayout_ & DataStorage::dslParticlePot) {
542	+	fill(snap_->atomData.particlePot.begin(),
543	+	snap_->atomData.particlePot.end(), 0.0);
544	+	}
545	+
546	+	if (storageLayout_ & DataStorage::dslDensity) {
547	+	fill(snap_->atomData.density.begin(),
548	+	snap_->atomData.density.end(), 0.0);
549	+	}
550	+	if (storageLayout_ & DataStorage::dslFunctional) {
551	+	fill(snap_->atomData.functional.begin(),
552	+	snap_->atomData.functional.end(), 0.0);
553	+	}
554	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
555	+	fill(snap_->atomData.functionalDerivative.begin(),
556	+	snap_->atomData.functionalDerivative.end(), 0.0);
557	+	}
558	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
559	+	fill(snap_->atomData.skippedCharge.begin(),
560	+	snap_->atomData.skippedCharge.end(), 0.0);
561	+	}
562	+
563	+	}
564	+
565	+
566	+	void ForceMatrixDecomposition::distributeData()  {
567	+	snap_ = sman_->getCurrentSnapshot();
568	+	storageLayout_ = sman_->getStorageLayout();
569	+	#ifdef IS_MPI
570	+
571		// gather up the atomic positions
572	<	AtomCommVectorI->gather(snap->atomData.position,
573	<	snap->atomIData.position);
574	<	AtomCommVectorJ->gather(snap->atomData.position,
575	<	snap->atomJData.position);
572	>	AtomPlanVectorRow->gather(snap_->atomData.position,
573	>	atomRowData.position);
574	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
575	>	atomColData.position);
576
577		// gather up the cutoff group positions
578	<	cgCommVectorI->gather(snap->cgData.position,
579	<	snap->cgIData.position);
580	<	cgCommVectorJ->gather(snap->cgData.position,
581	<	snap->cgJData.position);
578	>
579	>	cerr  << "before gather\n";
580	>	for (int i = 0; i < snap_->cgData.position.size(); i++) {
581	>	cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
582	>	}
583	>
584	>	cgPlanVectorRow->gather(snap_->cgData.position,
585	>	cgRowData.position);
586	>
587	>	cerr  << "after gather\n";
588	>	for (int i = 0; i < cgRowData.position.size(); i++) {
589	>	cerr << "cgRpos = " << cgRowData.position[i] << "\n";
590	>	}
591	>
592	>	cgPlanVectorColumn->gather(snap_->cgData.position,
593	>	cgColData.position);
594	>	for (int i = 0; i < cgColData.position.size(); i++) {
595	>	cerr << "cgCpos = " << cgColData.position[i] << "\n";
596	>	}
597	>
598
599		// if needed, gather the atomic rotation matrices
600	<	if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
601	<	AtomCommMatrixI->gather(snap->atomData.aMat,
602	<	snap->atomIData.aMat);
603	<	AtomCommMatrixJ->gather(snap->atomData.aMat,
604	<	snap->atomJData.aMat);
600	>	if (storageLayout_ & DataStorage::dslAmat) {
601	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
602	>	atomRowData.aMat);
603	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
604	>	atomColData.aMat);
605		}
606
607		// if needed, gather the atomic eletrostatic frames
608	<	if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
609	<	AtomCommMatrixI->gather(snap->atomData.electroFrame,
610	<	snap->atomIData.electroFrame);
611	<	AtomCommMatrixJ->gather(snap->atomData.electroFrame,
612	<	snap->atomJData.electroFrame);
608	>	if (storageLayout_ & DataStorage::dslElectroFrame) {
609	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
610	>	atomRowData.electroFrame);
611	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
612	>	atomColData.electroFrame);
613		}
614	+
615		#endif
616		}
617
618	<	void ForceDecomposition::collectIntermediateData() {
618	>	/* collects information obtained during the pre-pair loop onto local
619	>	* data structures.
620	>	*/
621	>	void ForceMatrixDecomposition::collectIntermediateData() {
622	>	snap_ = sman_->getCurrentSnapshot();
623	>	storageLayout_ = sman_->getStorageLayout();
624		#ifdef IS_MPI
117	–	Snapshot* snap = sman_->getCurrentSnapshot();
625
626	<	if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
627	<
628	<	AtomCommRealI->scatter(snap->atomIData.density,
629	<	snap->atomData.density);
630	<
631	<	int n = snap->atomData.density.size();
632	<	std::vector<RealType> rho_tmp(n, 0.0);
633	<	AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
626	>	if (storageLayout_ & DataStorage::dslDensity) {
627	>
628	>	AtomPlanRealRow->scatter(atomRowData.density,
629	>	snap_->atomData.density);
630	>
631	>	int n = snap_->atomData.density.size();
632	>	vector<RealType> rho_tmp(n, 0.0);
633	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
634		for (int i = 0; i < n; i++)
635	<	snap->atomData.density[i] += rho_tmp[i];
635	>	snap_->atomData.density[i] += rho_tmp[i];
636		}
637		#endif
638		}
639	<
640	<	void ForceDecomposition::distributeIntermediateData() {
639	>
640	>	/*
641	>	* redistributes information obtained during the pre-pair loop out to
642	>	* row and column-indexed data structures
643	>	*/
644	>	void ForceMatrixDecomposition::distributeIntermediateData() {
645	>	snap_ = sman_->getCurrentSnapshot();
646	>	storageLayout_ = sman_->getStorageLayout();
647		#ifdef IS_MPI
648	<	Snapshot* snap = sman_->getCurrentSnapshot();
649	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
650	<	AtomCommRealI->gather(snap->atomData.functional,
651	<	snap->atomIData.functional);
652	<	AtomCommRealJ->gather(snap->atomData.functional,
140	<	snap->atomJData.functional);
648	>	if (storageLayout_ & DataStorage::dslFunctional) {
649	>	AtomPlanRealRow->gather(snap_->atomData.functional,
650	>	atomRowData.functional);
651	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
652	>	atomColData.functional);
653		}
654
655	<	if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
656	<	AtomCommRealI->gather(snap->atomData.functionalDerivative,
657	<	snap->atomIData.functionalDerivative);
658	<	AtomCommRealJ->gather(snap->atomData.functionalDerivative,
659	<	snap->atomJData.functionalDerivative);
655	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
656	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
657	>	atomRowData.functionalDerivative);
658	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
659	>	atomColData.functionalDerivative);
660		}
661		#endif
662		}
663
664
665	<	void ForceDecomposition::collectData() {
666	<	#ifdef IS_MPI
667	<	Snapshot* snap = sman_->getCurrentSnapshot();
665	>	void ForceMatrixDecomposition::collectData() {
666	>	snap_ = sman_->getCurrentSnapshot();
667	>	storageLayout_ = sman_->getStorageLayout();
668	>	#ifdef IS_MPI
669	>	int n = snap_->atomData.force.size();
670	>	vector<Vector3d> frc_tmp(n, V3Zero);
671
672	<	int n = snap->atomData.force.size();
158	<	std::vector<Vector3d> frc_tmp(n, 0.0);
159	<
160	<	AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
672	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
673		for (int i = 0; i < n; i++) {
674	<	snap->atomData.force[i] += frc_tmp[i];
674	>	snap_->atomData.force[i] += frc_tmp[i];
675		frc_tmp[i] = 0.0;
676		}
677
678	<	AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
679	<	for (int i = 0; i < n; i++)
680	<	snap->atomData.force[i] += frc_tmp[i];
681	<
682	<
683	<	if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
678	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
679	>	for (int i = 0; i < n; i++) {
680	>	snap_->atomData.force[i] += frc_tmp[i];
681	>	}
682	>
683	>	if (storageLayout_ & DataStorage::dslTorque) {
684
685	<	int nt = snap->atomData.force.size();
686	<	std::vector<Vector3d> trq_tmp(nt, 0.0);
685	>	int nt = snap_->atomData.torque.size();
686	>	vector<Vector3d> trq_tmp(nt, V3Zero);
687
688	<	AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
689	<	for (int i = 0; i < n; i++) {
690	<	snap->atomData.torque[i] += trq_tmp[i];
688	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
689	>	for (int i = 0; i < nt; i++) {
690	>	snap_->atomData.torque[i] += trq_tmp[i];
691		trq_tmp[i] = 0.0;
692		}
693
694	<	AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
695	<	for (int i = 0; i < n; i++)
696	<	snap->atomData.torque[i] += trq_tmp[i];
694	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
695	>	for (int i = 0; i < nt; i++)
696	>	snap_->atomData.torque[i] += trq_tmp[i];
697		}
698	<
699	<
700	<	vector<vector<RealType> > pot_temp(LR_POT_TYPES,
701	<	vector<RealType> (nAtoms, 0.0));
702	<
703	<	for (int i = 0; i < LR_POT_TYPES; i++) {
704	<	AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
705	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
706	<	pot_local[i] += pot_temp[i][ii];
698	>
699	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
700	>
701	>	int ns = snap_->atomData.skippedCharge.size();
702	>	vector<RealType> skch_tmp(ns, 0.0);
703	>
704	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
705	>	for (int i = 0; i < ns; i++) {
706	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
707	>	skch_tmp[i] = 0.0;
708		}
709	+
710	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
711	+	for (int i = 0; i < ns; i++)
712	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
713		}
714
715	+	nLocal_ = snap_->getNumberOfAtoms();
716
717	+	vector<potVec> pot_temp(nLocal_,
718	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
719
720	+	// scatter/gather pot_row into the members of my column
721	+
722	+	AtomPlanPotRow->scatter(pot_row, pot_temp);
723	+
724	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
725	+	pairwisePot += pot_temp[ii];
726	+
727	+	fill(pot_temp.begin(), pot_temp.end(),
728	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
729	+
730	+	AtomPlanPotColumn->scatter(pot_col, pot_temp);
731	+
732	+	for (int ii = 0;  ii < pot_temp.size(); ii++ )
733	+	pairwisePot += pot_temp[ii];
734		#endif
735	+
736	+	cerr << "pairwisePot = " <<  pairwisePot << "\n";
737		}
738	+
739	+	int ForceMatrixDecomposition::getNAtomsInRow() {
740	+	#ifdef IS_MPI
741	+	return nAtomsInRow_;
742	+	#else
743	+	return nLocal_;
744	+	#endif
745	+	}
746	+
747	+	/**
748	+	* returns the list of atoms belonging to this group.
749	+	*/
750	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
751	+	#ifdef IS_MPI
752	+	return groupListRow_[cg1];
753	+	#else
754	+	return groupList_[cg1];
755	+	#endif
756	+	}
757	+
758	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
759	+	#ifdef IS_MPI
760	+	return groupListCol_[cg2];
761	+	#else
762	+	return groupList_[cg2];
763	+	#endif
764	+	}
765
766	+	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
767	+	Vector3d d;
768	+
769	+	#ifdef IS_MPI
770	+	d = cgColData.position[cg2] - cgRowData.position[cg1];
771	+	cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
772	+	cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
773	+	#else
774	+	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
775	+	cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
776	+	cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
777	+	#endif
778	+
779	+	snap_->wrapVector(d);
780	+	return d;
781	+	}
782	+
783	+
784	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
785	+
786	+	Vector3d d;
787	+
788	+	#ifdef IS_MPI
789	+	d = cgRowData.position[cg1] - atomRowData.position[atom1];
790	+	#else
791	+	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
792	+	#endif
793	+
794	+	snap_->wrapVector(d);
795	+	return d;
796	+	}
797	+
798	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
799	+	Vector3d d;
800	+
801	+	#ifdef IS_MPI
802	+	d = cgColData.position[cg2] - atomColData.position[atom2];
803	+	#else
804	+	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
805	+	#endif
806	+
807	+	snap_->wrapVector(d);
808	+	return d;
809	+	}
810	+
811	+	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
812	+	#ifdef IS_MPI
813	+	return massFactorsRow[atom1];
814	+	#else
815	+	return massFactors[atom1];
816	+	#endif
817	+	}
818	+
819	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
820	+	#ifdef IS_MPI
821	+	return massFactorsCol[atom2];
822	+	#else
823	+	return massFactors[atom2];
824	+	#endif
825	+
826	+	}
827	+
828	+	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
829	+	Vector3d d;
830	+
831	+	#ifdef IS_MPI
832	+	d = atomColData.position[atom2] - atomRowData.position[atom1];
833	+	#else
834	+	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
835	+	#endif
836	+
837	+	snap_->wrapVector(d);
838	+	return d;
839	+	}
840	+
841	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
842	+	return excludesForAtom[atom1];
843	+	}
844	+
845	+	/**
846	+	* We need to exclude some overcounted interactions that result from
847	+	* the parallel decomposition.
848	+	*/
849	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
850	+	int unique_id_1, unique_id_2;
851	+
852	+
853	+	cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
854	+	#ifdef IS_MPI
855	+	// in MPI, we have to look up the unique IDs for each atom
856	+	unique_id_1 = AtomRowToGlobal[atom1];
857	+	unique_id_2 = AtomColToGlobal[atom2];
858	+
859	+	cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
860	+	// this situation should only arise in MPI simulations
861	+	if (unique_id_1 == unique_id_2) return true;
862	+
863	+	// this prevents us from doing the pair on multiple processors
864	+	if (unique_id_1 < unique_id_2) {
865	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
866	+	} else {
867	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
868	+	}
869	+	#endif
870	+	return false;
871	+	}
872	+
873	+	/**
874	+	* We need to handle the interactions for atoms who are involved in
875	+	* the same rigid body as well as some short range interactions
876	+	* (bonds, bends, torsions) differently from other interactions.
877	+	* We'll still visit the pairwise routines, but with a flag that
878	+	* tells those routines to exclude the pair from direct long range
879	+	* interactions.  Some indirect interactions (notably reaction
880	+	* field) must still be handled for these pairs.
881	+	*/
882	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
883	+	int unique_id_2;
884	+	#ifdef IS_MPI
885	+	// in MPI, we have to look up the unique IDs for the row atom.
886	+	unique_id_2 = AtomColToGlobal[atom2];
887	+	#else
888	+	// in the normal loop, the atom numbers are unique
889	+	unique_id_2 = atom2;
890	+	#endif
891	+
892	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
893	+	i != excludesForAtom[atom1].end(); ++i) {
894	+	if ( (*i) == unique_id_2 ) return true;
895	+	}
896	+
897	+	return false;
898	+	}
899	+
900	+
901	+	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
902	+	#ifdef IS_MPI
903	+	atomRowData.force[atom1] += fg;
904	+	#else
905	+	snap_->atomData.force[atom1] += fg;
906	+	#endif
907	+	}
908	+
909	+	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
910	+	#ifdef IS_MPI
911	+	atomColData.force[atom2] += fg;
912	+	#else
913	+	snap_->atomData.force[atom2] += fg;
914	+	#endif
915	+	}
916	+
917	+	// filling interaction blocks with pointers
918	+	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
919	+	int atom1, int atom2) {
920	+
921	+	idat.excluded = excludeAtomPair(atom1, atom2);
922	+
923	+	#ifdef IS_MPI
924	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
925	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
926	+	//                         ff_->getAtomType(identsCol[atom2]) );
927	+
928	+	if (storageLayout_ & DataStorage::dslAmat) {
929	+	idat.A1 = &(atomRowData.aMat[atom1]);
930	+	idat.A2 = &(atomColData.aMat[atom2]);
931	+	}
932	+
933	+	if (storageLayout_ & DataStorage::dslElectroFrame) {
934	+	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
935	+	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
936	+	}
937	+
938	+	if (storageLayout_ & DataStorage::dslTorque) {
939	+	idat.t1 = &(atomRowData.torque[atom1]);
940	+	idat.t2 = &(atomColData.torque[atom2]);
941	+	}
942	+
943	+	if (storageLayout_ & DataStorage::dslDensity) {
944	+	idat.rho1 = &(atomRowData.density[atom1]);
945	+	idat.rho2 = &(atomColData.density[atom2]);
946	+	}
947	+
948	+	if (storageLayout_ & DataStorage::dslFunctional) {
949	+	idat.frho1 = &(atomRowData.functional[atom1]);
950	+	idat.frho2 = &(atomColData.functional[atom2]);
951	+	}
952	+
953	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
954	+	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
955	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
956	+	}
957	+
958	+	if (storageLayout_ & DataStorage::dslParticlePot) {
959	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
960	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
961	+	}
962	+
963	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
964	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
965	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
966	+	}
967	+
968	+	#else
969	+
970	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
971	+	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
972	+	//                         ff_->getAtomType(idents[atom2]) );
973	+
974	+	if (storageLayout_ & DataStorage::dslAmat) {
975	+	idat.A1 = &(snap_->atomData.aMat[atom1]);
976	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
977	+	}
978	+
979	+	if (storageLayout_ & DataStorage::dslElectroFrame) {
980	+	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
981	+	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
982	+	}
983	+
984	+	if (storageLayout_ & DataStorage::dslTorque) {
985	+	idat.t1 = &(snap_->atomData.torque[atom1]);
986	+	idat.t2 = &(snap_->atomData.torque[atom2]);
987	+	}
988	+
989	+	if (storageLayout_ & DataStorage::dslDensity) {
990	+	idat.rho1 = &(snap_->atomData.density[atom1]);
991	+	idat.rho2 = &(snap_->atomData.density[atom2]);
992	+	}
993	+
994	+	if (storageLayout_ & DataStorage::dslFunctional) {
995	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
996	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
997	+	}
998	+
999	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1000	+	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1001	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1002	+	}
1003	+
1004	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1005	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1006	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1007	+	}
1008	+
1009	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1010	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1011	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1012	+	}
1013	+	#endif
1014	+	}
1015	+
1016	+
1017	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1018	+	#ifdef IS_MPI
1019	+	pot_row[atom1] += 0.5 *  *(idat.pot);
1020	+	pot_col[atom2] += 0.5 *  *(idat.pot);
1021	+
1022	+	atomRowData.force[atom1] += *(idat.f1);
1023	+	atomColData.force[atom2] -= *(idat.f1);
1024	+	#else
1025	+	pairwisePot += *(idat.pot);
1026	+
1027	+	snap_->atomData.force[atom1] += *(idat.f1);
1028	+	snap_->atomData.force[atom2] -= *(idat.f1);
1029	+	#endif
1030	+
1031	+	}
1032	+
1033	+	vector<vector<int> > ForceMatrixDecomposition::buildLayerBasedNeighborList() {
1034	+	printf("buildLayerBasedNeighborList; nGroups:%d\n", nGroups_);
1035	+	// Na = nGroups_
1036	+	/* cell occupancy counter */
1037	+	vector<int> k_c;
1038	+	/* c_i - has cell containing atom i (size Na) */
1039	+	vector<int> c;
1040	+	/* l_i - layer containing atom i (size Na) */
1041	+	vector<int> l;
1042	+
1043	+	//      cellList_.clear();
1044	+
1045	+	RealType rList_ = (largestRcut_ + skinThickness_);
1046	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1047	+	Mat3x3d Hmat = snap_->getHmat();
1048	+	Vector3d Hx = Hmat.getColumn(0);
1049	+	Vector3d Hy = Hmat.getColumn(1);
1050	+	Vector3d Hz = Hmat.getColumn(2);
1051	+
1052	+	nCells_.x() = (int) (Hx.length()) / rList_;
1053	+	nCells_.y() = (int) (Hy.length()) / rList_;
1054	+	nCells_.z() = (int) (Hz.length()) / rList_;
1055	+
1056	+	Mat3x3d invHmat = snap_->getInvHmat();
1057	+	Vector3d rs, scaled, dr;
1058	+	Vector3i whichCell;
1059	+	int cellIndex;
1060	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1061	+
1062	+	//      cellList_.resize(nCtot);
1063	+	k_c = vector<int>(nCtot, 0);
1064	+
1065	+	for (int i = 0; i < nGroups_; i++)
1066	+	{
1067	+	rs = snap_->cgData.position[i];
1068	+
1069	+	// scaled positions relative to the box vectors
1070	+	scaled = invHmat * rs;
1071	+
1072	+	// wrap the vector back into the unit box by subtracting integer box
1073	+	// numbers
1074	+	for (int j = 0; j < 3; j++)
1075	+	{
1076	+	scaled[j] -= roundMe(scaled[j]);
1077	+	scaled[j] += 0.5;
1078	+	}
1079	+
1080	+	// find xyz-indices of cell that cutoffGroup is in.
1081	+	whichCell.x() = nCells_.x() * scaled.x();
1082	+	whichCell.y() = nCells_.y() * scaled.y();
1083	+	whichCell.z() = nCells_.z() * scaled.z();
1084	+
1085	+	// find single index of this cell:
1086	+	cellIndex = Vlinear(whichCell, nCells_);
1087	+
1088	+	c.push_back(cellIndex);
1089	+
1090	+	//              // add this cutoff group to the list of groups in this cell;
1091	+	//              cellList_[cellIndex].push_back(i);
1092	+	}
1093	+
1094	+	int k_c_curr;
1095	+	int k_c_max = 0;
1096	+	/* the cell-layer occupancy matrix */
1097	+	vector<vector<int> > H_c_l = vector<vector<int> >(nCtot);
1098	+
1099	+	for(int i = 0; i < nGroups_; ++i)
1100	+	{
1101	+	k_c_curr = ++k_c[c[i]];
1102	+	l.push_back(k_c_curr);
1103	+
1104	+	/* determines the number of layers in use */
1105	+	if(k_c_max < k_c_curr)
1106	+	{
1107	+	k_c_max = k_c_curr;
1108	+	}
1109	+
1110	+	H_c_l[c[i]].push_back(/*l[*/i/*]*/);
1111	+	}
1112	+
1113	+	int m;
1114	+	/* the neighbor matrix */
1115	+	vector<vector<int> >neighborMatW = vector<vector<int> >(nGroups_);
1116	+
1117	+	//      vector<pair<int, int> > neighborList;
1118	+	groupCutoffs cuts;
1119	+
1120	+	/* loops over objects(atoms, rigidBodies, cutoffGroups, etc.) */
1121	+	for(int i = 0; i < nGroups_; ++i)
1122	+	{
1123	+	m = 0;
1124	+	/* c' */
1125	+	int c1 = c[i];
1126	+	Vector3i c1v = idxToV(c1, nCells_);
1127	+
1128	+	/* loops over the neighboring cells c'' */
1129	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1130	+	{
1131	+	Vector3i c2v = c1v + (*os);
1132	+
1133	+	if (c2v.x() >= nCells_.x())
1134	+	{
1135	+	c2v.x() = 0;
1136	+	} else if (c2v.x() < 0)
1137	+	{
1138	+	c2v.x() = nCells_.x() - 1;
1139	+	}
1140	+
1141	+	if (c2v.y() >= nCells_.y())
1142	+	{
1143	+	c2v.y() = 0;
1144	+	} else if (c2v.y() < 0)
1145	+	{
1146	+	c2v.y() = nCells_.y() - 1;
1147	+	}
1148	+
1149	+	if (c2v.z() >= nCells_.z())
1150	+	{
1151	+	c2v.z() = 0;
1152	+	} else if (c2v.z() < 0)
1153	+	{
1154	+	c2v.z() = nCells_.z() - 1;
1155	+	}
1156	+
1157	+	int c2 = Vlinear(c2v, nCells_);
1158	+	/* loops over layers l to access the neighbor atoms */
1159	+	for (vector<int>::iterator j = H_c_l[c2].begin(); j != H_c_l[c2].end(); ++j)
1160	+	{
1161	+	//                              if i'' = 0 then break // doesn't apply to vector implementation of matrix
1162	+	//                              if(i != *j)
1163	+	if (c2 != c1 || (*j) < (i))
1164	+	{
1165	+	dr = snap_->cgData.position[(*j)] - snap_->cgData.position[(i)];
1166	+	snap_->wrapVector(dr);
1167	+	cuts = getGroupCutoffs((i), (*j));
1168	+	if (dr.lengthSquare() < cuts.third)
1169	+	{
1170	+	++m;
1171	+	/* transposed version of Rapaport W mat, to occupy successive memory locations on CPU */
1172	+	neighborMatW[i].push_back(*j);
1173	+	//                                              neighborList.push_back(make_pair((i), (*j)));
1174	+	}
1175	+	}
1176	+	}
1177	+	}
1178	+	}
1179	+
1180	+	// save the local cutoff group positions for the check that is
1181	+	// done on each loop:
1182	+	saved_CG_positions_.clear();
1183	+	for (int i = 0; i < nGroups_; i++)
1184	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1185	+
1186	+	return neighborMatW;
1187	+	}
1188	+
1189	+	/*
1190	+	* buildNeighborList
1191	+	*
1192	+	* first element of pair is row-indexed CutoffGroup
1193	+	* second element of pair is column-indexed CutoffGroup
1194	+	*/
1195	+	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1196	+
1197	+	vector<pair<int, int> > neighborList;
1198	+	groupCutoffs cuts;
1199	+	bool doAllPairs = false;
1200	+
1201	+	#ifdef IS_MPI
1202	+	cellListRow_.clear();
1203	+	cellListCol_.clear();
1204	+	#else
1205	+	cellList_.clear();
1206	+	#endif
1207	+
1208	+	RealType rList_ = (largestRcut_ + skinThickness_);
1209	+	RealType rl2 = rList_ * rList_;
1210	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1211	+	Mat3x3d Hmat = snap_->getHmat();
1212	+	Vector3d Hx = Hmat.getColumn(0);
1213	+	Vector3d Hy = Hmat.getColumn(1);
1214	+	Vector3d Hz = Hmat.getColumn(2);
1215	+
1216	+	nCells_.x() = (int) ( Hx.length() )/ rList_;
1217	+	nCells_.y() = (int) ( Hy.length() )/ rList_;
1218	+	nCells_.z() = (int) ( Hz.length() )/ rList_;
1219	+
1220	+	// handle small boxes where the cell offsets can end up repeating cells
1221	+
1222	+	if (nCells_.x() < 3) doAllPairs = true;
1223	+	if (nCells_.y() < 3) doAllPairs = true;
1224	+	if (nCells_.z() < 3) doAllPairs = true;
1225	+
1226	+	Mat3x3d invHmat = snap_->getInvHmat();
1227	+	Vector3d rs, scaled, dr;
1228	+	Vector3i whichCell;
1229	+	int cellIndex;
1230	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1231	+
1232	+	#ifdef IS_MPI
1233	+	cellListRow_.resize(nCtot);
1234	+	cellListCol_.resize(nCtot);
1235	+	#else
1236	+	cellList_.resize(nCtot);
1237	+	#endif
1238	+
1239	+	if (!doAllPairs) {
1240	+	#ifdef IS_MPI
1241	+
1242	+	for (int i = 0; i < nGroupsInRow_; i++) {
1243	+	rs = cgRowData.position[i];
1244	+
1245	+	// scaled positions relative to the box vectors
1246	+	scaled = invHmat * rs;
1247	+
1248	+	// wrap the vector back into the unit box by subtracting integer box
1249	+	// numbers
1250	+	for (int j = 0; j < 3; j++) {
1251	+	scaled[j] -= roundMe(scaled[j]);
1252	+	scaled[j] += 0.5;
1253	+	}
1254	+
1255	+	// find xyz-indices of cell that cutoffGroup is in.
1256	+	whichCell.x() = nCells_.x() * scaled.x();
1257	+	whichCell.y() = nCells_.y() * scaled.y();
1258	+	whichCell.z() = nCells_.z() * scaled.z();
1259	+
1260	+	// find single index of this cell:
1261	+	cellIndex = Vlinear(whichCell, nCells_);
1262	+
1263	+	// add this cutoff group to the list of groups in this cell;
1264	+	cellListRow_[cellIndex].push_back(i);
1265	+	}
1266	+	for (int i = 0; i < nGroupsInCol_; i++) {
1267	+	rs = cgColData.position[i];
1268	+
1269	+	// scaled positions relative to the box vectors
1270	+	scaled = invHmat * rs;
1271	+
1272	+	// wrap the vector back into the unit box by subtracting integer box
1273	+	// numbers
1274	+	for (int j = 0; j < 3; j++) {
1275	+	scaled[j] -= roundMe(scaled[j]);
1276	+	scaled[j] += 0.5;
1277	+	}
1278	+
1279	+	// find xyz-indices of cell that cutoffGroup is in.
1280	+	whichCell.x() = nCells_.x() * scaled.x();
1281	+	whichCell.y() = nCells_.y() * scaled.y();
1282	+	whichCell.z() = nCells_.z() * scaled.z();
1283	+
1284	+	// find single index of this cell:
1285	+	cellIndex = Vlinear(whichCell, nCells_);
1286	+
1287	+	// add this cutoff group to the list of groups in this cell;
1288	+	cellListCol_[cellIndex].push_back(i);
1289	+	}
1290	+	#else
1291	+	for (int i = 0; i < nGroups_; i++) {
1292	+	rs = snap_->cgData.position[i];
1293	+
1294	+	// scaled positions relative to the box vectors
1295	+	scaled = invHmat * rs;
1296	+
1297	+	// wrap the vector back into the unit box by subtracting integer box
1298	+	// numbers
1299	+	for (int j = 0; j < 3; j++) {
1300	+	scaled[j] -= roundMe(scaled[j]);
1301	+	scaled[j] += 0.5;
1302	+	}
1303	+
1304	+	// find xyz-indices of cell that cutoffGroup is in.
1305	+	whichCell.x() = nCells_.x() * scaled.x();
1306	+	whichCell.y() = nCells_.y() * scaled.y();
1307	+	whichCell.z() = nCells_.z() * scaled.z();
1308	+
1309	+	// find single index of this cell:
1310	+	cellIndex = Vlinear(whichCell, nCells_);
1311	+
1312	+	// add this cutoff group to the list of groups in this cell;
1313	+	cellList_[cellIndex].push_back(i);
1314	+	}
1315	+	#endif
1316	+
1317	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1318	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1319	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1320	+	Vector3i m1v(m1x, m1y, m1z);
1321	+	int m1 = Vlinear(m1v, nCells_);
1322	+
1323	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1324	+	os != cellOffsets_.end(); ++os) {
1325	+
1326	+	Vector3i m2v = m1v + (*os);
1327	+
1328	+	if (m2v.x() >= nCells_.x()) {
1329	+	m2v.x() = 0;
1330	+	} else if (m2v.x() < 0) {
1331	+	m2v.x() = nCells_.x() - 1;
1332	+	}
1333	+
1334	+	if (m2v.y() >= nCells_.y()) {
1335	+	m2v.y() = 0;
1336	+	} else if (m2v.y() < 0) {
1337	+	m2v.y() = nCells_.y() - 1;
1338	+	}
1339	+
1340	+	if (m2v.z() >= nCells_.z()) {
1341	+	m2v.z() = 0;
1342	+	} else if (m2v.z() < 0) {
1343	+	m2v.z() = nCells_.z() - 1;
1344	+	}
1345	+
1346	+	int m2 = Vlinear (m2v, nCells_);
1347	+
1348	+	#ifdef IS_MPI
1349	+	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1350	+	j1 != cellListRow_[m1].end(); ++j1) {
1351	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1352	+	j2 != cellListCol_[m2].end(); ++j2) {
1353	+
1354	+	// In parallel, we need to visit *all* pairs of row &
1355	+	// column indicies and will truncate later on.
1356	+	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1357	+	snap_->wrapVector(dr);
1358	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1359	+	if (dr.lengthSquare() < cuts.third) {
1360	+	neighborList.push_back(make_pair((*j1), (*j2)));
1361	+	}
1362	+	}
1363	+	}
1364	+	#else
1365	+
1366	+	for (vector<int>::iterator j1 = cellList_[m1].begin();
1367	+	j1 != cellList_[m1].end(); ++j1) {
1368	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1369	+	j2 != cellList_[m2].end(); ++j2) {
1370	+
1371	+	// Always do this if we're in different cells or if
1372	+	// we're in the same cell and the global index of the
1373	+	// j2 cutoff group is less than the j1 cutoff group
1374	+
1375	+	if (m2 != m1 || (*j2) < (*j1)) {
1376	+	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1377	+	snap_->wrapVector(dr);
1378	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1379	+	if (dr.lengthSquare() < cuts.third) {
1380	+	neighborList.push_back(make_pair((*j1), (*j2)));
1381	+	}
1382	+	}
1383	+	}
1384	+	}
1385	+	#endif
1386	+	}
1387	+	}
1388	+	}
1389	+	}
1390	+	} else {
1391	+	// branch to do all cutoff group pairs
1392	+	#ifdef IS_MPI
1393	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1394	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1395	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1396	+	snap_->wrapVector(dr);
1397	+	cuts = getGroupCutoffs( j1, j2 );
1398	+	if (dr.lengthSquare() < cuts.third) {
1399	+	neighborList.push_back(make_pair(j1, j2));
1400	+	}
1401	+	}
1402	+	}
1403	+	#else
1404	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1405	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1406	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1407	+	snap_->wrapVector(dr);
1408	+	cuts = getGroupCutoffs( j1, j2 );
1409	+	if (dr.lengthSquare() < cuts.third) {
1410	+	neighborList.push_back(make_pair(j1, j2));
1411	+	}
1412	+	}
1413	+	}
1414	+	#endif
1415	+	}
1416	+
1417	+	// save the local cutoff group positions for the check that is
1418	+	// done on each loop:
1419	+	saved_CG_positions_.clear();
1420	+	for (int i = 0; i < nGroups_; i++)
1421	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1422	+
1423	+	return neighborList;
1424	+	}
1425		} //end namespace OpenMD

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines