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

Comparing branches/devel_omp/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1595 by chuckv, Tue Jul 19 18:50:04 2011 UTC vs.
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	<	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
51	>	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) :
52	>	ForceDecomposition(info, iMan) {
53
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)
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	<	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) );
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	<	}
72	>	}
73
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	<	/**
85	<	* distributeInitialData is essentially a copy of the older fortran
86	<	* SimulationSetup
87	<	*/
88	<	void ForceMatrixDecomposition::distributeInitialData() {
89	<	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();
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	<	massFactors = info_->getMassFactors();
91	>	massFactors = info_->getMassFactors();
92
93	<	PairList* excludes = info_->getExcludedInteractions();
94	<	PairList* oneTwo = info_->getOneTwoInteractions();
95	<	PairList* oneThree = info_->getOneThreeInteractions();
96	<	PairList* oneFour = info_->getOneFourInteractions();
93	>	PairList* excludes = info_->getExcludedInteractions();
94	>	PairList* oneTwo = info_->getOneTwoInteractions();
95	>	PairList* oneThree = info_->getOneThreeInteractions();
96	>	PairList* oneFour = info_->getOneFourInteractions();
97
98		#ifdef IS_MPI
98	–
99	–	MPI::Intracomm row = rowComm.getComm();
100	–	MPI::Intracomm col = colComm.getComm();
99
100	<	AtomPlanIntRow = new Plan<int>(row, nLocal_);
101	<	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_);
100	>	MPI::Intracomm row = rowComm.getComm();
101	>	MPI::Intracomm col = colComm.getComm();
102
103	<	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
104	<	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
105	<	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
106	<	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
107	<	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
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	<	cgPlanIntRow = new Plan<int>(row, nGroups_);
110	<	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
111	<	cgPlanIntColumn = new Plan<int>(col, nGroups_);
112	<	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
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	<	nAtomsInRow_ = AtomPlanIntRow->getSize();
116	<	nAtomsInCol_ = AtomPlanIntColumn->getSize();
117	<	nGroupsInRow_ = cgPlanIntRow->getSize();
118	<	nGroupsInCol_ = cgPlanIntColumn->getSize();
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	<	// Modify the data storage objects with the correct layouts and sizes:
121	<	atomRowData.resize(nAtomsInRow_);
122	<	atomRowData.setStorageLayout(storageLayout_);
123	<	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_);
120	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
121	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
122	>	nGroupsInRow_ = cgPlanIntRow->getSize();
123	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
124
125	<	for (int i = 0; i < nAtomsInRow_; i++)
126	<	atypesRow[i] = ff_->getAtomType(identsRow[i]);
127	<	for (int i = 0; i < nAtomsInCol_; i++)
128	<	atypesCol[i] = ff_->getAtomType(identsCol[i]);
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	<	pot_row.resize(nAtomsInRow_);
136	<	pot_col.resize(nAtomsInCol_);
135	>	identsRow.resize(nAtomsInRow_);
136	>	identsCol.resize(nAtomsInCol_);
137
138	<	AtomRowToGlobal.resize(nAtomsInRow_);
139	<	AtomColToGlobal.resize(nAtomsInCol_);
154	<	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155	<	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
138	>	AtomPlanIntRow->gather(idents, identsRow);
139	>	AtomPlanIntColumn->gather(idents, identsCol);
140
141	<	cerr << "Atoms in Local:\n";
142	<	for (int i = 0; i < AtomLocalToGlobal.size(); i++) {
143	<	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	<	}
141	>	// allocate memory for the parallel objects
142	>	atypesRow.resize(nAtomsInRow_);
143	>	atypesCol.resize(nAtomsInCol_);
144
145	<	cgRowToGlobal.resize(nGroupsInRow_);
146	<	cgColToGlobal.resize(nGroupsInCol_);
147	<	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
148	<	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
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	<	cerr << "Gruops in Local:\n";
151	<	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	<	}
150	>	pot_row.resize(nAtomsInRow_);
151	>	pot_col.resize(nAtomsInCol_);
152
153	+	AtomRowToGlobal.resize(nAtomsInRow_);
154	+	AtomColToGlobal.resize(nAtomsInCol_);
155	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
156	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
157
158	<	massFactorsRow.resize(nAtomsInRow_);
159	<	massFactorsCol.resize(nAtomsInCol_);
160	<	AtomPlanRealRow->gather(massFactors, massFactorsRow);
161	<	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
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	<	groupListRow_.clear();
175	<	groupListRow_.resize(nGroupsInRow_);
176	<	for (int i = 0; i < nGroupsInRow_; i++) {
177	<	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	<	}
174	>	cgRowToGlobal.resize(nGroupsInRow_);
175	>	cgColToGlobal.resize(nGroupsInCol_);
176	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
177	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
178
179	<	groupListCol_.clear();
180	<	groupListCol_.resize(nGroupsInCol_);
181	<	for (int i = 0; i < nGroupsInCol_; i++) {
182	<	int gid = cgColToGlobal[i];
183	<	for (int j = 0; j < nAtomsInCol_; j++) {
184	<	int aid = AtomColToGlobal[j];
185	<	if (globalGroupMembership[aid] == gid)
186	<	groupListCol_[i].push_back(j);
187	<	}
188	<	}
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	<	excludesForAtom.clear();
196	<	excludesForAtom.resize(nAtomsInRow_);
197	<	toposForAtom.clear();
198	<	toposForAtom.resize(nAtomsInRow_);
220	<	topoDist.clear();
221	<	topoDist.resize(nAtomsInRow_);
222	<	for (int i = 0; i < nAtomsInRow_; i++) {
223	<	int iglob = AtomRowToGlobal[i];
195	>	massFactorsRow.resize(nAtomsInRow_);
196	>	massFactorsCol.resize(nAtomsInCol_);
197	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
198	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
199
200	<	for (int j = 0; j < nAtomsInCol_; j++) {
201	<	int jglob = AtomColToGlobal[j];
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	<	if (excludes->hasPair(iglob, jglob))
214	<	excludesForAtom[i].push_back(j);
215	<
216	<	if (oneTwo->hasPair(iglob, jglob)) {
217	<	toposForAtom[i].push_back(j);
218	<	topoDist[i].push_back(1);
219	<	} else {
220	<	if (oneThree->hasPair(iglob, jglob)) {
221	<	toposForAtom[i].push_back(j);
222	<	topoDist[i].push_back(2);
223	<	} else {
224	<	if (oneFour->hasPair(iglob, jglob)) {
240	<	toposForAtom[i].push_back(j);
241	<	topoDist[i].push_back(3);
242	<	}
243	<	}
244	<	}
245	<	}
246	<	}
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	<	#endif
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	<	// allocate memory for the parallel objects
237	<	atypesLocal.resize(nLocal_);
236	>	for (int j = 0; j < nAtomsInCol_; j++)
237	>	{
238	>	int jglob = AtomColToGlobal[j];
239
240	<	for (int i = 0; i < nLocal_; i++)
241	<	atypesLocal[i] = ff_->getAtomType(idents[i]);
240	>	if (excludes->hasPair(iglob, jglob))
241	>	excludesForAtom[i].push_back(j);
242
243	<	groupList_.clear();
244	<	groupList_.resize(nGroups_);
245	<	for (int i = 0; i < nGroups_; i++) {
246	<	int gid = cgLocalToGlobal[i];
247	<	for (int j = 0; j < nLocal_; j++) {
248	<	int aid = AtomLocalToGlobal[j];
249	<	if (globalGroupMembership[aid] == gid) {
250	<	groupList_[i].push_back(j);
251	<	}
252	<	}
253	<	}
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
265	<	excludesForAtom.clear();
269	<	excludesForAtom.resize(nLocal_);
270	<	toposForAtom.clear();
271	<	toposForAtom.resize(nLocal_);
272	<	topoDist.clear();
273	<	topoDist.resize(nLocal_);
265	>	#endif
266
267	<	for (int i = 0; i < nLocal_; i++) {
268	<	int iglob = AtomLocalToGlobal[i];
267	>	// allocate memory for the parallel objects
268	>	atypesLocal.resize(nLocal_);
269
270	<	for (int j = 0; j < nLocal_; j++) {
271	<	int jglob = AtomLocalToGlobal[j];
270	>	for (int i = 0; i < nLocal_; i++)
271	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
272
273	<	if (excludes->hasPair(iglob, jglob))
274	<	excludesForAtom[i].push_back(j);
275	<
276	<	if (oneTwo->hasPair(iglob, jglob)) {
277	<	toposForAtom[i].push_back(j);
278	<	topoDist[i].push_back(1);
279	<	} else {
280	<	if (oneThree->hasPair(iglob, jglob)) {
281	<	toposForAtom[i].push_back(j);
282	<	topoDist[i].push_back(2);
283	<	} else {
284	<	if (oneFour->hasPair(iglob, jglob)) {
285	<	toposForAtom[i].push_back(j);
286	<	topoDist[i].push_back(3);
295	<	}
296	<	}
297	<	}
298	<	}
299	<	}
300	<
301	<	createGtypeCutoffMap();
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	<	}
289	<
290	<	void ForceMatrixDecomposition::createGtypeCutoffMap() {
291	<
292	<	RealType tol = 1e-6;
293	<	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	<	}
288	>	excludesForAtom.clear();
289	>	excludesForAtom.resize(nLocal_);
290	>	toposForAtom.clear();
291	>	toposForAtom.resize(nLocal_);
292	>	topoDist.clear();
293	>	topoDist.resize(nLocal_);
294
295	<	bool gTypeFound = false;
296	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
297	<	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
295	>	for (int i = 0; i < nLocal_; i++)
296	>	{
297	>	int iglob = AtomLocalToGlobal[i];
298
299	<	vector<RealType> groupCutoff(nGroups_, 0.0);
300	<	groupToGtype.resize(nGroups_);
301	<	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
299	>	for (int j = 0; j < nLocal_; j++)
300	>	{
301	>	int jglob = AtomLocalToGlobal[j];
302
303	<	// Now we find the maximum group cutoff value present in the simulation
303	>	if (excludes->hasPair(iglob, jglob))
304	>	excludesForAtom[i].push_back(j);
305
306	<	RealType groupMax = *max_element(gTypeCutoffs.begin(),
307	<	gTypeCutoffs.end());
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	<	#ifdef IS_MPI
413	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
414	<	MPI::MAX);
415	<	#endif
416	<
417	<	RealType tradRcut = groupMax;
328	>	createGtypeCutoffMap();
329
330	<	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	<	}
330	>	}
331
332	<	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	<	}
332	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
333
334	+	RealType tol = 1e-6;
335	+	largestRcut_ = 0.0;
336	+	RealType rc;
337	+	int atid;
338	+	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
339
340	<	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	<	}
340	>	map<int, RealType> atypeCutoff;
341
342	<	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
343	<	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
344	<	if (toposForAtom[atom1][j] == atom2)
345	<	return topoDist[atom1][j];
346	<	}
347	<	return 0;
348	<	}
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	<	void ForceMatrixDecomposition::zeroWorkArrays() {
352	<	pairwisePot = 0.0;
353	<	embeddingPot = 0.0;
487	<
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	<	if (storageLayout_ & DataStorage::dslForce) {
356	<	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
357	<	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
358	<	}
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::dslTorque) {
372	<	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
373	<	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
374	<	}
375	<
376	<	fill(pot_row.begin(), pot_row.end(),
377	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
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	<	fill(pot_col.begin(), pot_col.end(),
387	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
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(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
421	<	0.0);
422	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
423	<	0.0);
424	<	}
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	<	if (storageLayout_ & DataStorage::dslDensity) {
434	<	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
435	<	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
436	<	}
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
449
450	<	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	<	}
450	>	// Now we find the maximum group cutoff value present in the simulation
451
452	<	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	<	}
452	>	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
453
454	<	if (storageLayout_ & DataStorage::dslSkippedCharge) {
455	<	fill(atomRowData.skippedCharge.begin(),
456	<	atomRowData.skippedCharge.end(), 0.0);
534	<	fill(atomColData.skippedCharge.begin(),
535	<	atomColData.skippedCharge.end(), 0.0);
536	<	}
537	<
454	>	#ifdef IS_MPI
455	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
456	>	MPI::MAX);
457		#endif
539	–	// even in parallel, we need to zero out the local arrays:
458
459	<	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	<	}
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	<	void ForceMatrixDecomposition::distributeData()  {
486	<	snap_ = sman_->getCurrentSnapshot();
487	<	storageLayout_ = sman_->getStorageLayout();
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	>	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	>	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
509	>	int i, j;
510		#ifdef IS_MPI
511	<
512	<	// gather up the atomic positions
513	<	AtomPlanVectorRow->gather(snap_->atomData.position,
514	<	atomRowData.position);
515	<	AtomPlanVectorColumn->gather(snap_->atomData.position,
516	<	atomColData.position);
517	<
518	<	// gather up the cutoff group positions
511	>	i = groupRowToGtype[cg1];
512	>	j = groupColToGtype[cg2];
513	>	#else
514	>	i = groupToGtype[cg1];
515	>	j = groupToGtype[cg2];
516	>	#endif
517	>	return gTypeCutoffMap[make_pair(i, j)];
518	>	}
519
520	<	cerr  << "before gather\n";
521	<	for (int i = 0; i < snap_->cgData.position.size(); i++) {
522	<	cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
523	<	}
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	<	cgPlanVectorRow->gather(snap_->cgData.position,
530	<	cgRowData.position);
529	>	void ForceMatrixDecomposition::zeroWorkArrays() {
530	>	pairwisePot = 0.0;
531	>	embeddingPot = 0.0;
532
533	<	cerr  << "after gather\n";
534	<	for (int i = 0; i < cgRowData.position.size(); i++) {
535	<	cerr << "cgRpos = " << cgRowData.position[i] << "\n";
536	<	}
533	>	#ifdef IS_MPI
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	<	cgPlanVectorColumn->gather(snap_->cgData.position,
541	<	cgColData.position);
542	<	for (int i = 0; i < cgColData.position.size(); i++) {
543	<	cerr << "cgCpos = " << cgColData.position[i] << "\n";
544	<	}
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	<
547	<	// if needed, gather the atomic rotation matrices
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 (storageLayout_ & DataStorage::dslElectroFrame) {
609	<	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
610	<	atomRowData.electroFrame);
611	<	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
612	<	atomColData.electroFrame);
613	<	}
546	>	fill(pot_row.begin(), pot_row.end(),
547	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
548
549	<	#endif
550	<	}
551	<
552	<	/* collects information obtained during the pre-pair loop onto local
553	<	* data structures.
554	<	*/
555	<	void ForceMatrixDecomposition::collectIntermediateData() {
556	<	snap_ = sman_->getCurrentSnapshot();
557	<	storageLayout_ = sman_->getStorageLayout();
549	>	fill(pot_col.begin(), pot_col.end(),
550	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
551	>
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	>	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	>	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	>	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	>	if (storageLayout_ & DataStorage::dslParticlePot)
594	>	{
595	>	fill(snap_->atomData.particlePot.begin(), snap_->atomData.particlePot.end(), 0.0);
596	>	}
597	>
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	>	}
616	>
617	>	void ForceMatrixDecomposition::distributeData() {
618	>	snap_ = sman_->getCurrentSnapshot();
619	>	storageLayout_ = sman_->getStorageLayout();
620		#ifdef IS_MPI
621	<
622	<	if (storageLayout_ & DataStorage::dslDensity) {
623	<
624	<	AtomPlanRealRow->scatter(atomRowData.density,
625	<	snap_->atomData.density);
626	<
627	<	int n = snap_->atomData.density.size();
628	<	vector<RealType> rho_tmp(n, 0.0);
629	<	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
630	<	for (int i = 0; i < n; i++)
631	<	snap_->atomData.density[i] += rho_tmp[i];
632	<	}
621	>
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	>	// 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	>	cgPlanVectorRow->gather(snap_->cgData.position,
637	>	cgRowData.position);
638	>
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	>	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 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 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	>	#endif
671	>	}
672	>
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::dslDensity)
682	>	{
683	>
684	>	AtomPlanRealRow->scatter(atomRowData.density,
685	>	snap_->atomData.density);
686	>
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	<	}
694	>	}
695
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();
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	<	AtomPlanRealRow->gather(snap_->atomData.functional,
706	<	atomRowData.functional);
707	<	AtomPlanRealColumn->gather(snap_->atomData.functional,
708	<	atomColData.functional);
709	<	}
710	<
711	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
712	<	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
713	<	atomRowData.functionalDerivative);
714	<	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
715	<	atomColData.functionalDerivative);
716	<	}
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::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	<
723	<	void ForceMatrixDecomposition::collectData() {
724	<	snap_ = sman_->getCurrentSnapshot();
667	<	storageLayout_ = sman_->getStorageLayout();
720	>	}
721	>
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);
671	<
672	<	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
673	<	for (int i = 0; i < n; i++) {
674	<	snap_->atomData.force[i] += frc_tmp[i];
675	<	frc_tmp[i] = 0.0;
676	<	}
677	<
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) {
726	>	int n = snap_->atomData.force.size();
727	>	vector<Vector3d> frc_tmp(n, V3Zero);
728
729	<	int nt = snap_->atomData.torque.size();
730	<	vector<Vector3d> trq_tmp(nt, V3Zero);
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	<	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
737	<	for (int i = 0; i < nt; i++) {
738	<	snap_->atomData.torque[i] += trq_tmp[i];
739	<	trq_tmp[i] = 0.0;
740	<	}
693	<
694	<	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
695	<	for (int i = 0; i < nt; i++)
696	<	snap_->atomData.torque[i] += trq_tmp[i];
697	<	}
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::dslSkippedCharge) {
742	>	if (storageLayout_ & DataStorage::dslTorque)
743	>	{
744
745	<	int ns = snap_->atomData.skippedCharge.size();
746	<	vector<RealType> skch_tmp(ns, 0.0);
745	>	int nt = snap_->atomData.torque.size();
746	>	vector<Vector3d> trq_tmp(nt, V3Zero);
747
748	<	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
749	<	for (int i = 0; i < ns; i++) {
750	<	snap_->atomData.skippedCharge[i] += skch_tmp[i];
751	<	skch_tmp[i] = 0.0;
752	<	}
753	<
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();
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	<	vector<potVec> pot_temp(nLocal_,
756	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
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	<	// scatter/gather pot_row into the members of my column
761	<
722	<	AtomPlanPotRow->scatter(pot_row, pot_temp);
760	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
761	>	{
762
763	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
764	<	pairwisePot += pot_temp[ii];
765	<
766	<	fill(pot_temp.begin(), pot_temp.end(),
767	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
768	<
769	<	AtomPlanPotColumn->scatter(pot_col, pot_temp);
770	<
771	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
772	<	pairwisePot += pot_temp[ii];
763	>	int ns = snap_->atomData.skippedCharge.size();
764	>	vector<RealType> skch_tmp(ns, 0.0);
765	>
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	>	nLocal_ = snap_->getNumberOfAtoms();
779	>
780	>	vector<potVec> pot_temp(nLocal_,
781	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
782	>
783	>	// scatter/gather pot_row into the members of my column
784	>
785	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
786	>
787	>	for (int ii = 0; ii < pot_temp.size(); ii++ )
788	>	pairwisePot += pot_temp[ii];
789	>
790	>	fill(pot_temp.begin(), pot_temp.end(),
791	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
792	>
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	<	cerr << "pairwisePot = " <<  pairwisePot << "\n";
800	<	}
799	>	cerr << "pairwisePot = " << pairwisePot << "\n";
800	>	}
801
802	<	int ForceMatrixDecomposition::getNAtomsInRow() {
802	>	int ForceMatrixDecomposition::getNAtomsInRow() {
803		#ifdef IS_MPI
804	<	return nAtomsInRow_;
804	>	return nAtomsInRow_;
805		#else
806	<	return nLocal_;
806	>	return nLocal_;
807		#endif
808	<	}
808	>	}
809
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];
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	<	}
819	>	}
820
821	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
821	>	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2) {
822		#ifdef IS_MPI
823	<	return groupListCol_[cg2];
823	>	return groupListCol_[cg2];
824		#else
825	<	return groupList_[cg2];
825	>	return groupList_[cg2];
826		#endif
827	<	}
828	<
829	<	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
830	<	Vector3d d;
831	<
827	>	}
828	>
829	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2) {
830	>	Vector3d d;
831	>
832		#ifdef IS_MPI
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";
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	<	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";
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
778	–
779	–	snap_->wrapVector(d);
780	–	return d;
781	–	}
841
842	+	snap_->wrapVector(d);
843	+	return d;
844	+	}
845
846	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
846	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2) {
847	>	Vector3d d;
848
849	<	Vector3d d;
850	<
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	<	d = cgRowData.position[cg1] - atomRowData.position[atom1];
864	>	d = cgRowData.position[cg1] - atomRowData.position[atom1];
865		#else
866	<	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
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	<
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	<	d = cgColData.position[cg2] - atomColData.position[atom2];
877	>	d = cgColData.position[cg2] - atomColData.position[atom2];
878		#else
879	<	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
879	>	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
880		#endif
806	–
807	–	snap_->wrapVector(d);
808	–	return d;
809	–	}
881
882	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
882	>	snap_->wrapVector(d);
883	>	return d;
884	>	}
885	>
886	>	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
887		#ifdef IS_MPI
888	<	return massFactorsRow[atom1];
888	>	return massFactorsRow[atom1];
889		#else
890	<	return massFactors[atom1];
890	>	return massFactors[atom1];
891		#endif
892	<	}
892	>	}
893
894	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
894	>	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
895		#ifdef IS_MPI
896	<	return massFactorsCol[atom2];
896	>	return massFactorsCol[atom2];
897		#else
898	<	return massFactors[atom2];
898	>	return massFactors[atom2];
899		#endif
900
901	<	}
902	<
903	<	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
904	<	Vector3d d;
905	<
901	>	}
902	>
903	>	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2) {
904	>	Vector3d d;
905	>
906		#ifdef IS_MPI
907	<	d = atomColData.position[atom2] - atomRowData.position[atom1];
907	>	d = atomColData.position[atom2] - atomRowData.position[atom1];
908		#else
909	<	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
909	>	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
910		#endif
911
912	<	snap_->wrapVector(d);
913	<	return d;
914	<	}
912	>	snap_->wrapVector(d);
913	>	return d;
914	>	}
915
916	<	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
917	<	return excludesForAtom[atom1];
918	<	}
916	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
917	>	return excludesForAtom[atom1];
918	>	}
919
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;
851	<
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	<	cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
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];
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	<	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;
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	<	}
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	<	/**
938	<	* We need to handle the interactions for atoms who are involved in
939	<	* the same rigid body as well as some short range interactions
940	<	* (bonds, bends, torsions) differently from other interactions.
941	<	* We'll still visit the pairwise routines, but with a flag that
942	<	* tells those routines to exclude the pair from direct long range
943	<	* interactions.  Some indirect interactions (notably reaction
944	<	* field) must still be handled for these pairs.
945	<	*/
946	<	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
947	<	int unique_id_2;
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	>	/**
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];
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;
964	>	// in the normal loop, the atom numbers are unique
965	>	unique_id_2 = atom2;
966		#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	–	}
967
968	<	return false;
969	<	}
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	+	return false;
975	+	}
976
977	<	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
977	>	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg) {
978		#ifdef IS_MPI
979	<	atomRowData.force[atom1] += fg;
979	>	atomRowData.force[atom1] += fg;
980		#else
981	<	snap_->atomData.force[atom1] += fg;
981	>	snap_->atomData.force[atom1] += fg;
982		#endif
983	<	}
983	>	}
984
985	<	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
985	>	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg) {
986		#ifdef IS_MPI
987	<	atomColData.force[atom2] += fg;
987	>	atomColData.force[atom2] += fg;
988		#else
989	<	snap_->atomData.force[atom2] += fg;
989	>	snap_->atomData.force[atom2] += fg;
990		#endif
991	<	}
991	>	}
992
993	<	// filling interaction blocks with pointers
994	<	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
919	<	int atom1, int atom2) {
993	>	// filling interaction blocks with pointers
994	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, int atom1, int atom2) {
995
996	<	idat.excluded = excludeAtomPair(atom1, atom2);
997	<
996	>	idat.excluded = excludeAtomPair(atom1, atom2);
997	>
998		#ifdef IS_MPI
999	<	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1000	<	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1001	<	//                         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	<	}
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 (storageLayout_ & DataStorage::dslTorque) {
1004	<	idat.t1 = &(atomRowData.torque[atom1]);
1005	<	idat.t2 = &(atomColData.torque[atom2]);
1006	<	}
1003	>	if (storageLayout_ & DataStorage::dslAmat)
1004	>	{
1005	>	idat.A1 = &(atomRowData.aMat[atom1]);
1006	>	idat.A2 = &(atomColData.aMat[atom2]);
1007	>	}
1008
1009	<	if (storageLayout_ & DataStorage::dslDensity) {
1010	<	idat.rho1 = &(atomRowData.density[atom1]);
1011	<	idat.rho2 = &(atomColData.density[atom2]);
1012	<	}
1009	>	if (storageLayout_ & DataStorage::dslElectroFrame)
1010	>	{
1011	>	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1012	>	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1013	>	}
1014
1015	<	if (storageLayout_ & DataStorage::dslFunctional) {
1016	<	idat.frho1 = &(atomRowData.functional[atom1]);
1017	<	idat.frho2 = &(atomColData.functional[atom2]);
1018	<	}
1015	>	if (storageLayout_ & DataStorage::dslTorque)
1016	>	{
1017	>	idat.t1 = &(atomRowData.torque[atom1]);
1018	>	idat.t2 = &(atomColData.torque[atom2]);
1019	>	}
1020
1021	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1022	<	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1023	<	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1024	<	}
1021	>	if (storageLayout_ & DataStorage::dslDensity)
1022	>	{
1023	>	idat.rho1 = &(atomRowData.density[atom1]);
1024	>	idat.rho2 = &(atomColData.density[atom2]);
1025	>	}
1026
1027	<	if (storageLayout_ & DataStorage::dslParticlePot) {
1028	<	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1029	<	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1030	<	}
1027	>	if (storageLayout_ & DataStorage::dslFunctional)
1028	>	{
1029	>	idat.frho1 = &(atomRowData.functional[atom1]);
1030	>	idat.frho2 = &(atomColData.functional[atom2]);
1031	>	}
1032
1033	<	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1034	<	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1035	<	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1036	<	}
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	<	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1054	<	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1055	<	//                         ff_->getAtomType(idents[atom2]) );
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	<	if (storageLayout_ & DataStorage::dslAmat) {
1058	<	idat.A1 = &(snap_->atomData.aMat[atom1]);
1059	<	idat.A2 = &(snap_->atomData.aMat[atom2]);
1060	<	}
1057	>	if (storageLayout_ & DataStorage::dslAmat)
1058	>	{
1059	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1060	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1061	>	}
1062
1063	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1064	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1065	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1066	<	}
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	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1071	<	idat.t2 = &(snap_->atomData.torque[atom2]);
1072	<	}
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	<	idat.rho1 = &(snap_->atomData.density[atom1]);
1077	<	idat.rho2 = &(snap_->atomData.density[atom2]);
1078	<	}
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	<	idat.frho1 = &(snap_->atomData.functional[atom1]);
1083	<	idat.frho2 = &(snap_->atomData.functional[atom2]);
1084	<	}
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	<	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1089	<	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1090	<	}
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	<	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1095	<	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1096	<	}
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	<	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1101	<	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1102	<	}
1099	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
1100	>	{
1101	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1102	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1103	>	}
1104		#endif
1105	<	}
1105	>	}
1106
1107	<
1017	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
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);
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);
1112	>	atomRowData.force[atom1] += *(idat.f1);
1113	>	atomColData.force[atom2] -= *(idat.f1);
1114		#else
1115	<	pairwisePot += *(idat.pot);
1115	>	pairwisePot += *(idat.pot);
1116
1117	<	snap_->atomData.force[atom1] += *(idat.f1);
1118	<	snap_->atomData.force[atom2] -= *(idat.f1);
1117	>	snap_->atomData.force[atom1] += *(idat.f1);
1118	>	snap_->atomData.force[atom2] -= *(idat.f1);
1119		#endif
1030	–
1031	–	}
1120
1121	<	vector<vector<int> > ForceMatrixDecomposition::buildLayerBasedNeighborList() {
1122	<	printf("buildLayerBasedNeighborList; nGroups:%d\n", nGroups_);
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;
1228	>	//      vector<int> k_c;
1229		/* c_i - has cell containing atom i (size Na) */
1230	<	vector<int> c;
1230	>	vector<int> c = vector<int> (nGroups_);
1231		/* l_i - layer containing atom i (size Na) */
1232	<	vector<int> l;
1232	>	//      vector<int> l;
1233
1043	–	//      cellList_.clear();
1044	–
1234		RealType rList_ = (largestRcut_ + skinThickness_);
1235		Snapshot* snap_ = sman_->getCurrentSnapshot();
1236		Mat3x3d Hmat = snap_->getHmat();
#	Line 1059 | Line 1248 | vector<vector<int> > ForceMatrixDecomposition::buildLa
1248		int cellIndex;
1249		int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1250
1251	<	//      cellList_.resize(nCtot);
1063	<	k_c = vector<int>(nCtot, 0);
1251	>	//      k_c = vector<int> (nCtot, 0);
1252
1253	<	for (int i = 0; i < nGroups_; i++)
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	<	rs = snap_->cgData.position[i];
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;
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	<	}
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();
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	<	// find single index of this cell:
1281	<	cellIndex = Vlinear(whichCell, nCells_);
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	<	c.push_back(cellIndex);
1283	>	// find single index of this cell:
1284	>	cellIndex = Vlinear(whichCell, nCells_);
1285
1286	<	//              // add this cutoff group to the list of groups in this cell;
1287	<	//              cellList_[cellIndex].push_back(i);
1286	>	c[cg->getGlobalIndex()] = cellIndex;
1287	>	}
1288		}
1289
1290	<	int k_c_curr;
1291	<	int k_c_max = 0;
1290	>	//      int k_c_curr;
1291	>	//      int k_c_max = 0;
1292		/* the cell-layer occupancy matrix */
1293	<	vector<vector<int> > H_c_l = vector<vector<int> >(nCtot);
1293	>	vector<vector<CutoffGroup *> > H_c_l = vector<vector<CutoffGroup *> > (nCtot);
1294
1295	<	for(int i = 0; i < nGroups_; ++i)
1295	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1296		{
1297	<	k_c_curr = ++k_c[c[i]];
1102	<	l.push_back(k_c_curr);
1297	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1298
1104	–	/* determines the number of layers in use */
1105	–	if(k_c_max < k_c_curr)
1299		{
1300	<	k_c_max = k_c_curr;
1301	<	}
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[i]].push_back(/*l[*/i/*]*/);
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<int> >neighborMatW = vector<vector<int> >(nGroups_);
1317	>	vector<vector<CutoffGroup *> > neighborMatW = vector<vector<CutoffGroup *> > (nGroups_);
1318
1117	–	//      vector<pair<int, int> > neighborList;
1319		groupCutoffs cuts;
1320	+	CutoffGroup *cg1;
1321
1322		/* loops over objects(atoms, rigidBodies, cutoffGroups, etc.) */
1323	<	for(int i = 0; i < nGroups_; ++i)
1323	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1324		{
1325	<	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)
1325	>	for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
1326		{
1327	<	Vector3i c2v = c1v + (*os);
1327	>	/* c' */
1328	>	int c1 = c[cg1->getGlobalIndex()];
1329	>	Vector3i c1v = idxToV(c1, nCells_);
1330
1331	<	if (c2v.x() >= nCells_.x())
1331	>	/* loops over the neighboring cells c'' */
1332	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1333		{
1334	<	c2v.x() = 0;
1136	<	} else if (c2v.x() < 0)
1137	<	{
1138	<	c2v.x() = nCells_.x() - 1;
1139	<	}
1334	>	Vector3i c2v = c1v + (*os);
1335
1336	<	if (c2v.y() >= nCells_.y())
1337	<	{
1338	<	c2v.y() = 0;
1339	<	} else if (c2v.y() < 0)
1340	<	{
1341	<	c2v.y() = nCells_.y() - 1;
1342	<	}
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.z() >= nCells_.z())
1345	<	{
1346	<	c2v.z() = 0;
1347	<	} else if (c2v.z() < 0)
1348	<	{
1349	<	c2v.z() = nCells_.z() - 1;
1350	<	}
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	<	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))
1352	>	if (c2v.z() >= nCells_.z())
1353		{
1354	<	dr = snap_->cgData.position[(*j)] - snap_->cgData.position[(i)];
1355	<	snap_->wrapVector(dr);
1356	<	cuts = getGroupCutoffs((i), (*j));
1357	<	if (dr.lengthSquare() < cuts.third)
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	<	++m;
1369	<	/* transposed version of Rapaport W mat, to occupy successive memory locations on CPU */
1370	<	neighborMatW[i].push_back(*j);
1371	<	//                                              neighborList.push_back(make_pair((i), (*j)));
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		}
#	Line 1186 | Line 1388 | vector<vector<int> > ForceMatrixDecomposition::buildLa
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() {
1196	<
1197	<	vector<pair<int, int> > neighborList;
1198	<	groupCutoffs cuts;
1199	<	bool doAllPairs = false;
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();
1404	>	cellListRow_.clear();
1405	>	cellListCol_.clear();
1406		#else
1407	<	cellList_.clear();
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);
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_;
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
1221	<
1222	<	if (nCells_.x() < 3) doAllPairs = true;
1223	<	if (nCells_.y() < 3) doAllPairs = true;
1224	<	if (nCells_.z() < 3) doAllPairs = true;
1422	>	// handle small boxes where the cell offsets can end up repeating cells
1423
1424	<	Mat3x3d invHmat = snap_->getInvHmat();
1425	<	Vector3d rs, scaled, dr;
1426	<	Vector3i whichCell;
1427	<	int cellIndex;
1428	<	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
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);
1438	>	cellListRow_.resize(nCtot);
1439	>	cellListCol_.resize(nCtot);
1440		#else
1441	<	cellList_.resize(nCtot);
1441	>	cellList_.resize(nCtot);
1442		#endif
1443
1444	<	if (!doAllPairs) {
1444	>	if (!doAllPairs)
1445	>	{
1446		#ifdef IS_MPI
1447
1448	<	for (int i = 0; i < nGroupsInRow_; i++) {
1449	<	rs = cgRowData.position[i];
1450	<
1451	<	// scaled positions relative to the box vectors
1452	<	scaled = invHmat * rs;
1453	<
1454	<	// wrap the vector back into the unit box by subtracting integer box
1455	<	// numbers
1456	<	for (int j = 0; j < 3; j++) {
1457	<	scaled[j] -= roundMe(scaled[j]);
1458	<	scaled[j] += 0.5;
1459	<	}
1460	<
1461	<	// find xyz-indices of cell that cutoffGroup is in.
1462	<	whichCell.x() = nCells_.x() * scaled.x();
1463	<	whichCell.y() = nCells_.y() * scaled.y();
1464	<	whichCell.z() = nCells_.z() * scaled.z();
1465	<
1466	<	// find single index of this cell:
1467	<	cellIndex = Vlinear(whichCell, nCells_);
1468	<
1469	<	// add this cutoff group to the list of groups in this cell;
1470	<	cellListRow_[cellIndex].push_back(i);
1471	<	}
1472	<	for (int i = 0; i < nGroupsInCol_; i++) {
1473	<	rs = cgColData.position[i];
1474	<
1475	<	// scaled positions relative to the box vectors
1476	<	scaled = invHmat * rs;
1477	<
1478	<	// wrap the vector back into the unit box by subtracting integer box
1479	<	// numbers
1480	<	for (int j = 0; j < 3; j++) {
1481	<	scaled[j] -= roundMe(scaled[j]);
1482	<	scaled[j] += 0.5;
1483	<	}
1484	<
1485	<	// find xyz-indices of cell that cutoffGroup is in.
1486	<	whichCell.x() = nCells_.x() * scaled.x();
1487	<	whichCell.y() = nCells_.y() * scaled.y();
1488	<	whichCell.z() = nCells_.z() * scaled.z();
1489	<
1490	<	// find single index of this cell:
1491	<	cellIndex = Vlinear(whichCell, nCells_);
1492	<
1493	<	// add this cutoff group to the list of groups in this cell;
1494	<	cellListCol_[cellIndex].push_back(i);
1495	<	}
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	<	rs = snap_->cgData.position[i];
1503	<
1504	<	// scaled positions relative to the box vectors
1505	<	scaled = invHmat * rs;
1506	<
1507	<	// wrap the vector back into the unit box by subtracting integer box
1508	<	// numbers
1509	<	for (int j = 0; j < 3; j++) {
1510	<	scaled[j] -= roundMe(scaled[j]);
1511	<	scaled[j] += 0.5;
1512	<	}
1513	<
1514	<	// find xyz-indices of cell that cutoffGroup is in.
1515	<	whichCell.x() = nCells_.x() * scaled.x();
1516	<	whichCell.y() = nCells_.y() * scaled.y();
1517	<	whichCell.z() = nCells_.z() * scaled.z();
1518	<
1519	<	// find single index of this cell:
1520	<	cellIndex = Vlinear(whichCell, nCells_);
1521	<
1522	<	// add this cutoff group to the list of groups in this cell;
1523	<	cellList_[cellIndex].push_back(i);
1524	<	}
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	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1531	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1532	<	Vector3i m1v(m1x, m1y, m1z);
1533	<	int m1 = Vlinear(m1v, nCells_);
1534	<
1535	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1536	<	os != cellOffsets_.end(); ++os) {
1537	<
1538	<	Vector3i m2v = m1v + (*os);
1539	<
1540	<	if (m2v.x() >= nCells_.x()) {
1541	<	m2v.x() = 0;
1542	<	} else if (m2v.x() < 0) {
1543	<	m2v.x() = nCells_.x() - 1;
1544	<	}
1545	<
1546	<	if (m2v.y() >= nCells_.y()) {
1547	<	m2v.y() = 0;
1548	<	} else if (m2v.y() < 0) {
1549	<	m2v.y() = nCells_.y() - 1;
1550	<	}
1551	<
1552	<	if (m2v.z() >= nCells_.z()) {
1553	<	m2v.z() = 0;
1554	<	} else if (m2v.z() < 0) {
1555	<	m2v.z() = nCells_.z() - 1;
1556	<	}
1557	<
1558	<	int m2 = Vlinear (m2v, nCells_);
1559	<
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	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1573	<	j2 != cellListCol_[m2].end(); ++j2) {
1574	<
1575	<	// In parallel, we need to visit *all* pairs of row &
1576	<	// column indicies and will truncate later on.
1577	<	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1578	<	snap_->wrapVector(dr);
1579	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1580	<	if (dr.lengthSquare() < cuts.third) {
1581	<	neighborList.push_back(make_pair((*j1), (*j2)));
1582	<	}
1583	<	}
1584	<	}
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();
1591	<	j1 != cellList_[m1].end(); ++j1) {
1592	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1593	<	j2 != cellList_[m2].end(); ++j2) {
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	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1601	<	snap_->wrapVector(dr);
1602	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1603	<	if (dr.lengthSquare() < cuts.third) {
1604	<	neighborList.push_back(make_pair((*j1), (*j2)));
1605	<	}
1606	<	}
1607	<	}
1608	<	}
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	<	// branch to do all cutoff group pairs
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	<	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1622	<	dr = cgColData.position[j2] - cgRowData.position[j1];
1623	<	snap_->wrapVector(dr);
1624	<	cuts = getGroupCutoffs( j1, j2 );
1625	<	if (dr.lengthSquare() < cuts.third) {
1626	<	neighborList.push_back(make_pair(j1, j2));
1627	<	}
1628	<	}
1629	<	}
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	<	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1636	<	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1637	<	snap_->wrapVector(dr);
1638	<	cuts = getGroupCutoffs( j1, j2 );
1639	<	if (dr.lengthSquare() < cuts.third) {
1640	<	neighborList.push_back(make_pair(j1, j2));
1641	<	}
1642	<	}
1643	<	}
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	<	}
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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