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

Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC vs.
branches/devel_omp/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1598 by mciznick, Wed Jul 27 14:26:53 2011 UTC

#	Line 43 | Line 43
43		#include "nonbonded/NonBondedInteraction.hpp"
44		#include "brains/SnapshotManager.hpp"
45		#include "brains/PairList.hpp"
46	+	#include "primitives/Molecule.hpp"
47
48		using namespace std;
49		namespace OpenMD {
50
51	<	/**
52	<	* distributeInitialData is essentially a copy of the older fortran
52	<	* SimulationSetup
53	<	*/
54	<
55	<	void ForceMatrixDecomposition::distributeInitialData() {
56	<	snap_ = sman_->getCurrentSnapshot();
57	<	storageLayout_ = sman_->getStorageLayout();
58	<	ff_ = info_->getForceField();
59	<	nLocal_ = snap_->getNumberOfAtoms();
51	>	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) :
52	>	ForceDecomposition(info, iMan) {
53
54	<	nGroups_ = info_->getNLocalCutoffGroups();
55	<	cerr << "in dId, nGroups = " << nGroups_ << "\n";
56	<	// gather the information for atomtype IDs (atids):
64	<	idents = info_->getIdentArray();
65	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
66	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
67	<	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68	<	massFactors = info_->getMassFactors();
69	<
70	<	PairList excludes = info_->getExcludedInteractions();
71	<	PairList oneTwo = info_->getOneTwoInteractions();
72	<	PairList oneThree = info_->getOneThreeInteractions();
73	<	PairList oneFour = info_->getOneFourInteractions();
74	<
54	>	// In a parallel computation, row and colum scans must visit all
55	>	// surrounding cells (not just the 14 upper triangular blocks that
56	>	// are used when the processor can see all pairs)
57		#ifdef IS_MPI
58	<
59	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
60	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
61	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
62	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
63	<	AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
58	>	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
59	>	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
60	>	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
61	>	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
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, 0,-1) );
68	>	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
69	>	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
70	>	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
71	>	#endif
72	>	}
73
74	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
75	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
76	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
77	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
78	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
74	>	/**
75	>	* distributeInitialData is essentially a copy of the older fortran
76	>	* SimulationSetup
77	>	*/
78	>	void ForceMatrixDecomposition::distributeInitialData() {
79	>	snap_ = sman_->getCurrentSnapshot();
80	>	storageLayout_ = sman_->getStorageLayout();
81	>	ff_ = info_->getForceField();
82	>	nLocal_ = snap_->getNumberOfAtoms();
83
84	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
85	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
86	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
87	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
84	>	nGroups_ = info_->getNLocalCutoffGroups();
85	>	// gather the information for atomtype IDs (atids):
86	>	idents = info_->getIdentArray();
87	>	AtomLocalToGlobal = info_->getGlobalAtomIndices();
88	>	cgLocalToGlobal = info_->getGlobalGroupIndices();
89	>	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
90
91	<	nAtomsInRow_ = AtomCommIntRow->getSize();
95	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
96	<	nGroupsInRow_ = cgCommIntRow->getSize();
97	<	nGroupsInCol_ = cgCommIntColumn->getSize();
91	>	massFactors = info_->getMassFactors();
92
93	<	// Modify the data storage objects with the correct layouts and sizes:
94	<	atomRowData.resize(nAtomsInRow_);
95	<	atomRowData.setStorageLayout(storageLayout_);
96	<	atomColData.resize(nAtomsInCol_);
103	<	atomColData.setStorageLayout(storageLayout_);
104	<	cgRowData.resize(nGroupsInRow_);
105	<	cgRowData.setStorageLayout(DataStorage::dslPosition);
106	<	cgColData.resize(nGroupsInCol_);
107	<	cgColData.setStorageLayout(DataStorage::dslPosition);
108	<
109	<	identsRow.resize(nAtomsInRow_);
110	<	identsCol.resize(nAtomsInCol_);
111	<
112	<	AtomCommIntRow->gather(idents, identsRow);
113	<	AtomCommIntColumn->gather(idents, identsCol);
114	<
115	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
117	<
118	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
93	>	PairList* excludes = info_->getExcludedInteractions();
94	>	PairList* oneTwo = info_->getOneTwoInteractions();
95	>	PairList* oneThree = info_->getOneThreeInteractions();
96	>	PairList* oneFour = info_->getOneFourInteractions();
97
98	<	AtomCommRealRow->gather(massFactors, massFactorsRow);
122	<	AtomCommRealColumn->gather(massFactors, massFactorsCol);
98	>	#ifdef IS_MPI
99
100	<	groupListRow_.clear();
101	<	groupListRow_.resize(nGroupsInRow_);
126	<	for (int i = 0; i < nGroupsInRow_; i++) {
127	<	int gid = cgRowToGlobal[i];
128	<	for (int j = 0; j < nAtomsInRow_; j++) {
129	<	int aid = AtomRowToGlobal[j];
130	<	if (globalGroupMembership[aid] == gid)
131	<	groupListRow_[i].push_back(j);
132	<	}
133	<	}
100	>	MPI::Intracomm row = rowComm.getComm();
101	>	MPI::Intracomm col = colComm.getComm();
102
103	<	groupListCol_.clear();
104	<	groupListCol_.resize(nGroupsInCol_);
105	<	for (int i = 0; i < nGroupsInCol_; i++) {
106	<	int gid = cgColToGlobal[i];
107	<	for (int j = 0; j < nAtomsInCol_; j++) {
140	<	int aid = AtomColToGlobal[j];
141	<	if (globalGroupMembership[aid] == gid)
142	<	groupListCol_[i].push_back(j);
143	<	}
144	<	}
103	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
104	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
105	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
106	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
107	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
108
109	<	skipsForAtom.clear();
110	<	skipsForAtom.resize(nAtomsInRow_);
111	<	toposForAtom.clear();
112	<	toposForAtom.resize(nAtomsInRow_);
113	<	topoDist.clear();
151	<	topoDist.resize(nAtomsInRow_);
152	<	for (int i = 0; i < nAtomsInRow_; i++) {
153	<	int iglob = AtomRowToGlobal[i];
109	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
110	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
111	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
112	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
113	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
114
115	<	for (int j = 0; j < nAtomsInCol_; j++) {
116	<	int jglob = AtomColToGlobal[j];
115	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
116	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
117	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
118	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
119
120	<	if (excludes.hasPair(iglob, jglob))
121	<	skipsForAtom[i].push_back(j);
122	<
123	<	if (oneTwo.hasPair(iglob, jglob)) {
162	<	toposForAtom[i].push_back(j);
163	<	topoDist[i].push_back(1);
164	<	} else {
165	<	if (oneThree.hasPair(iglob, jglob)) {
166	<	toposForAtom[i].push_back(j);
167	<	topoDist[i].push_back(2);
168	<	} else {
169	<	if (oneFour.hasPair(iglob, jglob)) {
170	<	toposForAtom[i].push_back(j);
171	<	topoDist[i].push_back(3);
172	<	}
173	<	}
174	<	}
175	<	}
176	<	}
120	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
121	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
122	>	nGroupsInRow_ = cgPlanIntRow->getSize();
123	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
124
125	<	#endif
125	>	// Modify the data storage objects with the correct layouts and sizes:
126	>	atomRowData.resize(nAtomsInRow_);
127	>	atomRowData.setStorageLayout(storageLayout_);
128	>	atomColData.resize(nAtomsInCol_);
129	>	atomColData.setStorageLayout(storageLayout_);
130	>	cgRowData.resize(nGroupsInRow_);
131	>	cgRowData.setStorageLayout(DataStorage::dslPosition);
132	>	cgColData.resize(nGroupsInCol_);
133	>	cgColData.setStorageLayout(DataStorage::dslPosition);
134
135	<	groupList_.clear();
136	<	groupList_.resize(nGroups_);
182	<	for (int i = 0; i < nGroups_; i++) {
183	<	int gid = cgLocalToGlobal[i];
184	<	for (int j = 0; j < nLocal_; j++) {
185	<	int aid = AtomLocalToGlobal[j];
186	<	if (globalGroupMembership[aid] == gid) {
187	<	groupList_[i].push_back(j);
188	<	}
189	<	}
190	<	}
135	>	identsRow.resize(nAtomsInRow_);
136	>	identsCol.resize(nAtomsInCol_);
137
138	<	skipsForAtom.clear();
139	<	skipsForAtom.resize(nLocal_);
194	<	toposForAtom.clear();
195	<	toposForAtom.resize(nLocal_);
196	<	topoDist.clear();
197	<	topoDist.resize(nLocal_);
138	>	AtomPlanIntRow->gather(idents, identsRow);
139	>	AtomPlanIntColumn->gather(idents, identsCol);
140
141	<	for (int i = 0; i < nLocal_; i++) {
142	<	int iglob = AtomLocalToGlobal[i];
141	>	// allocate memory for the parallel objects
142	>	atypesRow.resize(nAtomsInRow_);
143	>	atypesCol.resize(nAtomsInCol_);
144
145	<	for (int j = 0; j < nLocal_; j++) {
146	<	int jglob = AtomLocalToGlobal[j];
145	>	for (int i = 0; i < nAtomsInRow_; i++)
146	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
147	>	for (int i = 0; i < nAtomsInCol_; i++)
148	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
149
150	<	if (excludes.hasPair(iglob, jglob))
151	<	skipsForAtom[i].push_back(j);
207	<
208	<	if (oneTwo.hasPair(iglob, jglob)) {
209	<	toposForAtom[i].push_back(j);
210	<	topoDist[i].push_back(1);
211	<	} else {
212	<	if (oneThree.hasPair(iglob, jglob)) {
213	<	toposForAtom[i].push_back(j);
214	<	topoDist[i].push_back(2);
215	<	} else {
216	<	if (oneFour.hasPair(iglob, jglob)) {
217	<	toposForAtom[i].push_back(j);
218	<	topoDist[i].push_back(3);
219	<	}
220	<	}
221	<	}
222	<	}
223	<	}
224	<
225	<	createGtypeCutoffMap();
226	<	}
227	<
228	<	void ForceMatrixDecomposition::createGtypeCutoffMap() {
150	>	pot_row.resize(nAtomsInRow_);
151	>	pot_col.resize(nAtomsInCol_);
152
153	<	RealType tol = 1e-6;
154	<	RealType rc;
155	<	int atid;
156	<	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
234	<	vector<RealType> atypeCutoff;
235	<	atypeCutoff.resize( atypes.size() );
236	<
237	<	for (set<AtomType*>::iterator at = atypes.begin();
238	<	at != atypes.end(); ++at){
239	<	atid = (*at)->getIdent();
153	>	AtomRowToGlobal.resize(nAtomsInRow_);
154	>	AtomColToGlobal.resize(nAtomsInCol_);
155	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
156	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
157
158	<	if (userChoseCutoff_)
159	<	atypeCutoff[atid] = userCutoff_;
160	<	else
161	<	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
162	<	}
158	>	cerr << "Atoms in Local:\n";
159	>	for (int i = 0; i < AtomLocalToGlobal.size(); i++)
160	>	{
161	>	cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
162	>	}
163	>	cerr << "Atoms in Row:\n";
164	>	for (int i = 0; i < AtomRowToGlobal.size(); i++)
165	>	{
166	>	cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
167	>	}
168	>	cerr << "Atoms in Col:\n";
169	>	for (int i = 0; i < AtomColToGlobal.size(); i++)
170	>	{
171	>	cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
172	>	}
173
174	<	vector<RealType> gTypeCutoffs;
174	>	cgRowToGlobal.resize(nGroupsInRow_);
175	>	cgColToGlobal.resize(nGroupsInCol_);
176	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
177	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
178	>
179	>	cerr << "Gruops in Local:\n";
180	>	for (int i = 0; i < cgLocalToGlobal.size(); i++)
181	>	{
182	>	cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
183	>	}
184	>	cerr << "Groups in Row:\n";
185	>	for (int i = 0; i < cgRowToGlobal.size(); i++)
186	>	{
187	>	cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
188	>	}
189	>	cerr << "Groups in Col:\n";
190	>	for (int i = 0; i < cgColToGlobal.size(); i++)
191	>	{
192	>	cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
193	>	}
194
195	<	// first we do a single loop over the cutoff groups to find the
196	<	// largest cutoff for any atypes present in this group.
197	<	#ifdef IS_MPI
198	<	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
253	<	groupRowToGtype.resize(nGroupsInRow_);
254	<	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
255	<	vector<int> atomListRow = getAtomsInGroupRow(cg1);
256	<	for (vector<int>::iterator ia = atomListRow.begin();
257	<	ia != atomListRow.end(); ++ia) {
258	<	int atom1 = (*ia);
259	<	atid = identsRow[atom1];
260	<	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
261	<	groupCutoffRow[cg1] = atypeCutoff[atid];
262	<	}
263	<	}
195	>	massFactorsRow.resize(nAtomsInRow_);
196	>	massFactorsCol.resize(nAtomsInCol_);
197	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
198	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
199
200	<	bool gTypeFound = false;
201	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
202	<	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
203	<	groupRowToGtype[cg1] = gt;
204	<	gTypeFound = true;
205	<	}
206	<	}
207	<	if (!gTypeFound) {
208	<	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
209	<	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
210	<	}
211	<
277	<	}
278	<	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
279	<	groupColToGtype.resize(nGroupsInCol_);
280	<	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
281	<	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
282	<	for (vector<int>::iterator jb = atomListCol.begin();
283	<	jb != atomListCol.end(); ++jb) {
284	<	int atom2 = (*jb);
285	<	atid = identsCol[atom2];
286	<	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
287	<	groupCutoffCol[cg2] = atypeCutoff[atid];
288	<	}
289	<	}
290	<	bool gTypeFound = false;
291	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
292	<	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
293	<	groupColToGtype[cg2] = gt;
294	<	gTypeFound = true;
295	<	}
296	<	}
297	<	if (!gTypeFound) {
298	<	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
299	<	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
300	<	}
301	<	}
302	<	#else
200	>	groupListRow_.clear();
201	>	groupListRow_.resize(nGroupsInRow_);
202	>	for (int i = 0; i < nGroupsInRow_; i++)
203	>	{
204	>	int gid = cgRowToGlobal[i];
205	>	for (int j = 0; j < nAtomsInRow_; j++)
206	>	{
207	>	int aid = AtomRowToGlobal[j];
208	>	if (globalGroupMembership[aid] == gid)
209	>	groupListRow_[i].push_back(j);
210	>	}
211	>	}
212
213	<	vector<RealType> groupCutoff(nGroups_, 0.0);
214	<	groupToGtype.resize(nGroups_);
213	>	groupListCol_.clear();
214	>	groupListCol_.resize(nGroupsInCol_);
215	>	for (int i = 0; i < nGroupsInCol_; i++)
216	>	{
217	>	int gid = cgColToGlobal[i];
218	>	for (int j = 0; j < nAtomsInCol_; j++)
219	>	{
220	>	int aid = AtomColToGlobal[j];
221	>	if (globalGroupMembership[aid] == gid)
222	>	groupListCol_[i].push_back(j);
223	>	}
224	>	}
225
226	<	cerr << "nGroups = " << nGroups_ << "\n";
227	<	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
226	>	excludesForAtom.clear();
227	>	excludesForAtom.resize(nAtomsInRow_);
228	>	toposForAtom.clear();
229	>	toposForAtom.resize(nAtomsInRow_);
230	>	topoDist.clear();
231	>	topoDist.resize(nAtomsInRow_);
232	>	for (int i = 0; i < nAtomsInRow_; i++)
233	>	{
234	>	int iglob = AtomRowToGlobal[i];
235
236	<	groupCutoff[cg1] = 0.0;
237	<	vector<int> atomList = getAtomsInGroupRow(cg1);
236	>	for (int j = 0; j < nAtomsInCol_; j++)
237	>	{
238	>	int jglob = AtomColToGlobal[j];
239
240	<	for (vector<int>::iterator ia = atomList.begin();
241	<	ia != atomList.end(); ++ia) {
315	<	int atom1 = (*ia);
316	<	atid = idents[atom1];
317	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
318	<	groupCutoff[cg1] = atypeCutoff[atid];
319	<	}
320	<	}
240	>	if (excludes->hasPair(iglob, jglob))
241	>	excludesForAtom[i].push_back(j);
242
243	<	bool gTypeFound = false;
244	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
245	<	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
246	<	groupToGtype[cg1] = gt;
247	<	gTypeFound = true;
248	<	}
249	<	}
250	<	if (!gTypeFound) {
251	<	gTypeCutoffs.push_back( groupCutoff[cg1] );
252	<	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
253	<	}
254	<	}
255	<	#endif
243	>	if (oneTwo->hasPair(iglob, jglob))
244	>	{
245	>	toposForAtom[i].push_back(j);
246	>	topoDist[i].push_back(1);
247	>	} else
248	>	{
249	>	if (oneThree->hasPair(iglob, jglob))
250	>	{
251	>	toposForAtom[i].push_back(j);
252	>	topoDist[i].push_back(2);
253	>	} else
254	>	{
255	>	if (oneFour->hasPair(iglob, jglob))
256	>	{
257	>	toposForAtom[i].push_back(j);
258	>	topoDist[i].push_back(3);
259	>	}
260	>	}
261	>	}
262	>	}
263	>	}
264
336	–	cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
337	–	// Now we find the maximum group cutoff value present in the simulation
338	–
339	–	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
340	–
341	–	#ifdef IS_MPI
342	–	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
265		#endif
344	–
345	–	RealType tradRcut = groupMax;
266
267	<	for (int i = 0; i < gTypeCutoffs.size();  i++) {
268	<	for (int j = 0; j < gTypeCutoffs.size();  j++) {
349	<	RealType thisRcut;
350	<	switch(cutoffPolicy_) {
351	<	case TRADITIONAL:
352	<	thisRcut = tradRcut;
353	<	break;
354	<	case MIX:
355	<	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
356	<	break;
357	<	case MAX:
358	<	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
359	<	break;
360	<	default:
361	<	sprintf(painCave.errMsg,
362	<	"ForceMatrixDecomposition::createGtypeCutoffMap "
363	<	"hit an unknown cutoff policy!\n");
364	<	painCave.severity = OPENMD_ERROR;
365	<	painCave.isFatal = 1;
366	<	simError();
367	<	break;
368	<	}
267	>	// allocate memory for the parallel objects
268	>	atypesLocal.resize(nLocal_);
269
270	<	pair<int,int> key = make_pair(i,j);
271	<	gTypeCutoffMap[key].first = thisRcut;
270	>	for (int i = 0; i < nLocal_; i++)
271	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
272
273	<	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
273	>	groupList_.clear();
274	>	groupList_.resize(nGroups_);
275	>	for (int i = 0; i < nGroups_; i++)
276	>	{
277	>	int gid = cgLocalToGlobal[i];
278	>	for (int j = 0; j < nLocal_; j++)
279	>	{
280	>	int aid = AtomLocalToGlobal[j];
281	>	if (globalGroupMembership[aid] == gid)
282	>	{
283	>	groupList_[i].push_back(j);
284	>	}
285	>	}
286	>	}
287
288	<	gTypeCutoffMap[key].second = thisRcut*thisRcut;
289	<
290	<	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
288	>	excludesForAtom.clear();
289	>	excludesForAtom.resize(nLocal_);
290	>	toposForAtom.clear();
291	>	toposForAtom.resize(nLocal_);
292	>	topoDist.clear();
293	>	topoDist.resize(nLocal_);
294
295	<	// sanity check
296	<
297	<	if (userChoseCutoff_) {
382	<	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
383	<	sprintf(painCave.errMsg,
384	<	"ForceMatrixDecomposition::createGtypeCutoffMap "
385	<	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
386	<	painCave.severity = OPENMD_ERROR;
387	<	painCave.isFatal = 1;
388	<	simError();
389	<	}
390	<	}
391	<	}
392	<	}
393	<	}
295	>	for (int i = 0; i < nLocal_; i++)
296	>	{
297	>	int iglob = AtomLocalToGlobal[i];
298
299	+	for (int j = 0; j < nLocal_; j++)
300	+	{
301	+	int jglob = AtomLocalToGlobal[j];
302
303	<	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
304	<	int i, j;
398	<	#ifdef IS_MPI
399	<	i = groupRowToGtype[cg1];
400	<	j = groupColToGtype[cg2];
401	<	#else
402	<	i = groupToGtype[cg1];
403	<	j = groupToGtype[cg2];
404	<	#endif
405	<	return gTypeCutoffMap[make_pair(i,j)];
406	<	}
303	>	if (excludes->hasPair(iglob, jglob))
304	>	excludesForAtom[i].push_back(j);
305
306	<	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
307	<	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
308	<	if (toposForAtom[atom1][j] == atom2)
309	<	return topoDist[atom1][j];
310	<	}
311	<	return 0;
312	<	}
306	>	if (oneTwo->hasPair(iglob, jglob))
307	>	{
308	>	toposForAtom[i].push_back(j);
309	>	topoDist[i].push_back(1);
310	>	} else
311	>	{
312	>	if (oneThree->hasPair(iglob, jglob))
313	>	{
314	>	toposForAtom[i].push_back(j);
315	>	topoDist[i].push_back(2);
316	>	} else
317	>	{
318	>	if (oneFour->hasPair(iglob, jglob))
319	>	{
320	>	toposForAtom[i].push_back(j);
321	>	topoDist[i].push_back(3);
322	>	}
323	>	}
324	>	}
325	>	}
326	>	}
327
328	<	void ForceMatrixDecomposition::zeroWorkArrays() {
417	<	pairwisePot = 0.0;
418	<	embeddingPot = 0.0;
328	>	createGtypeCutoffMap();
329
330	<	#ifdef IS_MPI
421	<	if (storageLayout_ & DataStorage::dslForce) {
422	<	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
423	<	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
424	<	}
330	>	}
331
332	<	if (storageLayout_ & DataStorage::dslTorque) {
427	<	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
428	<	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
429	<	}
430	<
431	<	fill(pot_row.begin(), pot_row.end(),
432	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
332	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
333
334	<	fill(pot_col.begin(), pot_col.end(),
335	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
334	>	RealType tol = 1e-6;
335	>	largestRcut_ = 0.0;
336	>	RealType rc;
337	>	int atid;
338	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
339
340	<	if (storageLayout_ & DataStorage::dslParticlePot) {
438	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
439	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
440	<	}
340	>	map<int, RealType> atypeCutoff;
341
342	<	if (storageLayout_ & DataStorage::dslDensity) {
343	<	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
344	<	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
345	<	}
342	>	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at)
343	>	{
344	>	atid = (*at)->getIdent();
345	>	if (userChoseCutoff_)
346	>	atypeCutoff[atid] = userCutoff_;
347	>	else
348	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
349	>	}
350
351	<	if (storageLayout_ & DataStorage::dslFunctional) {
352	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
353	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
354	<	}
351	>	vector<RealType> gTypeCutoffs;
352	>	// first we do a single loop over the cutoff groups to find the
353	>	// largest cutoff for any atypes present in this group.
354	>	#ifdef IS_MPI
355	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
356	>	groupRowToGtype.resize(nGroupsInRow_);
357	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++)
358	>	{
359	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
360	>	for (vector<int>::iterator ia = atomListRow.begin();
361	>	ia != atomListRow.end(); ++ia)
362	>	{
363	>	int atom1 = (*ia);
364	>	atid = identsRow[atom1];
365	>	if (atypeCutoff[atid] > groupCutoffRow[cg1])
366	>	{
367	>	groupCutoffRow[cg1] = atypeCutoff[atid];
368	>	}
369	>	}
370
371	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
372	<	fill(atomRowData.functionalDerivative.begin(),
373	<	atomRowData.functionalDerivative.end(), 0.0);
374	<	fill(atomColData.functionalDerivative.begin(),
375	<	atomColData.functionalDerivative.end(), 0.0);
376	<	}
371	>	bool gTypeFound = false;
372	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
373	>	{
374	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol)
375	>	{
376	>	groupRowToGtype[cg1] = gt;
377	>	gTypeFound = true;
378	>	}
379	>	}
380	>	if (!gTypeFound)
381	>	{
382	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
383	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
384	>	}
385
386	+	}
387	+	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
388	+	groupColToGtype.resize(nGroupsInCol_);
389	+	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++)
390	+	{
391	+	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
392	+	for (vector<int>::iterator jb = atomListCol.begin();
393	+	jb != atomListCol.end(); ++jb)
394	+	{
395	+	int atom2 = (*jb);
396	+	atid = identsCol[atom2];
397	+	if (atypeCutoff[atid] > groupCutoffCol[cg2])
398	+	{
399	+	groupCutoffCol[cg2] = atypeCutoff[atid];
400	+	}
401	+	}
402	+	bool gTypeFound = false;
403	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
404	+	{
405	+	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol)
406	+	{
407	+	groupColToGtype[cg2] = gt;
408	+	gTypeFound = true;
409	+	}
410	+	}
411	+	if (!gTypeFound)
412	+	{
413	+	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
414	+	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
415	+	}
416	+	}
417		#else
418	<
419	<	if (storageLayout_ & DataStorage::dslParticlePot) {
420	<	fill(snap_->atomData.particlePot.begin(),
421	<	snap_->atomData.particlePot.end(), 0.0);
422	<	}
423	<
424	<	if (storageLayout_ & DataStorage::dslDensity) {
425	<	fill(snap_->atomData.density.begin(),
426	<	snap_->atomData.density.end(), 0.0);
427	<	}
428	<	if (storageLayout_ & DataStorage::dslFunctional) {
429	<	fill(snap_->atomData.functional.begin(),
430	<	snap_->atomData.functional.end(), 0.0);
431	<	}
432	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
433	<	fill(snap_->atomData.functionalDerivative.begin(),
434	<	snap_->atomData.functionalDerivative.end(), 0.0);
435	<	}
418	>
419	>	vector<RealType> groupCutoff(nGroups_, 0.0);
420	>	groupToGtype.resize(nGroups_);
421	>	for (int cg1 = 0; cg1 < nGroups_; cg1++)
422	>	{
423	>	groupCutoff[cg1] = 0.0;
424	>	vector<int> atomList = getAtomsInGroupRow(cg1);
425	>	for (vector<int>::iterator ia = atomList.begin(); ia != atomList.end(); ++ia)
426	>	{
427	>	int atom1 = (*ia);
428	>	atid = idents[atom1];
429	>	if (atypeCutoff[atid] > groupCutoff[cg1])
430	>	groupCutoff[cg1] = atypeCutoff[atid];
431	>	}
432	>
433	>	bool gTypeFound = false;
434	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
435	>	{
436	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol)
437	>	{
438	>	groupToGtype[cg1] = gt;
439	>	gTypeFound = true;
440	>	}
441	>	}
442	>	if (!gTypeFound)
443	>	{
444	>	gTypeCutoffs.push_back(groupCutoff[cg1]);
445	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
446	>	}
447	>	}
448		#endif
479	–
480	–	}
449
450	+	// Now we find the maximum group cutoff value present in the simulation
451
452	<	void ForceMatrixDecomposition::distributeData()  {
453	<	snap_ = sman_->getCurrentSnapshot();
485	<	storageLayout_ = sman_->getStorageLayout();
452	>	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
453	>
454		#ifdef IS_MPI
455	<
456	<	// gather up the atomic positions
489	<	AtomCommVectorRow->gather(snap_->atomData.position,
490	<	atomRowData.position);
491	<	AtomCommVectorColumn->gather(snap_->atomData.position,
492	<	atomColData.position);
493	<
494	<	// gather up the cutoff group positions
495	<	cgCommVectorRow->gather(snap_->cgData.position,
496	<	cgRowData.position);
497	<	cgCommVectorColumn->gather(snap_->cgData.position,
498	<	cgColData.position);
499	<
500	<	// if needed, gather the atomic rotation matrices
501	<	if (storageLayout_ & DataStorage::dslAmat) {
502	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
503	<	atomRowData.aMat);
504	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
505	<	atomColData.aMat);
506	<	}
507	<
508	<	// if needed, gather the atomic eletrostatic frames
509	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
510	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
511	<	atomRowData.electroFrame);
512	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
513	<	atomColData.electroFrame);
514	<	}
515	<	#endif
516	<	}
517	<
518	<	/* collects information obtained during the pre-pair loop onto local
519	<	* data structures.
520	<	*/
521	<	void ForceMatrixDecomposition::collectIntermediateData() {
522	<	snap_ = sman_->getCurrentSnapshot();
523	<	storageLayout_ = sman_->getStorageLayout();
524	<	#ifdef IS_MPI
525	<
526	<	if (storageLayout_ & DataStorage::dslDensity) {
527	<
528	<	AtomCommRealRow->scatter(atomRowData.density,
529	<	snap_->atomData.density);
530	<
531	<	int n = snap_->atomData.density.size();
532	<	vector<RealType> rho_tmp(n, 0.0);
533	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
534	<	for (int i = 0; i < n; i++)
535	<	snap_->atomData.density[i] += rho_tmp[i];
536	<	}
455	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
456	>	MPI::MAX);
457		#endif
538	–	}
458
459	<	/*
460	<	* redistributes information obtained during the pre-pair loop out to
461	<	* row and column-indexed data structures
462	<	*/
463	<	void ForceMatrixDecomposition::distributeIntermediateData() {
464	<	snap_ = sman_->getCurrentSnapshot();
465	<	storageLayout_ = sman_->getStorageLayout();
466	<	#ifdef IS_MPI
467	<	if (storageLayout_ & DataStorage::dslFunctional) {
468	<	AtomCommRealRow->gather(snap_->atomData.functional,
469	<	atomRowData.functional);
470	<	AtomCommRealColumn->gather(snap_->atomData.functional,
471	<	atomColData.functional);
472	<	}
473	<
474	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
475	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
476	<	atomRowData.functionalDerivative);
477	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
478	<	atomColData.functionalDerivative);
479	<	}
480	<	#endif
481	<	}
482	<
483	<
565	<	void ForceMatrixDecomposition::collectData() {
566	<	snap_ = sman_->getCurrentSnapshot();
567	<	storageLayout_ = sman_->getStorageLayout();
568	<	#ifdef IS_MPI
569	<	int n = snap_->atomData.force.size();
570	<	vector<Vector3d> frc_tmp(n, V3Zero);
571	<
572	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
573	<	for (int i = 0; i < n; i++) {
574	<	snap_->atomData.force[i] += frc_tmp[i];
575	<	frc_tmp[i] = 0.0;
576	<	}
577	<
578	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
579	<	for (int i = 0; i < n; i++)
580	<	snap_->atomData.force[i] += frc_tmp[i];
581	<
582	<
583	<	if (storageLayout_ & DataStorage::dslTorque) {
459	>	RealType tradRcut = groupMax;
460	>
461	>	for (int i = 0; i < gTypeCutoffs.size(); i++)
462	>	{
463	>	for (int j = 0; j < gTypeCutoffs.size(); j++)
464	>	{
465	>	RealType thisRcut;
466	>	switch (cutoffPolicy_) {
467	>	case TRADITIONAL:
468	>	thisRcut = tradRcut;
469	>	break;
470	>	case MIX:
471	>	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
472	>	break;
473	>	case MAX:
474	>	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
475	>	break;
476	>	default:
477	>	sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap "
478	>	"hit an unknown cutoff policy!\n");
479	>	painCave.severity = OPENMD_ERROR;
480	>	painCave.isFatal = 1;
481	>	simError();
482	>	break;
483	>	}
484
485	<	int nt = snap_->atomData.force.size();
486	<	vector<Vector3d> trq_tmp(nt, V3Zero);
485	>	pair<int, int> key = make_pair(i, j);
486	>	gTypeCutoffMap[key].first = thisRcut;
487	>	if (thisRcut > largestRcut_)
488	>	largestRcut_ = thisRcut;
489	>	gTypeCutoffMap[key].second = thisRcut * thisRcut;
490	>	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
491	>	// sanity check
492
493	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
494	<	for (int i = 0; i < n; i++) {
495	<	snap_->atomData.torque[i] += trq_tmp[i];
496	<	trq_tmp[i] = 0.0;
497	<	}
498	<
499	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
500	<	for (int i = 0; i < n; i++)
501	<	snap_->atomData.torque[i] += trq_tmp[i];
502	<	}
503	<
504	<	nLocal_ = snap_->getNumberOfAtoms();
493	>	if (userChoseCutoff_)
494	>	{
495	>	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001)
496	>	{
497	>	sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap "
498	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
499	>	painCave.severity = OPENMD_ERROR;
500	>	painCave.isFatal = 1;
501	>	simError();
502	>	}
503	>	}
504	>	}
505	>	}
506	>	}
507
508	<	vector<potVec> pot_temp(nLocal_,
509	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
603	<
604	<	// scatter/gather pot_row into the members of my column
605	<
606	<	AtomCommPotRow->scatter(pot_row, pot_temp);
607	<
608	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
609	<	pairwisePot += pot_temp[ii];
610	<
611	<	fill(pot_temp.begin(), pot_temp.end(),
612	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
613	<
614	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
615	<
616	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
617	<	pairwisePot += pot_temp[ii];
618	<	#endif
619	<
620	<	}
621	<
622	<	int ForceMatrixDecomposition::getNAtomsInRow() {
508	>	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
509	>	int i, j;
510		#ifdef IS_MPI
511	<	return nAtomsInRow_;
511	>	i = groupRowToGtype[cg1];
512	>	j = groupColToGtype[cg2];
513		#else
514	<	return nLocal_;
515	<	#endif
516	<	}
514	>	i = groupToGtype[cg1];
515	>	j = groupToGtype[cg2];
516	>	#endif
517	>	return gTypeCutoffMap[make_pair(i, j)];
518	>	}
519
520	<	/**
521	<	* returns the list of atoms belonging to this group.
522	<	*/
523	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
524	<	#ifdef IS_MPI
525	<	return groupListRow_[cg1];
526	<	#else
527	<	return groupList_[cg1];
638	<	#endif
639	<	}
520	>	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
521	>	for (int j = 0; j < toposForAtom[atom1].size(); j++)
522	>	{
523	>	if (toposForAtom[atom1][j] == atom2)
524	>	return topoDist[atom1][j];
525	>	}
526	>	return 0;
527	>	}
528
529	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
529	>	void ForceMatrixDecomposition::zeroWorkArrays() {
530	>	pairwisePot = 0.0;
531	>	embeddingPot = 0.0;
532	>
533		#ifdef IS_MPI
534	<	return groupListCol_[cg2];
535	<	#else
536	<	return groupList_[cg2];
537	<	#endif
538	<	}
648	<
649	<	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
650	<	Vector3d d;
651	<
652	<	#ifdef IS_MPI
653	<	d = cgColData.position[cg2] - cgRowData.position[cg1];
654	<	#else
655	<	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
656	<	#endif
657	<
658	<	snap_->wrapVector(d);
659	<	return d;
660	<	}
534	>	if (storageLayout_ & DataStorage::dslForce)
535	>	{
536	>	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
537	>	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
538	>	}
539
540	+	if (storageLayout_ & DataStorage::dslTorque)
541	+	{
542	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
543	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
544	+	}
545
546	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
546	>	fill(pot_row.begin(), pot_row.end(),
547	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
548
549	<	Vector3d d;
550	<
667	<	#ifdef IS_MPI
668	<	d = cgRowData.position[cg1] - atomRowData.position[atom1];
669	<	#else
670	<	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
671	<	#endif
549	>	fill(pot_col.begin(), pot_col.end(),
550	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
551
552	<	snap_->wrapVector(d);
553	<	return d;
554	<	}
555	<
556	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
557	<	Vector3d d;
558	<
680	<	#ifdef IS_MPI
681	<	d = cgColData.position[cg2] - atomColData.position[atom2];
682	<	#else
683	<	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
684	<	#endif
685	<
686	<	snap_->wrapVector(d);
687	<	return d;
688	<	}
552	>	if (storageLayout_ & DataStorage::dslParticlePot)
553	>	{
554	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
555	>	0.0);
556	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
557	>	0.0);
558	>	}
559
560	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
561	<	#ifdef IS_MPI
562	<	return massFactorsRow[atom1];
563	<	#else
564	<	cerr << "mfs = " << massFactors.size() << " atom1 = " << atom1 << "\n";
695	<	return massFactors[atom1];
696	<	#endif
697	<	}
560	>	if (storageLayout_ & DataStorage::dslDensity)
561	>	{
562	>	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
563	>	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
564	>	}
565
566	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
567	<	#ifdef IS_MPI
568	<	return massFactorsCol[atom2];
569	<	#else
570	<	return massFactors[atom2];
571	<	#endif
566	>	if (storageLayout_ & DataStorage::dslFunctional)
567	>	{
568	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
569	>	0.0);
570	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
571	>	0.0);
572	>	}
573
574	<	}
575	<
576	<	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
577	<	Vector3d d;
578	<
579	<	#ifdef IS_MPI
580	<	d = atomColData.position[atom2] - atomRowData.position[atom1];
581	<	#else
582	<	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
574	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
575	>	{
576	>	fill(atomRowData.functionalDerivative.begin(),
577	>	atomRowData.functionalDerivative.end(), 0.0);
578	>	fill(atomColData.functionalDerivative.begin(),
579	>	atomColData.functionalDerivative.end(), 0.0);
580	>	}
581	>
582	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
583	>	{
584	>	fill(atomRowData.skippedCharge.begin(),
585	>	atomRowData.skippedCharge.end(), 0.0);
586	>	fill(atomColData.skippedCharge.begin(),
587	>	atomColData.skippedCharge.end(), 0.0);
588	>	}
589	>
590		#endif
591	+	// even in parallel, we need to zero out the local arrays:
592
593	<	snap_->wrapVector(d);
594	<	return d;
595	<	}
593	>	if (storageLayout_ & DataStorage::dslParticlePot)
594	>	{
595	>	fill(snap_->atomData.particlePot.begin(), snap_->atomData.particlePot.end(), 0.0);
596	>	}
597
598	<	vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
599	<	return skipsForAtom[atom1];
600	<	}
598	>	if (storageLayout_ & DataStorage::dslDensity)
599	>	{
600	>	fill(snap_->atomData.density.begin(), snap_->atomData.density.end(), 0.0);
601	>	}
602	>	if (storageLayout_ & DataStorage::dslFunctional)
603	>	{
604	>	fill(snap_->atomData.functional.begin(), snap_->atomData.functional.end(), 0.0);
605	>	}
606	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
607	>	{
608	>	fill(snap_->atomData.functionalDerivative.begin(), snap_->atomData.functionalDerivative.end(), 0.0);
609	>	}
610	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
611	>	{
612	>	fill(snap_->atomData.skippedCharge.begin(), snap_->atomData.skippedCharge.end(), 0.0);
613	>	}
614
615	<	/**
726	<	* There are a number of reasons to skip a pair or a
727	<	* particle. Mostly we do this to exclude atoms who are involved in
728	<	* short range interactions (bonds, bends, torsions), but we also
729	<	* need to exclude some overcounted interactions that result from
730	<	* the parallel decomposition.
731	<	*/
732	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
733	<	int unique_id_1, unique_id_2;
615	>	}
616
617	+	void ForceMatrixDecomposition::distributeData() {
618	+	snap_ = sman_->getCurrentSnapshot();
619	+	storageLayout_ = sman_->getStorageLayout();
620		#ifdef IS_MPI
736	–	// in MPI, we have to look up the unique IDs for each atom
737	–	unique_id_1 = AtomRowToGlobal[atom1];
738	–	unique_id_2 = AtomColToGlobal[atom2];
621
622	<	// this situation should only arise in MPI simulations
623	<	if (unique_id_1 == unique_id_2) return true;
624	<
625	<	// this prevents us from doing the pair on multiple processors
626	<	if (unique_id_1 < unique_id_2) {
745	<	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
746	<	} else {
747	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
748	<	}
749	<	#else
750	<	// in the normal loop, the atom numbers are unique
751	<	unique_id_1 = atom1;
752	<	unique_id_2 = atom2;
753	<	#endif
754	<
755	<	for (vector<int>::iterator i = skipsForAtom[atom1].begin();
756	<	i != skipsForAtom[atom1].end(); ++i) {
757	<	if ( (*i) == unique_id_2 ) return true;
758	<	}
622	>	// gather up the atomic positions
623	>	AtomPlanVectorRow->gather(snap_->atomData.position,
624	>	atomRowData.position);
625	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
626	>	atomColData.position);
627
628	<	return false;
761	<	}
628	>	// gather up the cutoff group positions
629
630	+	cerr << "before gather\n";
631	+	for (int i = 0; i < snap_->cgData.position.size(); i++)
632	+	{
633	+	cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
634	+	}
635
636	<	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
637	<	#ifdef IS_MPI
766	<	atomRowData.force[atom1] += fg;
767	<	#else
768	<	snap_->atomData.force[atom1] += fg;
769	<	#endif
770	<	}
636	>	cgPlanVectorRow->gather(snap_->cgData.position,
637	>	cgRowData.position);
638
639	<	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
640	<	#ifdef IS_MPI
641	<	atomColData.force[atom2] += fg;
642	<	#else
643	<	snap_->atomData.force[atom2] += fg;
777	<	#endif
778	<	}
639	>	cerr << "after gather\n";
640	>	for (int i = 0; i < cgRowData.position.size(); i++)
641	>	{
642	>	cerr << "cgRpos = " << cgRowData.position[i] << "\n";
643	>	}
644
645	<	// filling interaction blocks with pointers
646	<	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
647	<	int atom1, int atom2) {
648	<	#ifdef IS_MPI
649	<
650	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
786	<	ff_->getAtomType(identsCol[atom2]) );
787	<
788	<	if (storageLayout_ & DataStorage::dslAmat) {
789	<	idat.A1 = &(atomRowData.aMat[atom1]);
790	<	idat.A2 = &(atomColData.aMat[atom2]);
791	<	}
792	<
793	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
794	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
795	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
796	<	}
645	>	cgPlanVectorColumn->gather(snap_->cgData.position,
646	>	cgColData.position);
647	>	for (int i = 0; i < cgColData.position.size(); i++)
648	>	{
649	>	cerr << "cgCpos = " << cgColData.position[i] << "\n";
650	>	}
651
652	<	if (storageLayout_ & DataStorage::dslTorque) {
653	<	idat.t1 = &(atomRowData.torque[atom1]);
654	<	idat.t2 = &(atomColData.torque[atom2]);
655	<	}
652	>	// if needed, gather the atomic rotation matrices
653	>	if (storageLayout_ & DataStorage::dslAmat)
654	>	{
655	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
656	>	atomRowData.aMat);
657	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
658	>	atomColData.aMat);
659	>	}
660
661	<	if (storageLayout_ & DataStorage::dslDensity) {
662	<	idat.rho1 = &(atomRowData.density[atom1]);
663	<	idat.rho2 = &(atomColData.density[atom2]);
664	<	}
661	>	// if needed, gather the atomic eletrostatic frames
662	>	if (storageLayout_ & DataStorage::dslElectroFrame)
663	>	{
664	>	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
665	>	atomRowData.electroFrame);
666	>	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
667	>	atomColData.electroFrame);
668	>	}
669
670	<	if (storageLayout_ & DataStorage::dslFunctional) {
671	<	idat.frho1 = &(atomRowData.functional[atom1]);
810	<	idat.frho2 = &(atomColData.functional[atom2]);
811	<	}
670	>	#endif
671	>	}
672
673	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
674	<	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
675	<	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
676	<	}
673	>	/* collects information obtained during the pre-pair loop onto local
674	>	* data structures.
675	>	*/
676	>	void ForceMatrixDecomposition::collectIntermediateData() {
677	>	snap_ = sman_->getCurrentSnapshot();
678	>	storageLayout_ = sman_->getStorageLayout();
679	>	#ifdef IS_MPI
680
681	<	if (storageLayout_ & DataStorage::dslParticlePot) {
682	<	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
820	<	idat.particlePot2 = &(atomColData.particlePot[atom2]);
821	<	}
681	>	if (storageLayout_ & DataStorage::dslDensity)
682	>	{
683
684	<	#else
684	>	AtomPlanRealRow->scatter(atomRowData.density,
685	>	snap_->atomData.density);
686
687	<	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
688	<	ff_->getAtomType(idents[atom2]) );
687	>	int n = snap_->atomData.density.size();
688	>	vector<RealType> rho_tmp(n, 0.0);
689	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
690	>	for (int i = 0; i < n; i++)
691	>	snap_->atomData.density[i] += rho_tmp[i];
692	>	}
693	>	#endif
694	>	}
695
696	<	if (storageLayout_ & DataStorage::dslAmat) {
697	<	idat.A1 = &(snap_->atomData.aMat[atom1]);
698	<	idat.A2 = &(snap_->atomData.aMat[atom2]);
699	<	}
696	>	/*
697	>	* redistributes information obtained during the pre-pair loop out to
698	>	* row and column-indexed data structures
699	>	*/
700	>	void ForceMatrixDecomposition::distributeIntermediateData() {
701	>	snap_ = sman_->getCurrentSnapshot();
702	>	storageLayout_ = sman_->getStorageLayout();
703	>	#ifdef IS_MPI
704	>	if (storageLayout_ & DataStorage::dslFunctional)
705	>	{
706	>	AtomPlanRealRow->gather(snap_->atomData.functional,
707	>	atomRowData.functional);
708	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
709	>	atomColData.functional);
710	>	}
711
712	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
713	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
714	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
715	<	}
712	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
713	>	{
714	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
715	>	atomRowData.functionalDerivative);
716	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
717	>	atomColData.functionalDerivative);
718	>	}
719	>	#endif
720	>	}
721
722	<	if (storageLayout_ & DataStorage::dslTorque) {
723	<	idat.t1 = &(snap_->atomData.torque[atom1]);
724	<	idat.t2 = &(snap_->atomData.torque[atom2]);
725	<	}
722	>	void ForceMatrixDecomposition::collectData() {
723	>	snap_ = sman_->getCurrentSnapshot();
724	>	storageLayout_ = sman_->getStorageLayout();
725	>	#ifdef IS_MPI
726	>	int n = snap_->atomData.force.size();
727	>	vector<Vector3d> frc_tmp(n, V3Zero);
728
729	<	if (storageLayout_ & DataStorage::dslDensity) {
730	<	idat.rho1 = &(snap_->atomData.density[atom1]);
731	<	idat.rho2 = &(snap_->atomData.density[atom2]);
732	<	}
729	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
730	>	for (int i = 0; i < n; i++)
731	>	{
732	>	snap_->atomData.force[i] += frc_tmp[i];
733	>	frc_tmp[i] = 0.0;
734	>	}
735
736	<	if (storageLayout_ & DataStorage::dslFunctional) {
737	<	idat.frho1 = &(snap_->atomData.functional[atom1]);
738	<	idat.frho2 = &(snap_->atomData.functional[atom2]);
739	<	}
736	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
737	>	for (int i = 0; i < n; i++)
738	>	{
739	>	snap_->atomData.force[i] += frc_tmp[i];
740	>	}
741
742	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
743	<	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
855	<	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
856	<	}
742	>	if (storageLayout_ & DataStorage::dslTorque)
743	>	{
744
745	<	if (storageLayout_ & DataStorage::dslParticlePot) {
746	<	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
860	<	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
861	<	}
745	>	int nt = snap_->atomData.torque.size();
746	>	vector<Vector3d> trq_tmp(nt, V3Zero);
747
748	<	#endif
749	<	}
748	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
749	>	for (int i = 0; i < nt; i++)
750	>	{
751	>	snap_->atomData.torque[i] += trq_tmp[i];
752	>	trq_tmp[i] = 0.0;
753	>	}
754
755	<
756	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
757	<	#ifdef IS_MPI
758	<	pot_row[atom1] += 0.5 *  *(idat.pot);
870	<	pot_col[atom2] += 0.5 *  *(idat.pot);
755	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
756	>	for (int i = 0; i < nt; i++)
757	>	snap_->atomData.torque[i] += trq_tmp[i];
758	>	}
759
760	<	atomRowData.force[atom1] += *(idat.f1);
761	<	atomColData.force[atom2] -= *(idat.f1);
874	<	#else
875	<	pairwisePot += *(idat.pot);
760	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
761	>	{
762
763	<	snap_->atomData.force[atom1] += *(idat.f1);
764	<	snap_->atomData.force[atom2] -= *(idat.f1);
879	<	#endif
763	>	int ns = snap_->atomData.skippedCharge.size();
764	>	vector<RealType> skch_tmp(ns, 0.0);
765
766	<	}
766	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
767	>	for (int i = 0; i < ns; i++)
768	>	{
769	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
770	>	skch_tmp[i] = 0.0;
771	>	}
772
773	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
774	+	for (int i = 0; i < ns; i++)
775	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
776	+	}
777
778	<	void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
885	<	int atom1, int atom2) {
886	<	#ifdef IS_MPI
887	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
888	<	ff_->getAtomType(identsCol[atom2]) );
778	>	nLocal_ = snap_->getNumberOfAtoms();
779
780	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
781	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
892	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
893	<	}
780	>	vector<potVec> pot_temp(nLocal_,
781	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
782
783	<	if (storageLayout_ & DataStorage::dslTorque) {
896	<	idat.t1 = &(atomRowData.torque[atom1]);
897	<	idat.t2 = &(atomColData.torque[atom2]);
898	<	}
783	>	// scatter/gather pot_row into the members of my column
784
785	<	if (storageLayout_ & DataStorage::dslSkippedCharge) {
901	<	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
902	<	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
903	<	}
904	<	#else
905	<	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
906	<	ff_->getAtomType(idents[atom2]) );
785	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
786
787	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
788	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
910	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
911	<	}
787	>	for (int ii = 0; ii < pot_temp.size(); ii++ )
788	>	pairwisePot += pot_temp[ii];
789
790	<	if (storageLayout_ & DataStorage::dslTorque) {
791	<	idat.t1 = &(snap_->atomData.torque[atom1]);
915	<	idat.t2 = &(snap_->atomData.torque[atom2]);
916	<	}
790	>	fill(pot_temp.begin(), pot_temp.end(),
791	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
792
793	<	if (storageLayout_ & DataStorage::dslSkippedCharge) {
919	<	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
920	<	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
921	<	}
922	<	#endif
923	<	}
793	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
794
795	+	for (int ii = 0; ii < pot_temp.size(); ii++ )
796	+	pairwisePot += pot_temp[ii];
797	+	#endif
798
799	<	void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {
799	>	cerr << "pairwisePot = " << pairwisePot << "\n";
800	>	}
801	>
802	>	int ForceMatrixDecomposition::getNAtomsInRow() {
803		#ifdef IS_MPI
804	<	pot_row[atom1] += 0.5 *  *(idat.pot);
929	<	pot_col[atom2] += 0.5 *  *(idat.pot);
804	>	return nAtomsInRow_;
805		#else
806	<	pairwisePot += *(idat.pot);
806	>	return nLocal_;
807		#endif
808	+	}
809
810	<	}
810	>	/**
811	>	* returns the list of atoms belonging to this group.
812	>	*/
813	>	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1) {
814	>	#ifdef IS_MPI
815	>	return groupListRow_[cg1];
816	>	#else
817	>	return groupList_[cg1];
818	>	#endif
819	>	}
820
821	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2) {
822	+	#ifdef IS_MPI
823	+	return groupListCol_[cg2];
824	+	#else
825	+	return groupList_[cg2];
826	+	#endif
827	+	}
828
829	<	/*
830	<	* buildNeighborList
831	<	*
940	<	* first element of pair is row-indexed CutoffGroup
941	<	* second element of pair is column-indexed CutoffGroup
942	<	*/
943	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
944	<
945	<	vector<pair<int, int> > neighborList;
946	<	groupCutoffs cuts;
829	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2) {
830	>	Vector3d d;
831	>
832		#ifdef IS_MPI
833	<	cellListRow_.clear();
834	<	cellListCol_.clear();
833	>	d = cgColData.position[cg2] - cgRowData.position[cg1];
834	>	cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
835	>	cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
836		#else
837	<	cellList_.clear();
837	>	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
838	>	cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
839	>	cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
840		#endif
841
842	<	RealType rList_ = (largestRcut_ + skinThickness_);
843	<	RealType rl2 = rList_ * rList_;
844	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
957	<	Mat3x3d Hmat = snap_->getHmat();
958	<	Vector3d Hx = Hmat.getColumn(0);
959	<	Vector3d Hy = Hmat.getColumn(1);
960	<	Vector3d Hz = Hmat.getColumn(2);
842	>	snap_->wrapVector(d);
843	>	return d;
844	>	}
845
846	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
847	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
964	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
846	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2) {
847	>	Vector3d d;
848
849	<	Mat3x3d invHmat = snap_->getInvHmat();
850	<	Vector3d rs, scaled, dr;
851	<	Vector3i whichCell;
852	<	int cellIndex;
853	<	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
849	>	d = snap_->cgData.position[cg2->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
850	>	/*      cerr << "cg1_gid = " << cg1->getGlobalIndex() << "\tcg1_lid = " << cg1->getLocalIndex() << "\tcg1p = "
851	>	<< snap_->cgData.position[cg1->getLocalIndex()] << "\n";
852	>	cerr << "cg2_gid = " << cg2->getGlobalIndex() << "\tcg2_lid = " << cg2->getLocalIndex() << "\tcg2p = "
853	>	<< snap_->cgData.position[cg2->getLocalIndex()] << "\n";*/
854
855	+	snap_->wrapVector(d);
856	+	return d;
857	+	}
858	+
859	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1) {
860	+
861	+	Vector3d d;
862	+
863		#ifdef IS_MPI
864	<	cellListRow_.resize(nCtot);
974	<	cellListCol_.resize(nCtot);
864	>	d = cgRowData.position[cg1] - atomRowData.position[atom1];
865		#else
866	<	cellList_.resize(nCtot);
866	>	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
867		#endif
868
869	+	snap_->wrapVector(d);
870	+	return d;
871	+	}
872	+
873	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2) {
874	+	Vector3d d;
875	+
876		#ifdef IS_MPI
877	<	for (int i = 0; i < nGroupsInRow_; i++) {
878	<	rs = cgRowData.position[i];
877	>	d = cgColData.position[cg2] - atomColData.position[atom2];
878	>	#else
879	>	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
880	>	#endif
881
882	<	// scaled positions relative to the box vectors
883	<	scaled = invHmat * rs;
882	>	snap_->wrapVector(d);
883	>	return d;
884	>	}
885
886	<	// wrap the vector back into the unit box by subtracting integer box
887	<	// numbers
888	<	for (int j = 0; j < 3; j++) {
889	<	scaled[j] -= roundMe(scaled[j]);
890	<	scaled[j] += 0.5;
891	<	}
892	<
993	<	// find xyz-indices of cell that cutoffGroup is in.
994	<	whichCell.x() = nCells_.x() * scaled.x();
995	<	whichCell.y() = nCells_.y() * scaled.y();
996	<	whichCell.z() = nCells_.z() * scaled.z();
886	>	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
887	>	#ifdef IS_MPI
888	>	return massFactorsRow[atom1];
889	>	#else
890	>	return massFactors[atom1];
891	>	#endif
892	>	}
893
894	<	// find single index of this cell:
895	<	cellIndex = Vlinear(whichCell, nCells_);
894	>	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
895	>	#ifdef IS_MPI
896	>	return massFactorsCol[atom2];
897	>	#else
898	>	return massFactors[atom2];
899	>	#endif
900
901	<	// add this cutoff group to the list of groups in this cell;
1002	<	cellListRow_[cellIndex].push_back(i);
1003	<	}
901	>	}
902
903	<	for (int i = 0; i < nGroupsInCol_; i++) {
904	<	rs = cgColData.position[i];
903	>	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2) {
904	>	Vector3d d;
905
906	<	// scaled positions relative to the box vectors
907	<	scaled = invHmat * rs;
906	>	#ifdef IS_MPI
907	>	d = atomColData.position[atom2] - atomRowData.position[atom1];
908	>	#else
909	>	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
910	>	#endif
911
912	<	// wrap the vector back into the unit box by subtracting integer box
913	<	// numbers
914	<	for (int j = 0; j < 3; j++) {
1014	<	scaled[j] -= roundMe(scaled[j]);
1015	<	scaled[j] += 0.5;
1016	<	}
912	>	snap_->wrapVector(d);
913	>	return d;
914	>	}
915
916	<	// find xyz-indices of cell that cutoffGroup is in.
917	<	whichCell.x() = nCells_.x() * scaled.x();
918	<	whichCell.y() = nCells_.y() * scaled.y();
1021	<	whichCell.z() = nCells_.z() * scaled.z();
916	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
917	>	return excludesForAtom[atom1];
918	>	}
919
920	<	// find single index of this cell:
921	<	cellIndex = Vlinear(whichCell, nCells_);
920	>	/**
921	>	* We need to exclude some overcounted interactions that result from
922	>	* the parallel decomposition.
923	>	*/
924	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
925	>	int unique_id_1, unique_id_2;
926
927	<	// add this cutoff group to the list of groups in this cell;
928	<	cellListCol_[cellIndex].push_back(i);
929	<	}
930	<	#else
931	<	for (int i = 0; i < nGroups_; i++) {
1031	<	rs = snap_->cgData.position[i];
927	>	//      cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
928	>	#ifdef IS_MPI
929	>	// in MPI, we have to look up the unique IDs for each atom
930	>	unique_id_1 = AtomRowToGlobal[atom1];
931	>	unique_id_2 = AtomColToGlobal[atom2];
932
933	<	// scaled positions relative to the box vectors
934	<	scaled = invHmat * rs;
933	>	cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
934	>	// this situation should only arise in MPI simulations
935	>	if (unique_id_1 == unique_id_2) return true;
936
937	<	// wrap the vector back into the unit box by subtracting integer box
938	<	// numbers
939	<	for (int j = 0; j < 3; j++) {
940	<	scaled[j] -= roundMe(scaled[j]);
941	<	scaled[j] += 0.5;
942	<	}
937	>	// this prevents us from doing the pair on multiple processors
938	>	if (unique_id_1 < unique_id_2)
939	>	{
940	>	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
941	>	} else
942	>	{
943	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
944	>	}
945	>	#endif
946	>	return false;
947	>	}
948
949	<	// find xyz-indices of cell that cutoffGroup is in.
950	<	whichCell.x() = nCells_.x() * scaled.x();
951	<	whichCell.y() = nCells_.y() * scaled.y();
952	<	whichCell.z() = nCells_.z() * scaled.z();
949	>	/**
950	>	* We need to handle the interactions for atoms who are involved in
951	>	* the same rigid body as well as some short range interactions
952	>	* (bonds, bends, torsions) differently from other interactions.
953	>	* We'll still visit the pairwise routines, but with a flag that
954	>	* tells those routines to exclude the pair from direct long range
955	>	* interactions.  Some indirect interactions (notably reaction
956	>	* field) must still be handled for these pairs.
957	>	*/
958	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
959	>	int unique_id_2;
960	>	#ifdef IS_MPI
961	>	// in MPI, we have to look up the unique IDs for the row atom.
962	>	unique_id_2 = AtomColToGlobal[atom2];
963	>	#else
964	>	// in the normal loop, the atom numbers are unique
965	>	unique_id_2 = atom2;
966	>	#endif
967
968	<	// find single index of this cell:
969	<	cellIndex = Vlinear(whichCell, nCells_);
968	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin(); i != excludesForAtom[atom1].end(); ++i)
969	>	{
970	>	if ((*i) == unique_id_2)
971	>	return true;
972	>	}
973
974	<	// add this cutoff group to the list of groups in this cell;
975	<	cellList_[cellIndex].push_back(i);
976	<	}
974	>	return false;
975	>	}
976	>
977	>	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg) {
978	>	#ifdef IS_MPI
979	>	atomRowData.force[atom1] += fg;
980	>	#else
981	>	snap_->atomData.force[atom1] += fg;
982		#endif
983	+	}
984
985	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
986	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
987	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
988	<	Vector3i m1v(m1x, m1y, m1z);
989	<	int m1 = Vlinear(m1v, nCells_);
985	>	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg) {
986	>	#ifdef IS_MPI
987	>	atomColData.force[atom2] += fg;
988	>	#else
989	>	snap_->atomData.force[atom2] += fg;
990	>	#endif
991	>	}
992
993	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
994	<	os != cellOffsets_.end(); ++os) {
1064	<
1065	<	Vector3i m2v = m1v + (*os);
1066	<
1067	<	if (m2v.x() >= nCells_.x()) {
1068	<	m2v.x() = 0;
1069	<	} else if (m2v.x() < 0) {
1070	<	m2v.x() = nCells_.x() - 1;
1071	<	}
1072	<
1073	<	if (m2v.y() >= nCells_.y()) {
1074	<	m2v.y() = 0;
1075	<	} else if (m2v.y() < 0) {
1076	<	m2v.y() = nCells_.y() - 1;
1077	<	}
1078	<
1079	<	if (m2v.z() >= nCells_.z()) {
1080	<	m2v.z() = 0;
1081	<	} else if (m2v.z() < 0) {
1082	<	m2v.z() = nCells_.z() - 1;
1083	<	}
1084	<
1085	<	int m2 = Vlinear (m2v, nCells_);
993	>	// filling interaction blocks with pointers
994	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, int atom1, int atom2) {
995
996	+	idat.excluded = excludeAtomPair(atom1, atom2);
997	+
998		#ifdef IS_MPI
999	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1000	<	j1 != cellListRow_[m1].end(); ++j1) {
1001	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1091	<	j2 != cellListCol_[m2].end(); ++j2) {
1092	<
1093	<	// Always do this if we're in different cells or if
1094	<	// we're in the same cell and the global index of the
1095	<	// j2 cutoff group is less than the j1 cutoff group
999	>	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1000	>	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1001	>	//                         ff_->getAtomType(identsCol[atom2]) );
1002
1003	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1004	<	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1005	<	snap_->wrapVector(dr);
1006	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1007	<	if (dr.lengthSquare() < cuts.third) {
1008	<	neighborList.push_back(make_pair((*j1), (*j2)));
1009	<	}
1010	<	}
1011	<	}
1012	<	}
1003	>	if (storageLayout_ & DataStorage::dslAmat)
1004	>	{
1005	>	idat.A1 = &(atomRowData.aMat[atom1]);
1006	>	idat.A2 = &(atomColData.aMat[atom2]);
1007	>	}
1008	>
1009	>	if (storageLayout_ & DataStorage::dslElectroFrame)
1010	>	{
1011	>	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1012	>	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1013	>	}
1014	>
1015	>	if (storageLayout_ & DataStorage::dslTorque)
1016	>	{
1017	>	idat.t1 = &(atomRowData.torque[atom1]);
1018	>	idat.t2 = &(atomColData.torque[atom2]);
1019	>	}
1020	>
1021	>	if (storageLayout_ & DataStorage::dslDensity)
1022	>	{
1023	>	idat.rho1 = &(atomRowData.density[atom1]);
1024	>	idat.rho2 = &(atomColData.density[atom2]);
1025	>	}
1026	>
1027	>	if (storageLayout_ & DataStorage::dslFunctional)
1028	>	{
1029	>	idat.frho1 = &(atomRowData.functional[atom1]);
1030	>	idat.frho2 = &(atomColData.functional[atom2]);
1031	>	}
1032	>
1033	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
1034	>	{
1035	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1036	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1037	>	}
1038	>
1039	>	if (storageLayout_ & DataStorage::dslParticlePot)
1040	>	{
1041	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1042	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1043	>	}
1044	>
1045	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
1046	>	{
1047	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1048	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1049	>	}
1050	>
1051		#else
1052
1053	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1054	<	j1 != cellList_[m1].end(); ++j1) {
1055	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1112	<	j2 != cellList_[m2].end(); ++j2) {
1053	>	idat.atypes = make_pair(atypesLocal[atom1], atypesLocal[atom2]);
1054	>	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1055	>	//                         ff_->getAtomType(idents[atom2]) );
1056
1057	<	// Always do this if we're in different cells or if
1058	<	// we're in the same cell and the global index of the
1059	<	// j2 cutoff group is less than the j1 cutoff group
1057	>	if (storageLayout_ & DataStorage::dslAmat)
1058	>	{
1059	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1060	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1061	>	}
1062
1063	<	if (m2 != m1 || (*j2) < (*j1)) {
1064	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1065	<	snap_->wrapVector(dr);
1066	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1067	<	if (dr.lengthSquare() < cuts.third) {
1068	<	neighborList.push_back(make_pair((*j1), (*j2)));
1069	<	}
1070	<	}
1071	<	}
1072	<	}
1063	>	if (storageLayout_ & DataStorage::dslElectroFrame)
1064	>	{
1065	>	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1066	>	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1067	>	}
1068	>
1069	>	if (storageLayout_ & DataStorage::dslTorque)
1070	>	{
1071	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1072	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1073	>	}
1074	>
1075	>	if (storageLayout_ & DataStorage::dslDensity)
1076	>	{
1077	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1078	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1079	>	}
1080	>
1081	>	if (storageLayout_ & DataStorage::dslFunctional)
1082	>	{
1083	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1084	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1085	>	}
1086	>
1087	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
1088	>	{
1089	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1090	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1091	>	}
1092	>
1093	>	if (storageLayout_ & DataStorage::dslParticlePot)
1094	>	{
1095	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1096	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1097	>	}
1098	>
1099	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
1100	>	{
1101	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1102	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1103	>	}
1104		#endif
1105	<	}
1106	<	}
1107	<	}
1108	<	}
1109	<
1110	<	// save the local cutoff group positions for the check that is
1111	<	// done on each loop:
1112	<	saved_CG_positions_.clear();
1113	<	for (int i = 0; i < nGroups_; i++)
1114	<	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1115	<
1116	<	return neighborList;
1117	<	}
1105	>	}
1106	>
1107	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1108	>	#ifdef IS_MPI
1109	>	pot_row[atom1] += 0.5 * *(idat.pot);
1110	>	pot_col[atom2] += 0.5 * *(idat.pot);
1111	>
1112	>	atomRowData.force[atom1] += *(idat.f1);
1113	>	atomColData.force[atom2] -= *(idat.f1);
1114	>	#else
1115	>	pairwisePot += *(idat.pot);
1116	>
1117	>	snap_->atomData.force[atom1] += *(idat.f1);
1118	>	snap_->atomData.force[atom2] -= *(idat.f1);
1119	>	#endif
1120	>
1121	>	}
1122	>
1123	>	void ForceMatrixDecomposition::reorderGroupCutoffs(vector<int> &order) {
1124	>	vector<int> tmp = vector<int> (groupToGtype.size());
1125	>
1126	>	for (int i = 0; i < groupToGtype.size(); ++i)
1127	>	{
1128	>	tmp[i] = groupToGtype[i];
1129	>	}
1130	>
1131	>	for (int i = 0; i < groupToGtype.size(); ++i)
1132	>	{
1133	>	groupToGtype[i] = tmp[order[i]];
1134	>	}
1135	>	}
1136	>
1137	>	void ForceMatrixDecomposition::reorderPosition(vector<int> &order) {
1138	>	Snapshot* snap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1139	>	DataStorage* cgConfig = &(snap_->cgData);
1140	>	vector<Vector3d> tmp = vector<Vector3d> (nGroups_);
1141	>
1142	>	for (int i = 0; i < nGroups_; ++i)
1143	>	{
1144	>	tmp[i] = snap_->cgData.position[i];
1145	>	}
1146	>
1147	>	vector<int> mapPos = vector<int>(nGroups_);
1148	>	for (int i = 0; i < nGroups_; ++i)
1149	>	{
1150	>	snap_->cgData.position[i] = tmp[order[i]];
1151	>	mapPos[order[i]] = i;
1152	>	}
1153	>
1154	>	SimInfo::MoleculeIterator mi;
1155	>	Molecule* mol;
1156	>	Molecule::CutoffGroupIterator ci;
1157	>	CutoffGroup* cg;
1158	>
1159	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1160	>	{
1161	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1162	>	{
1163	>	cg->setLocalIndex(mapPos[cg->getLocalIndex()]);
1164	>	}
1165	>	}
1166	>
1167	>	/*      if (info_->getNCutoffGroups() > 0)
1168	>	{
1169	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1170	>	{
1171	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1172	>	{
1173	>	printf("gbI:%d locI:%d x:%f y:%f z:%f\n", cg->getGlobalIndex(), cg->getLocalIndex(),
1174	>	cgConfig->position[cg->getLocalIndex()].x(), cgConfig->position[cg->getLocalIndex()].y(),
1175	>	cgConfig->position[cg->getLocalIndex()].z());
1176	>	}
1177	>	}
1178	>	} else
1179	>	{
1180	>	// center of mass of the group is the same as position of the atom
1181	>	// if cutoff group does not exist
1182	>	printf("ERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
1183	>	//                      cgConfig->position = config->position;
1184	>	}*/
1185	>	}
1186	>
1187	>	void ForceMatrixDecomposition::reorderGroupList(vector<int> &order) {
1188	>	vector<vector<int> > tmp = vector<vector<int> > (groupList_.size());
1189	>
1190	>	for (int i = 0; i < groupList_.size(); ++i)
1191	>	{
1192	>	tmp[i] = groupList_[i];
1193	>	}
1194	>
1195	>	for (int i = 0; i < groupList_.size(); ++i)
1196	>	{
1197	>	groupList_[i] = tmp[order[i]];
1198	>	}
1199	>	}
1200	>
1201	>	void ForceMatrixDecomposition::reorderMemory(vector<vector<CutoffGroup *> > &H_c_l) {
1202	>	int n = 0;
1203	>	//      printf("Reorder memory time:%f!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
1204	>	//                      info_->getSnapshotManager()->getCurrentSnapshot()->getTime());
1205	>
1206	>	/* record the reordered atom indices */
1207	>	vector<int> k = vector<int> (nGroups_);
1208	>
1209	>	for (int c = 0; c < H_c_l.size(); ++c)
1210	>	{
1211	>	for (vector<CutoffGroup *>::iterator cg = H_c_l[c].begin(); cg != H_c_l[c].end(); ++cg)
1212	>	{
1213	>	int i = (*cg)->getGlobalIndex();
1214	>	k[n] = i;
1215	>	++n;
1216	>	}
1217	>	}
1218	>
1219	>	//      reorderGroupCutoffs(k);
1220	>	//      reorderGroupList(k);
1221	>	reorderPosition(k);
1222	>	}
1223	>
1224	>	vector<vector<CutoffGroup *> > ForceMatrixDecomposition::buildLayerBasedNeighborList() {
1225	>	//      printf("buildLayerBasedNeighborList; nGroups:%d\n", nGroups_);
1226	>	// Na = nGroups_
1227	>	/* cell occupancy counter */
1228	>	//      vector<int> k_c;
1229	>	/* c_i - has cell containing atom i (size Na) */
1230	>	vector<int> c = vector<int> (nGroups_);
1231	>	/* l_i - layer containing atom i (size Na) */
1232	>	//      vector<int> l;
1233	>
1234	>	RealType rList_ = (largestRcut_ + skinThickness_);
1235	>	Snapshot* snap_ = sman_->getCurrentSnapshot();
1236	>	Mat3x3d Hmat = snap_->getHmat();
1237	>	Vector3d Hx = Hmat.getColumn(0);
1238	>	Vector3d Hy = Hmat.getColumn(1);
1239	>	Vector3d Hz = Hmat.getColumn(2);
1240	>
1241	>	nCells_.x() = (int) (Hx.length()) / rList_;
1242	>	nCells_.y() = (int) (Hy.length()) / rList_;
1243	>	nCells_.z() = (int) (Hz.length()) / rList_;
1244	>
1245	>	Mat3x3d invHmat = snap_->getInvHmat();
1246	>	Vector3d rs, scaled, dr;
1247	>	Vector3i whichCell;
1248	>	int cellIndex;
1249	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1250	>
1251	>	//      k_c = vector<int> (nCtot, 0);
1252	>
1253	>	SimInfo::MoleculeIterator mi;
1254	>	Molecule* mol;
1255	>	Molecule::CutoffGroupIterator ci;
1256	>	CutoffGroup* cg;
1257	>
1258	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1259	>	{
1260	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1261	>	{
1262	>	rs = snap_->cgData.position[cg->getLocalIndex()];
1263	>
1264	>	// scaled positions relative to the box vectors
1265	>	scaled = invHmat * rs;
1266	>
1267	>	// wrap the vector back into the unit box by subtracting integer box
1268	>	// numbers
1269	>	for (int j = 0; j < 3; j++)
1270	>	{
1271	>	scaled[j] -= roundMe(scaled[j]);
1272	>	scaled[j] += 0.5;
1273	>	}
1274	>
1275	>	// find xyz-indices of cell that cutoffGroup is in.
1276	>	whichCell.x() = nCells_.x() * scaled.x();
1277	>	whichCell.y() = nCells_.y() * scaled.y();
1278	>	whichCell.z() = nCells_.z() * scaled.z();
1279	>
1280	>	//                      printf("pos x:%f y:%f z:%f cell x:%d y:%d z:%d\n", rs.x(), rs.y(), rs.z(), whichCell.x(), whichCell.y(),
1281	>	//                                      whichCell.z());
1282	>
1283	>	// find single index of this cell:
1284	>	cellIndex = Vlinear(whichCell, nCells_);
1285	>
1286	>	c[cg->getGlobalIndex()] = cellIndex;
1287	>	}
1288	>	}
1289	>
1290	>	//      int k_c_curr;
1291	>	//      int k_c_max = 0;
1292	>	/* the cell-layer occupancy matrix */
1293	>	vector<vector<CutoffGroup *> > H_c_l = vector<vector<CutoffGroup *> > (nCtot);
1294	>
1295	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1296	>	{
1297	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1298	>
1299	>	{
1300	>	//                      k_c_curr = ++k_c[c[cg1->getGlobalIndex()]];
1301	>	//                      l.push_back(k_c_curr);
1302	>	//
1303	>	//                      /* determines the number of layers in use */
1304	>	//                      if (k_c_max < k_c_curr)
1305	>	//                      {
1306	>	//                              k_c_max = k_c_curr;
1307	>	//                      }
1308	>
1309	>	H_c_l[c[cg->getGlobalIndex()]].push_back(/*l[*/cg/*]*/);
1310	>	}
1311	>	}
1312	>
1313	>	reorderMemory(H_c_l);
1314	>
1315	>	int m;
1316	>	/* the neighbor matrix */
1317	>	vector<vector<CutoffGroup *> > neighborMatW = vector<vector<CutoffGroup *> > (nGroups_);
1318	>
1319	>	groupCutoffs cuts;
1320	>	CutoffGroup *cg1;
1321	>
1322	>	/* loops over objects(atoms, rigidBodies, cutoffGroups, etc.) */
1323	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1324	>	{
1325	>	for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
1326	>	{
1327	>	/* c' */
1328	>	int c1 = c[cg1->getGlobalIndex()];
1329	>	Vector3i c1v = idxToV(c1, nCells_);
1330	>
1331	>	/* loops over the neighboring cells c'' */
1332	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1333	>	{
1334	>	Vector3i c2v = c1v + (*os);
1335	>
1336	>	if (c2v.x() >= nCells_.x())
1337	>	{
1338	>	c2v.x() = 0;
1339	>	} else if (c2v.x() < 0)
1340	>	{
1341	>	c2v.x() = nCells_.x() - 1;
1342	>	}
1343	>
1344	>	if (c2v.y() >= nCells_.y())
1345	>	{
1346	>	c2v.y() = 0;
1347	>	} else if (c2v.y() < 0)
1348	>	{
1349	>	c2v.y() = nCells_.y() - 1;
1350	>	}
1351	>
1352	>	if (c2v.z() >= nCells_.z())
1353	>	{
1354	>	c2v.z() = 0;
1355	>	} else if (c2v.z() < 0)
1356	>	{
1357	>	c2v.z() = nCells_.z() - 1;
1358	>	}
1359	>
1360	>	int c2 = Vlinear(c2v, nCells_);
1361	>	/* loops over layers l to access the neighbor atoms */
1362	>	for (vector<CutoffGroup *>::iterator cg2 = H_c_l[c2].begin(); cg2 != H_c_l[c2].end(); ++cg2)
1363	>	{
1364	>	//                              if i'' = 0 then break // doesn't apply to vector implementation of matrix
1365	>	//                              if(i != *j)
1366	>	if (c2 != c1 || (*cg2)->getGlobalIndex() < cg1->getGlobalIndex())
1367	>	{
1368	>	dr = snap_->cgData.position[(*cg2)->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
1369	>	snap_->wrapVector(dr);
1370	>	cuts = getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex());
1371	>	if (dr.lengthSquare() < cuts.third)
1372	>	{
1373	>	/* transposed version of Rapaport W mat, to occupy successive memory locations on CPU */
1374	>	neighborMatW[cg1->getGlobalIndex()].push_back((*cg2));
1375	>	}
1376	>	}
1377	>	}
1378	>	}
1379	>	}
1380	>	}
1381	>
1382	>	// save the local cutoff group positions for the check that is
1383	>	// done on each loop:
1384	>	saved_CG_positions_.clear();
1385	>	for (int i = 0; i < nGroups_; i++)
1386	>	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1387	>
1388	>	return neighborMatW;
1389	>	}
1390	>
1391	>	/*
1392	>	* buildNeighborList
1393	>	*
1394	>	* first element of pair is row-indexed CutoffGroup
1395	>	* second element of pair is column-indexed CutoffGroup
1396	>	*/
1397	>	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1398	>
1399	>	vector<pair<int, int> > neighborList;
1400	>	groupCutoffs cuts;
1401	>	bool doAllPairs = false;
1402	>
1403	>	#ifdef IS_MPI
1404	>	cellListRow_.clear();
1405	>	cellListCol_.clear();
1406	>	#else
1407	>	cellList_.clear();
1408	>	#endif
1409	>
1410	>	RealType rList_ = (largestRcut_ + skinThickness_);
1411	>	RealType rl2 = rList_ * rList_;
1412	>	Snapshot* snap_ = sman_->getCurrentSnapshot();
1413	>	Mat3x3d Hmat = snap_->getHmat();
1414	>	Vector3d Hx = Hmat.getColumn(0);
1415	>	Vector3d Hy = Hmat.getColumn(1);
1416	>	Vector3d Hz = Hmat.getColumn(2);
1417	>
1418	>	nCells_.x() = (int) (Hx.length()) / rList_;
1419	>	nCells_.y() = (int) (Hy.length()) / rList_;
1420	>	nCells_.z() = (int) (Hz.length()) / rList_;
1421	>
1422	>	// handle small boxes where the cell offsets can end up repeating cells
1423	>
1424	>	if (nCells_.x() < 3)
1425	>	doAllPairs = true;
1426	>	if (nCells_.y() < 3)
1427	>	doAllPairs = true;
1428	>	if (nCells_.z() < 3)
1429	>	doAllPairs = true;
1430	>
1431	>	Mat3x3d invHmat = snap_->getInvHmat();
1432	>	Vector3d rs, scaled, dr;
1433	>	Vector3i whichCell;
1434	>	int cellIndex;
1435	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1436	>
1437	>	#ifdef IS_MPI
1438	>	cellListRow_.resize(nCtot);
1439	>	cellListCol_.resize(nCtot);
1440	>	#else
1441	>	cellList_.resize(nCtot);
1442	>	#endif
1443	>
1444	>	if (!doAllPairs)
1445	>	{
1446	>	#ifdef IS_MPI
1447	>
1448	>	for (int i = 0; i < nGroupsInRow_; i++)
1449	>	{
1450	>	rs = cgRowData.position[i];
1451	>
1452	>	// scaled positions relative to the box vectors
1453	>	scaled = invHmat * rs;
1454	>
1455	>	// wrap the vector back into the unit box by subtracting integer box
1456	>	// numbers
1457	>	for (int j = 0; j < 3; j++)
1458	>	{
1459	>	scaled[j] -= roundMe(scaled[j]);
1460	>	scaled[j] += 0.5;
1461	>	}
1462	>
1463	>	// find xyz-indices of cell that cutoffGroup is in.
1464	>	whichCell.x() = nCells_.x() * scaled.x();
1465	>	whichCell.y() = nCells_.y() * scaled.y();
1466	>	whichCell.z() = nCells_.z() * scaled.z();
1467	>
1468	>	// find single index of this cell:
1469	>	cellIndex = Vlinear(whichCell, nCells_);
1470	>
1471	>	// add this cutoff group to the list of groups in this cell;
1472	>	cellListRow_[cellIndex].push_back(i);
1473	>	}
1474	>	for (int i = 0; i < nGroupsInCol_; i++)
1475	>	{
1476	>	rs = cgColData.position[i];
1477	>
1478	>	// scaled positions relative to the box vectors
1479	>	scaled = invHmat * rs;
1480	>
1481	>	// wrap the vector back into the unit box by subtracting integer box
1482	>	// numbers
1483	>	for (int j = 0; j < 3; j++)
1484	>	{
1485	>	scaled[j] -= roundMe(scaled[j]);
1486	>	scaled[j] += 0.5;
1487	>	}
1488	>
1489	>	// find xyz-indices of cell that cutoffGroup is in.
1490	>	whichCell.x() = nCells_.x() * scaled.x();
1491	>	whichCell.y() = nCells_.y() * scaled.y();
1492	>	whichCell.z() = nCells_.z() * scaled.z();
1493	>
1494	>	// find single index of this cell:
1495	>	cellIndex = Vlinear(whichCell, nCells_);
1496	>
1497	>	// add this cutoff group to the list of groups in this cell;
1498	>	cellListCol_[cellIndex].push_back(i);
1499	>	}
1500	>	#else
1501	>	for (int i = 0; i < nGroups_; i++)
1502	>	{
1503	>	rs = snap_->cgData.position[i];
1504	>
1505	>	// scaled positions relative to the box vectors
1506	>	scaled = invHmat * rs;
1507	>
1508	>	// wrap the vector back into the unit box by subtracting integer box
1509	>	// numbers
1510	>	for (int j = 0; j < 3; j++)
1511	>	{
1512	>	scaled[j] -= roundMe(scaled[j]);
1513	>	scaled[j] += 0.5;
1514	>	}
1515	>
1516	>	// find xyz-indices of cell that cutoffGroup is in.
1517	>	whichCell.x() = nCells_.x() * scaled.x();
1518	>	whichCell.y() = nCells_.y() * scaled.y();
1519	>	whichCell.z() = nCells_.z() * scaled.z();
1520	>
1521	>	// find single index of this cell:
1522	>	cellIndex = Vlinear(whichCell, nCells_);
1523	>
1524	>	// add this cutoff group to the list of groups in this cell;
1525	>	cellList_[cellIndex].push_back(i);
1526	>	}
1527	>	#endif
1528	>
1529	>	for (int m1z = 0; m1z < nCells_.z(); m1z++)
1530	>	{
1531	>	for (int m1y = 0; m1y < nCells_.y(); m1y++)
1532	>	{
1533	>	for (int m1x = 0; m1x < nCells_.x(); m1x++)
1534	>	{
1535	>	Vector3i m1v(m1x, m1y, m1z);
1536	>	int m1 = Vlinear(m1v, nCells_);
1537	>
1538	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1539	>	{
1540	>
1541	>	Vector3i m2v = m1v + (*os);
1542	>
1543	>	if (m2v.x() >= nCells_.x())
1544	>	{
1545	>	m2v.x() = 0;
1546	>	} else if (m2v.x() < 0)
1547	>	{
1548	>	m2v.x() = nCells_.x() - 1;
1549	>	}
1550	>
1551	>	if (m2v.y() >= nCells_.y())
1552	>	{
1553	>	m2v.y() = 0;
1554	>	} else if (m2v.y() < 0)
1555	>	{
1556	>	m2v.y() = nCells_.y() - 1;
1557	>	}
1558	>
1559	>	if (m2v.z() >= nCells_.z())
1560	>	{
1561	>	m2v.z() = 0;
1562	>	} else if (m2v.z() < 0)
1563	>	{
1564	>	m2v.z() = nCells_.z() - 1;
1565	>	}
1566	>
1567	>	int m2 = Vlinear(m2v, nCells_);
1568	>
1569	>	#ifdef IS_MPI
1570	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1571	>	j1 != cellListRow_[m1].end(); ++j1)
1572	>	{
1573	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1574	>	j2 != cellListCol_[m2].end(); ++j2)
1575	>	{
1576	>
1577	>	// In parallel, we need to visit *all* pairs of row &
1578	>	// column indicies and will truncate later on.
1579	>	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1580	>	snap_->wrapVector(dr);
1581	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1582	>	if (dr.lengthSquare() < cuts.third)
1583	>	{
1584	>	neighborList.push_back(make_pair((*j1), (*j2)));
1585	>	}
1586	>	}
1587	>	}
1588	>	#else
1589	>
1590	>	for (vector<int>::iterator j1 = cellList_[m1].begin(); j1 != cellList_[m1].end(); ++j1)
1591	>	{
1592	>	for (vector<int>::iterator j2 = cellList_[m2].begin(); j2 != cellList_[m2].end(); ++j2)
1593	>	{
1594	>
1595	>	// Always do this if we're in different cells or if
1596	>	// we're in the same cell and the global index of the
1597	>	// j2 cutoff group is less than the j1 cutoff group
1598	>
1599	>	if (m2 != m1 || (*j2) < (*j1))
1600	>	{
1601	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1602	>	snap_->wrapVector(dr);
1603	>	cuts = getGroupCutoffs((*j1), (*j2));
1604	>	if (dr.lengthSquare() < cuts.third)
1605	>	{
1606	>	neighborList.push_back(make_pair((*j1), (*j2)));
1607	>	}
1608	>	}
1609	>	}
1610	>	}
1611	>	#endif
1612	>	}
1613	>	}
1614	>	}
1615	>	}
1616	>	} else
1617	>	{
1618	>	// branch to do all cutoff group pairs
1619	>	#ifdef IS_MPI
1620	>	for (int j1 = 0; j1 < nGroupsInRow_; j1++)
1621	>	{
1622	>	for (int j2 = 0; j2 < nGroupsInCol_; j2++)
1623	>	{
1624	>	dr = cgColData.position[j2] - cgRowData.position[j1];
1625	>	snap_->wrapVector(dr);
1626	>	cuts = getGroupCutoffs( j1, j2 );
1627	>	if (dr.lengthSquare() < cuts.third)
1628	>	{
1629	>	neighborList.push_back(make_pair(j1, j2));
1630	>	}
1631	>	}
1632	>	}
1633	>	#else
1634	>	for (int j1 = 0; j1 < nGroups_ - 1; j1++)
1635	>	{
1636	>	for (int j2 = j1 + 1; j2 < nGroups_; j2++)
1637	>	{
1638	>	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1639	>	snap_->wrapVector(dr);
1640	>	cuts = getGroupCutoffs(j1, j2);
1641	>	if (dr.lengthSquare() < cuts.third)
1642	>	{
1643	>	neighborList.push_back(make_pair(j1, j2));
1644	>	}
1645	>	}
1646	>	}
1647	>	#endif
1648	>	}
1649	>
1650	>	// save the local cutoff group positions for the check that is
1651	>	// done on each loop:
1652	>	saved_CG_positions_.clear();
1653	>	for (int i = 0; i < nGroups_; i++)
1654	>	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1655	>
1656	>	return neighborList;
1657	>	}
1658		} //end namespace OpenMD

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