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

Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs.
branches/devel_omp/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1614 by mciznick, Tue Aug 23 20:55:51 2011 UTC

#	Line 43 | Line 43
43		#include "nonbonded/NonBondedInteraction.hpp"
44		#include "brains/SnapshotManager.hpp"
45		#include "brains/PairList.hpp"
46	+	#include "primitives/Molecule.hpp"
47
48		using namespace std;
49		namespace OpenMD {
50
51	<	/**
52	<	* distributeInitialData is essentially a copy of the older fortran
53	<	* SimulationSetup
54	<	*/
55	<
56	<	void ForceMatrixDecomposition::distributeInitialData() {
57	<	snap_ = sman_->getCurrentSnapshot();
58	<	storageLayout_ = sman_->getStorageLayout();
59	<	nLocal_ = snap_->getNumberOfAtoms();
60	<	nGroups_ = snap_->getNumberOfCutoffGroups();
51	>	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) :
52	>	ForceDecomposition(info, iMan) {
53	>	// In a parallel computation, row and colum scans must visit all
54	>	// surrounding cells (not just the 14 upper triangular blocks that
55	>	// are used when the processor can see all pairs)
56	>	#ifdef IS_MPI
57	>	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
58	>	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
59	>	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
60	>	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
61	>	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
62	>	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
63	>	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
64	>	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
65	>	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
66	>	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
67	>	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
68	>	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
69	>	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
70	>	#endif
71	>	}
72
73	<	// gather the information for atomtype IDs (atids):
74	<	vector<int> identsLocal = info_->getIdentArray();
75	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
76	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
77	<	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
78	<	vector<RealType> massFactorsLocal = info_->getMassFactors();
79	<	PairList excludes = info_->getExcludedInteractions();
80	<	PairList oneTwo = info_->getOneTwoInteractions();
81	<	PairList oneThree = info_->getOneThreeInteractions();
70	<	PairList oneFour = info_->getOneFourInteractions();
71	<	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
73	>	/**
74	>	* distributeInitialData is essentially a copy of the older fortran
75	>	* SimulationSetup
76	>	*/
77	>	void ForceMatrixDecomposition::distributeInitialData() {
78	>	snap_ = sman_->getCurrentSnapshot();
79	>	storageLayout_ = sman_->getStorageLayout();
80	>	ff_ = info_->getForceField();
81	>	nLocal_ = snap_->getNumberOfAtoms();
82
83	+	nGroups_ = info_->getNLocalCutoffGroups();
84	+	// gather the information for atomtype IDs (atids):
85	+	idents = info_->getIdentArray();
86	+	AtomLocalToGlobal = info_->getGlobalAtomIndices();
87	+	cgLocalToGlobal = info_->getGlobalGroupIndices();
88	+	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
89	+
90	+	massFactors = info_->getMassFactors();
91	+
92	+	PairList* excludes = info_->getExcludedInteractions();
93	+	PairList* oneTwo = info_->getOneTwoInteractions();
94	+	PairList* oneThree = info_->getOneThreeInteractions();
95	+	PairList* oneFour = info_->getOneFourInteractions();
96	+
97		#ifdef IS_MPI
74	–
75	–	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
76	–	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
77	–	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
78	–	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
98
99	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
100	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
82	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
83	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
99	>	MPI::Intracomm row = rowComm.getComm();
100	>	MPI::Intracomm col = colComm.getComm();
101
102	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
103	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
104	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
105	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
102	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
103	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
104	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
105	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
106	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
107
108	<	nAtomsInRow_ = AtomCommIntRow->getSize();
109	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
110	<	nGroupsInRow_ = cgCommIntRow->getSize();
111	<	nGroupsInCol_ = cgCommIntColumn->getSize();
108	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
109	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
110	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
111	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
112	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
113
114	<	// Modify the data storage objects with the correct layouts and sizes:
115	<	atomRowData.resize(nAtomsInRow_);
116	<	atomRowData.setStorageLayout(storageLayout_);
117	<	atomColData.resize(nAtomsInCol_);
99	<	atomColData.setStorageLayout(storageLayout_);
100	<	cgRowData.resize(nGroupsInRow_);
101	<	cgRowData.setStorageLayout(DataStorage::dslPosition);
102	<	cgColData.resize(nGroupsInCol_);
103	<	cgColData.setStorageLayout(DataStorage::dslPosition);
104	<
105	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
106	<	vector<RealType> (nAtomsInRow_, 0.0));
107	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
108	<	vector<RealType> (nAtomsInCol_, 0.0));
109	<
110	<	identsRow.reserve(nAtomsInRow_);
111	<	identsCol.reserve(nAtomsInCol_);
112	<
113	<	AtomCommIntRow->gather(identsLocal, identsRow);
114	<	AtomCommIntColumn->gather(identsLocal, identsCol);
115	<
116	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
117	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
118	<
119	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
120	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
114	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
115	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
116	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
117	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
118
119	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
120	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
119	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
120	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
121	>	nGroupsInRow_ = cgPlanIntRow->getSize();
122	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
123
124	<	groupListRow_.clear();
125	<	groupListRow_.reserve(nGroupsInRow_);
126	<	for (int i = 0; i < nGroupsInRow_; i++) {
127	<	int gid = cgRowToGlobal[i];
128	<	for (int j = 0; j < nAtomsInRow_; j++) {
129	<	int aid = AtomRowToGlobal[j];
130	<	if (globalGroupMembership[aid] == gid)
131	<	groupListRow_[i].push_back(j);
132	<	}
134	<	}
124	>	// Modify the data storage objects with the correct layouts and sizes:
125	>	atomRowData.resize(nAtomsInRow_);
126	>	atomRowData.setStorageLayout(storageLayout_);
127	>	atomColData.resize(nAtomsInCol_);
128	>	atomColData.setStorageLayout(storageLayout_);
129	>	cgRowData.resize(nGroupsInRow_);
130	>	cgRowData.setStorageLayout(DataStorage::dslPosition);
131	>	cgColData.resize(nGroupsInCol_);
132	>	cgColData.setStorageLayout(DataStorage::dslPosition);
133
134	<	groupListCol_.clear();
135	<	groupListCol_.reserve(nGroupsInCol_);
138	<	for (int i = 0; i < nGroupsInCol_; i++) {
139	<	int gid = cgColToGlobal[i];
140	<	for (int j = 0; j < nAtomsInCol_; j++) {
141	<	int aid = AtomColToGlobal[j];
142	<	if (globalGroupMembership[aid] == gid)
143	<	groupListCol_[i].push_back(j);
144	<	}
145	<	}
134	>	identsRow.resize(nAtomsInRow_);
135	>	identsCol.resize(nAtomsInCol_);
136
137	<	skipsForRowAtom.clear();
138	<	skipsForRowAtom.reserve(nAtomsInRow_);
149	<	for (int i = 0; i < nAtomsInRow_; i++) {
150	<	int iglob = AtomColToGlobal[i];
151	<	for (int j = 0; j < nAtomsInCol_; j++) {
152	<	int jglob = AtomRowToGlobal[j];
153	<	if (excludes.hasPair(iglob, jglob))
154	<	skipsForRowAtom[i].push_back(j);
155	<	}
156	<	}
137	>	AtomPlanIntRow->gather(idents, identsRow);
138	>	AtomPlanIntColumn->gather(idents, identsCol);
139
140	<	toposForRowAtom.clear();
141	<	toposForRowAtom.reserve(nAtomsInRow_);
142	<	for (int i = 0; i < nAtomsInRow_; i++) {
161	<	int iglob = AtomColToGlobal[i];
162	<	int nTopos = 0;
163	<	for (int j = 0; j < nAtomsInCol_; j++) {
164	<	int jglob = AtomRowToGlobal[j];
165	<	if (oneTwo.hasPair(iglob, jglob)) {
166	<	toposForRowAtom[i].push_back(j);
167	<	topoDistRow[i][nTopos] = 1;
168	<	nTopos++;
169	<	}
170	<	if (oneThree.hasPair(iglob, jglob)) {
171	<	toposForRowAtom[i].push_back(j);
172	<	topoDistRow[i][nTopos] = 2;
173	<	nTopos++;
174	<	}
175	<	if (oneFour.hasPair(iglob, jglob)) {
176	<	toposForRowAtom[i].push_back(j);
177	<	topoDistRow[i][nTopos] = 3;
178	<	nTopos++;
179	<	}
180	<	}
181	<	}
140	>	// allocate memory for the parallel objects
141	>	atypesRow.resize(nAtomsInRow_);
142	>	atypesCol.resize(nAtomsInCol_);
143
144	<	#endif
144	>	for (int i = 0; i < nAtomsInRow_; i++)
145	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
146	>	for (int i = 0; i < nAtomsInCol_; i++)
147	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
148
149	<	groupList_.clear();
150	<	groupList_.reserve(nGroups_);
187	<	for (int i = 0; i < nGroups_; i++) {
188	<	int gid = cgLocalToGlobal[i];
189	<	for (int j = 0; j < nLocal_; j++) {
190	<	int aid = AtomLocalToGlobal[j];
191	<	if (globalGroupMembership[aid] == gid)
192	<	groupList_[i].push_back(j);
193	<	}
194	<	}
149	>	pot_row.resize(nAtomsInRow_);
150	>	pot_col.resize(nAtomsInCol_);
151
152	<	skipsForLocalAtom.clear();
153	<	skipsForLocalAtom.reserve(nLocal_);
152	>	AtomRowToGlobal.resize(nAtomsInRow_);
153	>	AtomColToGlobal.resize(nAtomsInCol_);
154	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156
157	<	for (int i = 0; i < nLocal_; i++) {
158	<	int iglob = AtomLocalToGlobal[i];
159	<	for (int j = 0; j < nLocal_; j++) {
160	<	int jglob = AtomLocalToGlobal[j];
161	<	if (excludes.hasPair(iglob, jglob))
162	<	skipsForLocalAtom[i].push_back(j);
163	<	}
164	<	}
157	>	cerr << "Atoms in Local:\n";
158	>	for (int i = 0; i < AtomLocalToGlobal.size(); i++)
159	>	{
160	>	cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
161	>	}
162	>	cerr << "Atoms in Row:\n";
163	>	for (int i = 0; i < AtomRowToGlobal.size(); i++)
164	>	{
165	>	cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
166	>	}
167	>	cerr << "Atoms in Col:\n";
168	>	for (int i = 0; i < AtomColToGlobal.size(); i++)
169	>	{
170	>	cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
171	>	}
172
173	<	toposForLocalAtom.clear();
174	<	toposForLocalAtom.reserve(nLocal_);
175	<	for (int i = 0; i < nLocal_; i++) {
176	<	int iglob = AtomLocalToGlobal[i];
212	<	int nTopos = 0;
213	<	for (int j = 0; j < nLocal_; j++) {
214	<	int jglob = AtomLocalToGlobal[j];
215	<	if (oneTwo.hasPair(iglob, jglob)) {
216	<	toposForLocalAtom[i].push_back(j);
217	<	topoDistLocal[i][nTopos] = 1;
218	<	nTopos++;
219	<	}
220	<	if (oneThree.hasPair(iglob, jglob)) {
221	<	toposForLocalAtom[i].push_back(j);
222	<	topoDistLocal[i][nTopos] = 2;
223	<	nTopos++;
224	<	}
225	<	if (oneFour.hasPair(iglob, jglob)) {
226	<	toposForLocalAtom[i].push_back(j);
227	<	topoDistLocal[i][nTopos] = 3;
228	<	nTopos++;
229	<	}
230	<	}
231	<	}
232	<	}
233	<
234	<	void ForceMatrixDecomposition::distributeData()  {
235	<	snap_ = sman_->getCurrentSnapshot();
236	<	storageLayout_ = sman_->getStorageLayout();
237	<	#ifdef IS_MPI
238	<
239	<	// gather up the atomic positions
240	<	AtomCommVectorRow->gather(snap_->atomData.position,
241	<	atomRowData.position);
242	<	AtomCommVectorColumn->gather(snap_->atomData.position,
243	<	atomColData.position);
244	<
245	<	// gather up the cutoff group positions
246	<	cgCommVectorRow->gather(snap_->cgData.position,
247	<	cgRowData.position);
248	<	cgCommVectorColumn->gather(snap_->cgData.position,
249	<	cgColData.position);
250	<
251	<	// if needed, gather the atomic rotation matrices
252	<	if (storageLayout_ & DataStorage::dslAmat) {
253	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
254	<	atomRowData.aMat);
255	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
256	<	atomColData.aMat);
257	<	}
258	<
259	<	// if needed, gather the atomic eletrostatic frames
260	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
261	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
262	<	atomRowData.electroFrame);
263	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
264	<	atomColData.electroFrame);
265	<	}
266	<	#endif
267	<	}
268	<
269	<	void ForceMatrixDecomposition::collectIntermediateData() {
270	<	snap_ = sman_->getCurrentSnapshot();
271	<	storageLayout_ = sman_->getStorageLayout();
272	<	#ifdef IS_MPI
273	<
274	<	if (storageLayout_ & DataStorage::dslDensity) {
275	<
276	<	AtomCommRealRow->scatter(atomRowData.density,
277	<	snap_->atomData.density);
278	<
279	<	int n = snap_->atomData.density.size();
280	<	std::vector<RealType> rho_tmp(n, 0.0);
281	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
282	<	for (int i = 0; i < n; i++)
283	<	snap_->atomData.density[i] += rho_tmp[i];
284	<	}
285	<	#endif
286	<	}
287	<
288	<	void ForceMatrixDecomposition::distributeIntermediateData() {
289	<	snap_ = sman_->getCurrentSnapshot();
290	<	storageLayout_ = sman_->getStorageLayout();
291	<	#ifdef IS_MPI
292	<	if (storageLayout_ & DataStorage::dslFunctional) {
293	<	AtomCommRealRow->gather(snap_->atomData.functional,
294	<	atomRowData.functional);
295	<	AtomCommRealColumn->gather(snap_->atomData.functional,
296	<	atomColData.functional);
297	<	}
298	<
299	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
300	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
301	<	atomRowData.functionalDerivative);
302	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
303	<	atomColData.functionalDerivative);
304	<	}
305	<	#endif
306	<	}
307	<
308	<
309	<	void ForceMatrixDecomposition::collectData() {
310	<	snap_ = sman_->getCurrentSnapshot();
311	<	storageLayout_ = sman_->getStorageLayout();
312	<	#ifdef IS_MPI
313	<	int n = snap_->atomData.force.size();
314	<	vector<Vector3d> frc_tmp(n, V3Zero);
315	<
316	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
317	<	for (int i = 0; i < n; i++) {
318	<	snap_->atomData.force[i] += frc_tmp[i];
319	<	frc_tmp[i] = 0.0;
320	<	}
321	<
322	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
323	<	for (int i = 0; i < n; i++)
324	<	snap_->atomData.force[i] += frc_tmp[i];
325	<
326	<
327	<	if (storageLayout_ & DataStorage::dslTorque) {
173	>	cgRowToGlobal.resize(nGroupsInRow_);
174	>	cgColToGlobal.resize(nGroupsInCol_);
175	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177
178	<	int nt = snap_->atomData.force.size();
179	<	vector<Vector3d> trq_tmp(nt, V3Zero);
178	>	cerr << "Gruops in Local:\n";
179	>	for (int i = 0; i < cgLocalToGlobal.size(); i++)
180	>	{
181	>	cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
182	>	}
183	>	cerr << "Groups in Row:\n";
184	>	for (int i = 0; i < cgRowToGlobal.size(); i++)
185	>	{
186	>	cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
187	>	}
188	>	cerr << "Groups in Col:\n";
189	>	for (int i = 0; i < cgColToGlobal.size(); i++)
190	>	{
191	>	cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
192	>	}
193
194	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
195	<	for (int i = 0; i < n; i++) {
196	<	snap_->atomData.torque[i] += trq_tmp[i];
197	<	trq_tmp[i] = 0.0;
336	<	}
337	<
338	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
339	<	for (int i = 0; i < n; i++)
340	<	snap_->atomData.torque[i] += trq_tmp[i];
341	<	}
342	<
343	<	nLocal_ = snap_->getNumberOfAtoms();
194	>	massFactorsRow.resize(nAtomsInRow_);
195	>	massFactorsCol.resize(nAtomsInCol_);
196	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
197	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
198
199	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
200	<	vector<RealType> (nLocal_, 0.0));
201	<
202	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
203	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
204	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
205	<	pot_local[i] += pot_temp[i][ii];
206	<	}
207	<	}
208	<	#endif
209	<	}
199	>	groupListRow_.clear();
200	>	groupListRow_.resize(nGroupsInRow_);
201	>	for (int i = 0; i < nGroupsInRow_; i++)
202	>	{
203	>	int gid = cgRowToGlobal[i];
204	>	for (int j = 0; j < nAtomsInRow_; j++)
205	>	{
206	>	int aid = AtomRowToGlobal[j];
207	>	if (globalGroupMembership[aid] == gid)
208	>	groupListRow_[i].push_back(j);
209	>	}
210	>	}
211
212	<	int ForceMatrixDecomposition::getNAtomsInRow() {
213	<	#ifdef IS_MPI
214	<	return nAtomsInRow_;
215	<	#else
216	<	return nLocal_;
217	<	#endif
218	<	}
212	>	groupListCol_.clear();
213	>	groupListCol_.resize(nGroupsInCol_);
214	>	for (int i = 0; i < nGroupsInCol_; i++)
215	>	{
216	>	int gid = cgColToGlobal[i];
217	>	for (int j = 0; j < nAtomsInCol_; j++)
218	>	{
219	>	int aid = AtomColToGlobal[j];
220	>	if (globalGroupMembership[aid] == gid)
221	>	groupListCol_[i].push_back(j);
222	>	}
223	>	}
224
225	<	/**
226	<	* returns the list of atoms belonging to this group.
227	<	*/
228	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
229	<	#ifdef IS_MPI
230	<	return groupListRow_[cg1];
231	<	#else
232	<	return groupList_[cg1];
233	<	#endif
374	<	}
225	>	excludesForAtom.clear();
226	>	excludesForAtom.resize(nAtomsInRow_);
227	>	toposForAtom.clear();
228	>	toposForAtom.resize(nAtomsInRow_);
229	>	topoDist.clear();
230	>	topoDist.resize(nAtomsInRow_);
231	>	for (int i = 0; i < nAtomsInRow_; i++)
232	>	{
233	>	int iglob = AtomRowToGlobal[i];
234
235	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
236	<	#ifdef IS_MPI
237	<	return groupListCol_[cg2];
379	<	#else
380	<	return groupList_[cg2];
381	<	#endif
382	<	}
383	<
384	<	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
385	<	Vector3d d;
386	<
387	<	#ifdef IS_MPI
388	<	d = cgColData.position[cg2] - cgRowData.position[cg1];
389	<	#else
390	<	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
391	<	#endif
392	<
393	<	snap_->wrapVector(d);
394	<	return d;
395	<	}
235	>	for (int j = 0; j < nAtomsInCol_; j++)
236	>	{
237	>	int jglob = AtomColToGlobal[j];
238
239	+	if (excludes->hasPair(iglob, jglob))
240	+	excludesForAtom[i].push_back(j);
241
242	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
242	>	if (oneTwo->hasPair(iglob, jglob))
243	>	{
244	>	toposForAtom[i].push_back(j);
245	>	topoDist[i].push_back(1);
246	>	} else
247	>	{
248	>	if (oneThree->hasPair(iglob, jglob))
249	>	{
250	>	toposForAtom[i].push_back(j);
251	>	topoDist[i].push_back(2);
252	>	} else
253	>	{
254	>	if (oneFour->hasPair(iglob, jglob))
255	>	{
256	>	toposForAtom[i].push_back(j);
257	>	topoDist[i].push_back(3);
258	>	}
259	>	}
260	>	}
261	>	}
262	>	}
263
400	–	Vector3d d;
401	–
402	–	#ifdef IS_MPI
403	–	d = cgRowData.position[cg1] - atomRowData.position[atom1];
404	–	#else
405	–	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
264		#endif
265
266	<	snap_->wrapVector(d);
267	<	return d;
268	<	}
269	<
270	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
413	<	Vector3d d;
414	<
415	<	#ifdef IS_MPI
416	<	d = cgColData.position[cg2] - atomColData.position[atom2];
417	<	#else
418	<	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
419	<	#endif
420	<
421	<	snap_->wrapVector(d);
422	<	return d;
423	<	}
424	<
425	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
426	<	#ifdef IS_MPI
427	<	return massFactorsRow[atom1];
428	<	#else
429	<	return massFactorsLocal[atom1];
430	<	#endif
431	<	}
432	<
433	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
434	<	#ifdef IS_MPI
435	<	return massFactorsCol[atom2];
436	<	#else
437	<	return massFactorsLocal[atom2];
438	<	#endif
266	>	// allocate memory for the parallel objects
267	>	atypesLocal.resize(nLocal_);
268	>
269	>	for (int i = 0; i < nLocal_; i++)
270	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
271
272	<	}
273	<
274	<	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
275	<	Vector3d d;
276	<
277	<	#ifdef IS_MPI
278	<	d = atomColData.position[atom2] - atomRowData.position[atom1];
279	<	#else
280	<	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
281	<	#endif
272	>	groupList_.clear();
273	>	groupList_.resize(nGroups_);
274	>	for (int i = 0; i < nGroups_; i++)
275	>	{
276	>	int gid = cgLocalToGlobal[i];
277	>	for (int j = 0; j < nLocal_; j++)
278	>	{
279	>	int aid = AtomLocalToGlobal[j];
280	>	if (globalGroupMembership[aid] == gid)
281	>	{
282	>	groupList_[i].push_back(j);
283	>	}
284	>	}
285	>	}
286
287	<	snap_->wrapVector(d);
288	<	return d;
289	<	}
287	>	excludesForAtom.clear();
288	>	excludesForAtom.resize(nLocal_);
289	>	toposForAtom.clear();
290	>	toposForAtom.resize(nLocal_);
291	>	topoDist.clear();
292	>	topoDist.resize(nLocal_);
293
294	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
295	<	#ifdef IS_MPI
296	<	return skipsForRowAtom[atom1];
458	<	#else
459	<	return skipsForLocalAtom[atom1];
460	<	#endif
461	<	}
294	>	for (int i = 0; i < nLocal_; i++)
295	>	{
296	>	int iglob = AtomLocalToGlobal[i];
297
298	<	/**
299	<	* there are a number of reasons to skip a pair or a particle mostly
300	<	* we do this to exclude atoms who are involved in short range
466	<	* interactions (bonds, bends, torsions), but we also need to
467	<	* exclude some overcounted interactions that result from the
468	<	* parallel decomposition.
469	<	*/
470	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
471	<	int unique_id_1, unique_id_2;
298	>	for (int j = 0; j < nLocal_; j++)
299	>	{
300	>	int jglob = AtomLocalToGlobal[j];
301
302	<	#ifdef IS_MPI
303	<	// in MPI, we have to look up the unique IDs for each atom
475	<	unique_id_1 = AtomRowToGlobal[atom1];
476	<	unique_id_2 = AtomColToGlobal[atom2];
302	>	if (excludes->hasPair(iglob, jglob))
303	>	excludesForAtom[i].push_back(j);
304
305	<	// this situation should only arise in MPI simulations
306	<	if (unique_id_1 == unique_id_2) return true;
307	<
308	<	// this prevents us from doing the pair on multiple processors
309	<	if (unique_id_1 < unique_id_2) {
310	<	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
311	<	} else {
312	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
313	<	}
314	<	#else
315	<	// in the normal loop, the atom numbers are unique
316	<	unique_id_1 = atom1;
317	<	unique_id_2 = atom2;
318	<	#endif
319	<
320	<	#ifdef IS_MPI
321	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
322	<	i != skipsForRowAtom[atom1].end(); ++i) {
323	<	if ( (*i) == unique_id_2 ) return true;
324	<	}
325	<	#else
499	<	for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
500	<	i != skipsForLocalAtom[atom1].end(); ++i) {
501	<	if ( (*i) == unique_id_2 ) return true;
502	<	}
503	<	#endif
504	<	}
305	>	if (oneTwo->hasPair(iglob, jglob))
306	>	{
307	>	toposForAtom[i].push_back(j);
308	>	topoDist[i].push_back(1);
309	>	} else
310	>	{
311	>	if (oneThree->hasPair(iglob, jglob))
312	>	{
313	>	toposForAtom[i].push_back(j);
314	>	topoDist[i].push_back(2);
315	>	} else
316	>	{
317	>	if (oneFour->hasPair(iglob, jglob))
318	>	{
319	>	toposForAtom[i].push_back(j);
320	>	topoDist[i].push_back(3);
321	>	}
322	>	}
323	>	}
324	>	}
325	>	}
326
327	<	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
328	<
329	<	#ifdef IS_MPI
330	<	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
331	<	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
332	<	}
333	<	#else
334	<	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
335	<	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
515	<	}
516	<	#endif
327	>	Globals* simParams_ = info_->getSimParams();
328	>	if (simParams_->haveNeighborListReorderFreq())
329	>	{
330	>	neighborListReorderFreq = simParams_->getNeighborListReorderFreq();
331	>	} else
332	>	{
333	>	neighborListReorderFreq = 0;
334	>	}
335	>	reorderFreqCounter = 1;
336
337	<	// zero is default for unconnected (i.e. normal) pair interactions
519	<	return 0;
520	<	}
337	>	createGtypeCutoffMap();
338
339	<	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
523	<	#ifdef IS_MPI
524	<	atomRowData.force[atom1] += fg;
525	<	#else
526	<	snap_->atomData.force[atom1] += fg;
527	<	#endif
528	<	}
339	>	}
340
341	<	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
531	<	#ifdef IS_MPI
532	<	atomColData.force[atom2] += fg;
533	<	#else
534	<	snap_->atomData.force[atom2] += fg;
535	<	#endif
536	<	}
341	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
342
343	<	// filling interaction blocks with pointers
344	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
345	<	InteractionData idat;
343	>	RealType tol = 1e-6;
344	>	largestRcut_ = 0.0;
345	>	RealType rc;
346	>	int atid;
347	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
348
349	<	#ifdef IS_MPI
543	<	if (storageLayout_ & DataStorage::dslAmat) {
544	<	idat.A1 = &(atomRowData.aMat[atom1]);
545	<	idat.A2 = &(atomColData.aMat[atom2]);
546	<	}
547	<
548	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
549	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
550	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
551	<	}
349	>	map<int, RealType> atypeCutoff;
350
351	<	if (storageLayout_ & DataStorage::dslTorque) {
352	<	idat.t1 = &(atomRowData.torque[atom1]);
353	<	idat.t2 = &(atomColData.torque[atom2]);
354	<	}
351	>	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at)
352	>	{
353	>	atid = (*at)->getIdent();
354	>	if (userChoseCutoff_)
355	>	atypeCutoff[atid] = userCutoff_;
356	>	else
357	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
358	>	}
359
360	<	if (storageLayout_ & DataStorage::dslDensity) {
361	<	idat.rho1 = &(atomRowData.density[atom1]);
362	<	idat.rho2 = &(atomColData.density[atom2]);
363	<	}
364	<
365	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
366	<	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
367	<	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
368	<	}
369	<
370	<	#else
371	<	if (storageLayout_ & DataStorage::dslAmat) {
372	<	idat.A1 = &(snap_->atomData.aMat[atom1]);
373	<	idat.A2 = &(snap_->atomData.aMat[atom2]);
374	<	}
375	<
376	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
377	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
378	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
577	<	}
578	<
579	<	if (storageLayout_ & DataStorage::dslTorque) {
580	<	idat.t1 = &(snap_->atomData.torque[atom1]);
581	<	idat.t2 = &(snap_->atomData.torque[atom2]);
582	<	}
583	<
584	<	if (storageLayout_ & DataStorage::dslDensity) {
585	<	idat.rho1 = &(snap_->atomData.density[atom1]);
586	<	idat.rho2 = &(snap_->atomData.density[atom2]);
587	<	}
588	<
589	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
590	<	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
591	<	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
592	<	}
593	<	#endif
594	<	return idat;
595	<	}
596	<
597	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
598	<
599	<	InteractionData idat;
600	<	#ifdef IS_MPI
601	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
602	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
603	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
604	<	}
605	<	if (storageLayout_ & DataStorage::dslTorque) {
606	<	idat.t1 = &(atomRowData.torque[atom1]);
607	<	idat.t2 = &(atomColData.torque[atom2]);
608	<	}
609	<	if (storageLayout_ & DataStorage::dslForce) {
610	<	idat.t1 = &(atomRowData.force[atom1]);
611	<	idat.t2 = &(atomColData.force[atom2]);
612	<	}
613	<	#else
614	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
615	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
616	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
617	<	}
618	<	if (storageLayout_ & DataStorage::dslTorque) {
619	<	idat.t1 = &(snap_->atomData.torque[atom1]);
620	<	idat.t2 = &(snap_->atomData.torque[atom2]);
621	<	}
622	<	if (storageLayout_ & DataStorage::dslForce) {
623	<	idat.t1 = &(snap_->atomData.force[atom1]);
624	<	idat.t2 = &(snap_->atomData.force[atom2]);
625	<	}
626	<	#endif
627	<
628	<	}
360	>	vector<RealType> gTypeCutoffs;
361	>	// first we do a single loop over the cutoff groups to find the
362	>	// largest cutoff for any atypes present in this group.
363	>	#ifdef IS_MPI
364	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
365	>	groupRowToGtype.resize(nGroupsInRow_);
366	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++)
367	>	{
368	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
369	>	for (vector<int>::iterator ia = atomListRow.begin();
370	>	ia != atomListRow.end(); ++ia)
371	>	{
372	>	int atom1 = (*ia);
373	>	atid = identsRow[atom1];
374	>	if (atypeCutoff[atid] > groupCutoffRow[cg1])
375	>	{
376	>	groupCutoffRow[cg1] = atypeCutoff[atid];
377	>	}
378	>	}
379
380	+	bool gTypeFound = false;
381	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
382	+	{
383	+	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol)
384	+	{
385	+	groupRowToGtype[cg1] = gt;
386	+	gTypeFound = true;
387	+	}
388	+	}
389	+	if (!gTypeFound)
390	+	{
391	+	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
392	+	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
393	+	}
394
395	+	}
396	+	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
397	+	groupColToGtype.resize(nGroupsInCol_);
398	+	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++)
399	+	{
400	+	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
401	+	for (vector<int>::iterator jb = atomListCol.begin();
402	+	jb != atomListCol.end(); ++jb)
403	+	{
404	+	int atom2 = (*jb);
405	+	atid = identsCol[atom2];
406	+	if (atypeCutoff[atid] > groupCutoffCol[cg2])
407	+	{
408	+	groupCutoffCol[cg2] = atypeCutoff[atid];
409	+	}
410	+	}
411	+	bool gTypeFound = false;
412	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
413	+	{
414	+	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol)
415	+	{
416	+	groupColToGtype[cg2] = gt;
417	+	gTypeFound = true;
418	+	}
419	+	}
420	+	if (!gTypeFound)
421	+	{
422	+	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
423	+	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
424	+	}
425	+	}
426	+	#else
427
428	+	vector<RealType> groupCutoff(nGroups_, 0.0);
429	+	groupToGtype.resize(nGroups_);
430	+	for (int cg1 = 0; cg1 < nGroups_; cg1++)
431	+	{
432	+	groupCutoff[cg1] = 0.0;
433	+	vector<int> atomList = getAtomsInGroupRow(cg1);
434	+	for (vector<int>::iterator ia = atomList.begin(); ia != atomList.end(); ++ia)
435	+	{
436	+	int atom1 = (*ia);
437	+	atid = idents[atom1];
438	+	if (atypeCutoff[atid] > groupCutoff[cg1])
439	+	groupCutoff[cg1] = atypeCutoff[atid];
440	+	}
441
442	<	/*
443	<	* buildNeighborList
444	<	*
445	<	* first element of pair is row-indexed CutoffGroup
446	<	* second element of pair is column-indexed CutoffGroup
447	<	*/
448	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
449	<
450	<	vector<pair<int, int> > neighborList;
442	>	bool gTypeFound = false;
443	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
444	>	{
445	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol)
446	>	{
447	>	groupToGtype[cg1] = gt;
448	>	gTypeFound = true;
449	>	}
450	>	}
451	>	if (!gTypeFound)
452	>	{
453	>	gTypeCutoffs.push_back(groupCutoff[cg1]);
454	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
455	>	}
456	>	}
457	>	#endif
458	>
459	>	// Now we find the maximum group cutoff value present in the simulation
460	>
461	>	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
462	>
463		#ifdef IS_MPI
464	<	cellListRow_.clear();
465	<	cellListCol_.clear();
645	<	#else
646	<	cellList_.clear();
464	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
465	>	MPI::MAX);
466		#endif
467
468	<	// dangerous to not do error checking.
650	<	RealType rCut_;
651	<
652	<	RealType rList_ = (rCut_ + skinThickness_);
653	<	RealType rl2 = rList_ * rList_;
654	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
655	<	Mat3x3d Hmat = snap_->getHmat();
656	<	Vector3d Hx = Hmat.getColumn(0);
657	<	Vector3d Hy = Hmat.getColumn(1);
658	<	Vector3d Hz = Hmat.getColumn(2);
468	>	RealType tradRcut = groupMax;
469
470	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
471	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
472	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
470	>	for (int i = 0; i < gTypeCutoffs.size(); i++)
471	>	{
472	>	for (int j = 0; j < gTypeCutoffs.size(); j++)
473	>	{
474	>	RealType thisRcut;
475	>	switch (cutoffPolicy_) {
476	>	case TRADITIONAL:
477	>	thisRcut = tradRcut;
478	>	break;
479	>	case MIX:
480	>	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
481	>	break;
482	>	case MAX:
483	>	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
484	>	break;
485	>	default:
486	>	sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap "
487	>	"hit an unknown cutoff policy!\n");
488	>	painCave.severity = OPENMD_ERROR;
489	>	painCave.isFatal = 1;
490	>	simError();
491	>	break;
492	>	}
493
494	<	Mat3x3d invHmat = snap_->getInvHmat();
495	<	Vector3d rs, scaled, dr;
496	<	Vector3i whichCell;
497	<	int cellIndex;
494	>	pair<int, int> key = make_pair(i, j);
495	>	gTypeCutoffMap[key].first = thisRcut;
496	>	if (thisRcut > largestRcut_)
497	>	largestRcut_ = thisRcut;
498	>	gTypeCutoffMap[key].second = thisRcut * thisRcut;
499	>	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
500	>	// sanity check
501
502	+	if (userChoseCutoff_)
503	+	{
504	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001)
505	+	{
506	+	sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap "
507	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
508	+	painCave.severity = OPENMD_ERROR;
509	+	painCave.isFatal = 1;
510	+	simError();
511	+	}
512	+	}
513	+	}
514	+	}
515	+	}
516	+
517	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
518	+	int i, j;
519		#ifdef IS_MPI
520	<	for (int i = 0; i < nGroupsInRow_; i++) {
521	<	rs = cgRowData.position[i];
522	<	// scaled positions relative to the box vectors
523	<	scaled = invHmat * rs;
524	<	// wrap the vector back into the unit box by subtracting integer box
525	<	// numbers
526	<	for (int j = 0; j < 3; j++)
527	<	scaled[j] -= roundMe(scaled[j]);
678	<
679	<	// find xyz-indices of cell that cutoffGroup is in.
680	<	whichCell.x() = nCells_.x() * scaled.x();
681	<	whichCell.y() = nCells_.y() * scaled.y();
682	<	whichCell.z() = nCells_.z() * scaled.z();
520	>	i = groupRowToGtype[cg1];
521	>	j = groupColToGtype[cg2];
522	>	#else
523	>	i = groupToGtype[cg1];
524	>	j = groupToGtype[cg2];
525	>	#endif
526	>	return gTypeCutoffMap[make_pair(i, j)];
527	>	}
528
529	<	// find single index of this cell:
530	<	cellIndex = Vlinear(whichCell, nCells_);
531	<	// add this cutoff group to the list of groups in this cell;
532	<	cellListRow_[cellIndex].push_back(i);
533	<	}
529	>	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
530	>	for (int j = 0; j < toposForAtom[atom1].size(); j++)
531	>	{
532	>	if (toposForAtom[atom1][j] == atom2)
533	>	return topoDist[atom1][j];
534	>	}
535	>	return 0;
536	>	}
537
538	<	for (int i = 0; i < nGroupsInCol_; i++) {
539	<	rs = cgColData.position[i];
540	<	// scaled positions relative to the box vectors
693	<	scaled = invHmat * rs;
694	<	// wrap the vector back into the unit box by subtracting integer box
695	<	// numbers
696	<	for (int j = 0; j < 3; j++)
697	<	scaled[j] -= roundMe(scaled[j]);
538	>	void ForceMatrixDecomposition::zeroWorkArrays() {
539	>	pairwisePot = 0.0;
540	>	embeddingPot = 0.0;
541
542	<	// find xyz-indices of cell that cutoffGroup is in.
543	<	whichCell.x() = nCells_.x() * scaled.x();
544	<	whichCell.y() = nCells_.y() * scaled.y();
545	<	whichCell.z() = nCells_.z() * scaled.z();
542	>	#ifdef IS_MPI
543	>	if (storageLayout_ & DataStorage::dslForce)
544	>	{
545	>	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
546	>	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
547	>	}
548	>
549	>	if (storageLayout_ & DataStorage::dslTorque)
550	>	{
551	>	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
552	>	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
553	>	}
554	>
555	>	fill(pot_row.begin(), pot_row.end(),
556	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
557	>
558	>	fill(pot_col.begin(), pot_col.end(),
559	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
560
561	<	// find single index of this cell:
562	<	cellIndex = Vlinear(whichCell, nCells_);
563	<	// add this cutoff group to the list of groups in this cell;
564	<	cellListCol_[cellIndex].push_back(i);
565	<	}
566	<	#else
567	<	for (int i = 0; i < nGroups_; i++) {
711	<	rs = snap_->cgData.position[i];
712	<	// scaled positions relative to the box vectors
713	<	scaled = invHmat * rs;
714	<	// wrap the vector back into the unit box by subtracting integer box
715	<	// numbers
716	<	for (int j = 0; j < 3; j++)
717	<	scaled[j] -= roundMe(scaled[j]);
561	>	if (storageLayout_ & DataStorage::dslParticlePot)
562	>	{
563	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
564	>	0.0);
565	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
566	>	0.0);
567	>	}
568
569	<	// find xyz-indices of cell that cutoffGroup is in.
570	<	whichCell.x() = nCells_.x() * scaled.x();
571	<	whichCell.y() = nCells_.y() * scaled.y();
572	<	whichCell.z() = nCells_.z() * scaled.z();
569	>	if (storageLayout_ & DataStorage::dslDensity)
570	>	{
571	>	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
572	>	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
573	>	}
574
575	<	// find single index of this cell:
576	<	cellIndex = Vlinear(whichCell, nCells_);
577	<	// add this cutoff group to the list of groups in this cell;
578	<	cellList_[cellIndex].push_back(i);
579	<	}
575	>	if (storageLayout_ & DataStorage::dslFunctional)
576	>	{
577	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
578	>	0.0);
579	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
580	>	0.0);
581	>	}
582	>
583	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
584	>	{
585	>	fill(atomRowData.functionalDerivative.begin(),
586	>	atomRowData.functionalDerivative.end(), 0.0);
587	>	fill(atomColData.functionalDerivative.begin(),
588	>	atomColData.functionalDerivative.end(), 0.0);
589	>	}
590	>
591	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
592	>	{
593	>	fill(atomRowData.skippedCharge.begin(),
594	>	atomRowData.skippedCharge.end(), 0.0);
595	>	fill(atomColData.skippedCharge.begin(),
596	>	atomColData.skippedCharge.end(), 0.0);
597	>	}
598	>
599		#endif
600	+	// even in parallel, we need to zero out the local arrays:
601
602	+	if (storageLayout_ & DataStorage::dslParticlePot)
603	+	{
604	+	fill(snap_->atomData.particlePot.begin(), snap_->atomData.particlePot.end(), 0.0);
605	+	}
606
607	+	if (storageLayout_ & DataStorage::dslDensity)
608	+	{
609	+	fill(snap_->atomData.density.begin(), snap_->atomData.density.end(), 0.0);
610	+	}
611	+	if (storageLayout_ & DataStorage::dslFunctional)
612	+	{
613	+	fill(snap_->atomData.functional.begin(), snap_->atomData.functional.end(), 0.0);
614	+	}
615	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
616	+	{
617	+	fill(snap_->atomData.functionalDerivative.begin(), snap_->atomData.functionalDerivative.end(), 0.0);
618	+	}
619	+	if (storageLayout_ & DataStorage::dslSkippedCharge)
620	+	{
621	+	fill(snap_->atomData.skippedCharge.begin(), snap_->atomData.skippedCharge.end(), 0.0);
622	+	}
623
624	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
734	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
735	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
736	<	Vector3i m1v(m1x, m1y, m1z);
737	<	int m1 = Vlinear(m1v, nCells_);
624	>	}
625
626	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
627	<	os != cellOffsets_.end(); ++os) {
628	<
629	<	Vector3i m2v = m1v + (*os);
743	<
744	<	if (m2v.x() >= nCells_.x()) {
745	<	m2v.x() = 0;
746	<	} else if (m2v.x() < 0) {
747	<	m2v.x() = nCells_.x() - 1;
748	<	}
749	<
750	<	if (m2v.y() >= nCells_.y()) {
751	<	m2v.y() = 0;
752	<	} else if (m2v.y() < 0) {
753	<	m2v.y() = nCells_.y() - 1;
754	<	}
755	<
756	<	if (m2v.z() >= nCells_.z()) {
757	<	m2v.z() = 0;
758	<	} else if (m2v.z() < 0) {
759	<	m2v.z() = nCells_.z() - 1;
760	<	}
761	<
762	<	int m2 = Vlinear (m2v, nCells_);
626	>	void ForceMatrixDecomposition::distributeData() {
627	>	snap_ = sman_->getCurrentSnapshot();
628	>	storageLayout_ = sman_->getStorageLayout();
629	>	#ifdef IS_MPI
630
631	+	// gather up the atomic positions
632	+	AtomPlanVectorRow->gather(snap_->atomData.position,
633	+	atomRowData.position);
634	+	AtomPlanVectorColumn->gather(snap_->atomData.position,
635	+	atomColData.position);
636	+
637	+	// gather up the cutoff group positions
638	+
639	+	cerr << "before gather\n";
640	+	for (int i = 0; i < snap_->cgData.position.size(); i++)
641	+	{
642	+	cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
643	+	}
644	+
645	+	cgPlanVectorRow->gather(snap_->cgData.position,
646	+	cgRowData.position);
647	+
648	+	cerr << "after gather\n";
649	+	for (int i = 0; i < cgRowData.position.size(); i++)
650	+	{
651	+	cerr << "cgRpos = " << cgRowData.position[i] << "\n";
652	+	}
653	+
654	+	cgPlanVectorColumn->gather(snap_->cgData.position,
655	+	cgColData.position);
656	+	for (int i = 0; i < cgColData.position.size(); i++)
657	+	{
658	+	cerr << "cgCpos = " << cgColData.position[i] << "\n";
659	+	}
660	+
661	+	// if needed, gather the atomic rotation matrices
662	+	if (storageLayout_ & DataStorage::dslAmat)
663	+	{
664	+	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
665	+	atomRowData.aMat);
666	+	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
667	+	atomColData.aMat);
668	+	}
669	+
670	+	// if needed, gather the atomic eletrostatic frames
671	+	if (storageLayout_ & DataStorage::dslElectroFrame)
672	+	{
673	+	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
674	+	atomRowData.electroFrame);
675	+	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
676	+	atomColData.electroFrame);
677	+	}
678	+
679	+	#endif
680	+	}
681	+
682	+	/* collects information obtained during the pre-pair loop onto local
683	+	* data structures.
684	+	*/
685	+	void ForceMatrixDecomposition::collectIntermediateData() {
686	+	snap_ = sman_->getCurrentSnapshot();
687	+	storageLayout_ = sman_->getStorageLayout();
688		#ifdef IS_MPI
765	–	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
766	–	j1 != cellListRow_[m1].end(); ++j1) {
767	–	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
768	–	j2 != cellListCol_[m2].end(); ++j2) {
769	–
770	–	// Always do this if we're in different cells or if
771	–	// we're in the same cell and the global index of the
772	–	// j2 cutoff group is less than the j1 cutoff group
689
690	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
691	<	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
776	<	snap_->wrapVector(dr);
777	<	if (dr.lengthSquare() < rl2) {
778	<	neighborList.push_back(make_pair((*j1), (*j2)));
779	<	}
780	<	}
781	<	}
782	<	}
783	<	#else
784	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
785	<	j1 != cellList_[m1].end(); ++j1) {
786	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
787	<	j2 != cellList_[m2].end(); ++j2) {
788	<
789	<	// Always do this if we're in different cells or if
790	<	// we're in the same cell and the global index of the
791	<	// j2 cutoff group is less than the j1 cutoff group
690	>	if (storageLayout_ & DataStorage::dslDensity)
691	>	{
692
693	<	if (m2 != m1 || (*j2) < (*j1)) {
694	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
695	<	snap_->wrapVector(dr);
696	<	if (dr.lengthSquare() < rl2) {
697	<	neighborList.push_back(make_pair((*j1), (*j2)));
698	<	}
699	<	}
700	<	}
701	<	}
693	>	AtomPlanRealRow->scatter(atomRowData.density,
694	>	snap_->atomData.density);
695	>
696	>	int n = snap_->atomData.density.size();
697	>	vector<RealType> rho_tmp(n, 0.0);
698	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
699	>	for (int i = 0; i < n; i++)
700	>	snap_->atomData.density[i] += rho_tmp[i];
701	>	}
702		#endif
703	<	}
804	<	}
805	<	}
806	<	}
703	>	}
704
705	<	// save the local cutoff group positions for the check that is
706	<	// done on each loop:
707	<	saved_CG_positions_.clear();
708	<	for (int i = 0; i < nGroups_; i++)
709	<	saved_CG_positions_.push_back(snap_->cgData.position[i]);
705	>	/*
706	>	* redistributes information obtained during the pre-pair loop out to
707	>	* row and column-indexed data structures
708	>	*/
709	>	void ForceMatrixDecomposition::distributeIntermediateData() {
710	>	snap_ = sman_->getCurrentSnapshot();
711	>	storageLayout_ = sman_->getStorageLayout();
712	>	#ifdef IS_MPI
713	>	if (storageLayout_ & DataStorage::dslFunctional)
714	>	{
715	>	AtomPlanRealRow->gather(snap_->atomData.functional,
716	>	atomRowData.functional);
717	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
718	>	atomColData.functional);
719	>	}
720
721	<	return neighborList;
722	<	}
721	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
722	>	{
723	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
724	>	atomRowData.functionalDerivative);
725	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
726	>	atomColData.functionalDerivative);
727	>	}
728	>	#endif
729	>	}
730	>
731	>	void ForceMatrixDecomposition::collectData() {
732	>	snap_ = sman_->getCurrentSnapshot();
733	>	storageLayout_ = sman_->getStorageLayout();
734	>	#ifdef IS_MPI
735	>	int n = snap_->atomData.force.size();
736	>	vector<Vector3d> frc_tmp(n, V3Zero);
737	>
738	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
739	>	for (int i = 0; i < n; i++)
740	>	{
741	>	snap_->atomData.force[i] += frc_tmp[i];
742	>	frc_tmp[i] = 0.0;
743	>	}
744	>
745	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
746	>	for (int i = 0; i < n; i++)
747	>	{
748	>	snap_->atomData.force[i] += frc_tmp[i];
749	>	}
750	>
751	>	if (storageLayout_ & DataStorage::dslTorque)
752	>	{
753	>
754	>	int nt = snap_->atomData.torque.size();
755	>	vector<Vector3d> trq_tmp(nt, V3Zero);
756	>
757	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
758	>	for (int i = 0; i < nt; i++)
759	>	{
760	>	snap_->atomData.torque[i] += trq_tmp[i];
761	>	trq_tmp[i] = 0.0;
762	>	}
763	>
764	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
765	>	for (int i = 0; i < nt; i++)
766	>	snap_->atomData.torque[i] += trq_tmp[i];
767	>	}
768	>
769	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
770	>	{
771	>
772	>	int ns = snap_->atomData.skippedCharge.size();
773	>	vector<RealType> skch_tmp(ns, 0.0);
774	>
775	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
776	>	for (int i = 0; i < ns; i++)
777	>	{
778	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
779	>	skch_tmp[i] = 0.0;
780	>	}
781	>
782	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
783	>	for (int i = 0; i < ns; i++)
784	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
785	>	}
786	>
787	>	nLocal_ = snap_->getNumberOfAtoms();
788	>
789	>	vector<potVec> pot_temp(nLocal_,
790	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
791	>
792	>	// scatter/gather pot_row into the members of my column
793	>
794	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
795	>
796	>	for (int ii = 0; ii < pot_temp.size(); ii++ )
797	>	pairwisePot += pot_temp[ii];
798	>
799	>	fill(pot_temp.begin(), pot_temp.end(),
800	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
801	>
802	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
803	>
804	>	for (int ii = 0; ii < pot_temp.size(); ii++ )
805	>	pairwisePot += pot_temp[ii];
806	>	#endif
807	>
808	>	//      cerr << "pairwisePot = " << pairwisePot << "\n";
809	>	}
810	>
811	>	int ForceMatrixDecomposition::getNAtomsInRow() {
812	>	#ifdef IS_MPI
813	>	return nAtomsInRow_;
814	>	#else
815	>	return nLocal_;
816	>	#endif
817	>	}
818	>
819	>	/**
820	>	* returns the list of atoms belonging to this group.
821	>	*/
822	>	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1) {
823	>	#ifdef IS_MPI
824	>	return groupListRow_[cg1];
825	>	#else
826	>	return groupList_[cg1];
827	>	#endif
828	>	}
829	>
830	>	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2) {
831	>	#ifdef IS_MPI
832	>	return groupListCol_[cg2];
833	>	#else
834	>	return groupList_[cg2];
835	>	#endif
836	>	}
837	>
838	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2) {
839	>	Vector3d d;
840	>
841	>	#ifdef IS_MPI
842	>	d = cgColData.position[cg2] - cgRowData.position[cg1];
843	>	cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
844	>	cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
845	>	#else
846	>	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
847	>	cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
848	>	cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
849	>	#endif
850	>
851	>	snap_->wrapVector(d);
852	>	return d;
853	>	}
854	>
855	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2) {
856	>	Vector3d d;
857	>
858	>	d = snap_->cgData.position[cg2->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
859	>	/*      cerr << "cg1_gid = " << cg1->getGlobalIndex() << "\tcg1_lid = " << cg1->getLocalIndex() << "\tcg1p = "
860	>	<< snap_->cgData.position[cg1->getLocalIndex()] << "\n";
861	>	cerr << "cg2_gid = " << cg2->getGlobalIndex() << "\tcg2_lid = " << cg2->getLocalIndex() << "\tcg2p = "
862	>	<< snap_->cgData.position[cg2->getLocalIndex()] << "\n";*/
863	>
864	>	snap_->wrapVector(d);
865	>	return d;
866	>	}
867	>
868	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1) {
869	>
870	>	Vector3d d;
871	>
872	>	#ifdef IS_MPI
873	>	d = cgRowData.position[cg1] - atomRowData.position[atom1];
874	>	#else
875	>	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
876	>	#endif
877	>
878	>	snap_->wrapVector(d);
879	>	return d;
880	>	}
881	>
882	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2) {
883	>	Vector3d d;
884	>
885	>	#ifdef IS_MPI
886	>	d = cgColData.position[cg2] - atomColData.position[atom2];
887	>	#else
888	>	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
889	>	#endif
890	>
891	>	snap_->wrapVector(d);
892	>	return d;
893	>	}
894	>
895	>	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
896	>	#ifdef IS_MPI
897	>	return massFactorsRow[atom1];
898	>	#else
899	>	return massFactors[atom1];
900	>	#endif
901	>	}
902	>
903	>	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
904	>	#ifdef IS_MPI
905	>	return massFactorsCol[atom2];
906	>	#else
907	>	return massFactors[atom2];
908	>	#endif
909	>
910	>	}
911	>
912	>	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2) {
913	>	Vector3d d;
914	>
915	>	#ifdef IS_MPI
916	>	d = atomColData.position[atom2] - atomRowData.position[atom1];
917	>	#else
918	>	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
919	>	#endif
920	>
921	>	snap_->wrapVector(d);
922	>	return d;
923	>	}
924	>
925	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
926	>	return excludesForAtom[atom1];
927	>	}
928	>
929	>	/**
930	>	* We need to exclude some overcounted interactions that result from
931	>	* the parallel decomposition.
932	>	*/
933	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
934	>	int unique_id_1, unique_id_2;
935	>
936	>	//      cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
937	>	#ifdef IS_MPI
938	>	// in MPI, we have to look up the unique IDs for each atom
939	>	unique_id_1 = AtomRowToGlobal[atom1];
940	>	unique_id_2 = AtomColToGlobal[atom2];
941	>
942	>	cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
943	>	// this situation should only arise in MPI simulations
944	>	if (unique_id_1 == unique_id_2) return true;
945	>
946	>	// this prevents us from doing the pair on multiple processors
947	>	if (unique_id_1 < unique_id_2)
948	>	{
949	>	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
950	>	} else
951	>	{
952	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
953	>	}
954	>	#endif
955	>	return false;
956	>	}
957	>
958	>	/**
959	>	* We need to handle the interactions for atoms who are involved in
960	>	* the same rigid body as well as some short range interactions
961	>	* (bonds, bends, torsions) differently from other interactions.
962	>	* We'll still visit the pairwise routines, but with a flag that
963	>	* tells those routines to exclude the pair from direct long range
964	>	* interactions.  Some indirect interactions (notably reaction
965	>	* field) must still be handled for these pairs.
966	>	*/
967	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
968	>	int unique_id_2;
969	>	#ifdef IS_MPI
970	>	// in MPI, we have to look up the unique IDs for the row atom.
971	>	unique_id_2 = AtomColToGlobal[atom2];
972	>	#else
973	>	// in the normal loop, the atom numbers are unique
974	>	unique_id_2 = atom2;
975	>	#endif
976	>
977	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin(); i != excludesForAtom[atom1].end(); ++i)
978	>	{
979	>	if ((*i) == unique_id_2)
980	>	return true;
981	>	}
982	>
983	>	return false;
984	>	}
985	>
986	>	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg) {
987	>	#ifdef IS_MPI
988	>	atomRowData.force[atom1] += fg;
989	>	#else
990	>	snap_->atomData.force[atom1] += fg;
991	>	#endif
992	>	}
993	>
994	>	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg) {
995	>	#ifdef IS_MPI
996	>	atomColData.force[atom2] += fg;
997	>	#else
998	>	snap_->atomData.force[atom2] += fg;
999	>	#endif
1000	>	}
1001	>
1002	>	// filling interaction blocks with pointers
1003	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, int atom1, int atom2) {
1004	>
1005	>	idat.excluded = excludeAtomPair(atom1, atom2);
1006	>
1007	>	#ifdef IS_MPI
1008	>	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1009	>	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1010	>	//                         ff_->getAtomType(identsCol[atom2]) );
1011	>
1012	>	if (storageLayout_ & DataStorage::dslAmat)
1013	>	{
1014	>	idat.A1 = &(atomRowData.aMat[atom1]);
1015	>	idat.A2 = &(atomColData.aMat[atom2]);
1016	>	}
1017	>
1018	>	if (storageLayout_ & DataStorage::dslElectroFrame)
1019	>	{
1020	>	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1021	>	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1022	>	}
1023	>
1024	>	if (storageLayout_ & DataStorage::dslTorque)
1025	>	{
1026	>	idat.t1 = &(atomRowData.torque[atom1]);
1027	>	idat.t2 = &(atomColData.torque[atom2]);
1028	>	}
1029	>
1030	>	if (storageLayout_ & DataStorage::dslDensity)
1031	>	{
1032	>	idat.rho1 = &(atomRowData.density[atom1]);
1033	>	idat.rho2 = &(atomColData.density[atom2]);
1034	>	}
1035	>
1036	>	if (storageLayout_ & DataStorage::dslFunctional)
1037	>	{
1038	>	idat.frho1 = &(atomRowData.functional[atom1]);
1039	>	idat.frho2 = &(atomColData.functional[atom2]);
1040	>	}
1041	>
1042	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
1043	>	{
1044	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1045	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1046	>	}
1047	>
1048	>	if (storageLayout_ & DataStorage::dslParticlePot)
1049	>	{
1050	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1051	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1052	>	}
1053	>
1054	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
1055	>	{
1056	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1057	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1058	>	}
1059	>
1060	>	#else
1061	>
1062	>	idat.atypes = make_pair(atypesLocal[atom1], atypesLocal[atom2]);
1063	>	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1064	>	//                         ff_->getAtomType(idents[atom2]) );
1065	>
1066	>	if (storageLayout_ & DataStorage::dslAmat)
1067	>	{
1068	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1069	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1070	>	}
1071	>
1072	>	if (storageLayout_ & DataStorage::dslElectroFrame)
1073	>	{
1074	>	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1075	>	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1076	>	}
1077	>
1078	>	if (storageLayout_ & DataStorage::dslTorque)
1079	>	{
1080	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1081	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1082	>	}
1083	>
1084	>	if (storageLayout_ & DataStorage::dslDensity)
1085	>	{
1086	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1087	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1088	>	}
1089	>
1090	>	if (storageLayout_ & DataStorage::dslFunctional)
1091	>	{
1092	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1093	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1094	>	}
1095	>
1096	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
1097	>	{
1098	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1099	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1100	>	}
1101	>
1102	>	if (storageLayout_ & DataStorage::dslParticlePot)
1103	>	{
1104	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1105	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1106	>	}
1107	>
1108	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
1109	>	{
1110	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1111	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1112	>	}
1113	>	#endif
1114	>	}
1115	>
1116	>	// filling interaction blocks with pointers
1117	>	void ForceMatrixDecomposition::fillInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2) {
1118	>
1119	>	idat.excluded = excludeAtomPair(atom1, atom2);
1120	>
1121	>	#ifdef IS_MPI
1122	>	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1123	>	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1124	>	//                         ff_->getAtomType(identsCol[atom2]) );
1125	>
1126	>	if (storageLayout_ & DataStorage::dslAmat)
1127	>	{
1128	>	idat.A1 = &(atomRowData.aMat[atom1]);
1129	>	idat.A2 = &(atomColData.aMat[atom2]);
1130	>	}
1131	>
1132	>	if (storageLayout_ & DataStorage::dslElectroFrame)
1133	>	{
1134	>	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1135	>	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1136	>	}
1137	>
1138	>	if (storageLayout_ & DataStorage::dslTorque)
1139	>	{
1140	>	idat.t1 = &(atomRowData.torque[atom1]);
1141	>	idat.t2 = &(atomColData.torque[atom2]);
1142	>	}
1143	>
1144	>	if (storageLayout_ & DataStorage::dslDensity)
1145	>	{
1146	>	idat.rho1 = &(atomRowData.density[atom1]);
1147	>	idat.rho2 = &(atomColData.density[atom2]);
1148	>	}
1149	>
1150	>	if (storageLayout_ & DataStorage::dslFunctional)
1151	>	{
1152	>	idat.frho1 = &(atomRowData.functional[atom1]);
1153	>	idat.frho2 = &(atomColData.functional[atom2]);
1154	>	}
1155	>
1156	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
1157	>	{
1158	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1159	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1160	>	}
1161	>
1162	>	if (storageLayout_ & DataStorage::dslParticlePot)
1163	>	{
1164	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1165	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1166	>	}
1167	>
1168	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
1169	>	{
1170	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1171	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1172	>	}
1173	>
1174	>	#else
1175	>
1176	>	idat.atypes = make_pair(atypesLocal[atom1], atypesLocal[atom2]);
1177	>	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1178	>	//                         ff_->getAtomType(idents[atom2]) );
1179	>
1180	>	if (storageLayout_ & DataStorage::dslAmat)
1181	>	{
1182	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1183	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1184	>	}
1185	>
1186	>	if (storageLayout_ & DataStorage::dslElectroFrame)
1187	>	{
1188	>	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1189	>	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1190	>	}
1191	>
1192	>	if (storageLayout_ & DataStorage::dslTorque)
1193	>	{
1194	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1195	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1196	>	}
1197	>
1198	>	if (storageLayout_ & DataStorage::dslDensity)
1199	>	{
1200	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1201	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1202	>	}
1203	>
1204	>	if (storageLayout_ & DataStorage::dslFunctional)
1205	>	{
1206	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1207	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1208	>	}
1209	>
1210	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
1211	>	{
1212	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1213	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1214	>	}
1215	>
1216	>	if (storageLayout_ & DataStorage::dslParticlePot)
1217	>	{
1218	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1219	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1220	>	}
1221	>
1222	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
1223	>	{
1224	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1225	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1226	>	}
1227	>	#endif
1228	>	}
1229	>
1230	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1231	>	#ifdef IS_MPI
1232	>	pot_row[atom1] += 0.5 * *(idat.pot);
1233	>	pot_col[atom2] += 0.5 * *(idat.pot);
1234	>
1235	>	atomRowData.force[atom1] += *(idat.f1);
1236	>	atomColData.force[atom2] -= *(idat.f1);
1237	>	#else
1238	>	pairwisePot += *(idat.pot);
1239	>
1240	>	snap_->atomData.force[atom1] += *(idat.f1);
1241	>	snap_->atomData.force[atom2] -= *(idat.f1);
1242	>	#endif
1243	>
1244	>	}
1245	>
1246	>	void ForceMatrixDecomposition::unpackInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2) {
1247	>	pairwisePot += idat.pot;
1248	>
1249	>	snap_->atomData.force[atom1] += idat.f1;
1250	>	snap_->atomData.force[atom2] -= idat.f1;
1251	>	}
1252	>
1253	>	void ForceMatrixDecomposition::reorderGroupCutoffs(vector<int> &order) {
1254	>	vector<int> tmp = vector<int> (groupToGtype.size());
1255	>
1256	>	for (int i = 0; i < groupToGtype.size(); ++i)
1257	>	{
1258	>	tmp[i] = groupToGtype[i];
1259	>	}
1260	>
1261	>	for (int i = 0; i < groupToGtype.size(); ++i)
1262	>	{
1263	>	groupToGtype[i] = tmp[order[i]];
1264	>	}
1265	>	}
1266	>
1267	>	void ForceMatrixDecomposition::reorderPosition(vector<int> &order) {
1268	>	Snapshot* snap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1269	>	DataStorage* cgConfig = &(snap_->cgData);
1270	>	vector<Vector3d> tmp = vector<Vector3d> (nGroups_);
1271	>
1272	>	for (int i = 0; i < nGroups_; ++i)
1273	>	{
1274	>	tmp[i] = snap_->cgData.position[i];
1275	>	}
1276	>
1277	>	vector<int> mapPos = vector<int> (nGroups_);
1278	>	for (int i = 0; i < nGroups_; ++i)
1279	>	{
1280	>	snap_->cgData.position[i] = tmp[order[i]];
1281	>	mapPos[order[i]] = i;
1282	>	}
1283	>
1284	>	SimInfo::MoleculeIterator mi;
1285	>	Molecule* mol;
1286	>	Molecule::CutoffGroupIterator ci;
1287	>	CutoffGroup* cg;
1288	>
1289	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1290	>	{
1291	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1292	>	{
1293	>	cg->setLocalIndex(mapPos[cg->getLocalIndex()]);
1294	>	}
1295	>	}
1296	>	}
1297	>
1298	>	void ForceMatrixDecomposition::reorderGroupList(vector<int> &order) {
1299	>	vector<vector<int> > tmp = vector<vector<int> > (groupList_.size());
1300	>
1301	>	for (int i = 0; i < groupList_.size(); ++i)
1302	>	{
1303	>	tmp[i] = groupList_[i];
1304	>	}
1305	>
1306	>	for (int i = 0; i < groupList_.size(); ++i)
1307	>	{
1308	>	groupList_[i] = tmp[order[i]];
1309	>	}
1310	>	}
1311	>
1312	>	void ForceMatrixDecomposition::reorderMemory(vector<vector<CutoffGroup *> > &H_c_l) {
1313	>	int n = 0;
1314	>
1315	>	/* record the reordered atom indices */
1316	>	vector<int> k = vector<int> (nGroups_);
1317	>
1318	>	for (int c = 0; c < H_c_l.size(); ++c)
1319	>	{
1320	>	for (vector<CutoffGroup *>::iterator cg = H_c_l[c].begin(); cg != H_c_l[c].end(); ++cg)
1321	>	{
1322	>	int i = (*cg)->getGlobalIndex();
1323	>	k[n] = i;
1324	>	++n;
1325	>	}
1326	>	}
1327	>
1328	>	//      reorderGroupCutoffs(k);
1329	>	//      reorderGroupList(k);
1330	>	reorderPosition(k);
1331	>	}
1332	>
1333	>	vector<vector<CutoffGroup *> > ForceMatrixDecomposition::buildLayerBasedNeighborList() {
1334	>	// Na = nGroups_
1335	>	/* cell occupancy counter */
1336	>	//      vector<int> k_c;
1337	>	/* c_i - has cell containing atom i (size Na) */
1338	>	vector<int> c = vector<int> (nGroups_);
1339	>	/* l_i - layer containing atom i (size Na) */
1340	>	//      vector<int> l;
1341	>
1342	>	RealType rList_ = (largestRcut_ + skinThickness_);
1343	>	Snapshot* snap_ = sman_->getCurrentSnapshot();
1344	>	Mat3x3d Hmat = snap_->getHmat();
1345	>	Vector3d Hx = Hmat.getColumn(0);
1346	>	Vector3d Hy = Hmat.getColumn(1);
1347	>	Vector3d Hz = Hmat.getColumn(2);
1348	>
1349	>	nCells_.x() = (int) (Hx.length()) / rList_;
1350	>	nCells_.y() = (int) (Hy.length()) / rList_;
1351	>	nCells_.z() = (int) (Hz.length()) / rList_;
1352	>
1353	>	Mat3x3d invHmat = snap_->getInvHmat();
1354	>	Vector3d rs, scaled, dr;
1355	>	Vector3i whichCell;
1356	>	int cellIndex;
1357	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1358	>
1359	>	//      k_c = vector<int> (nCtot, 0);
1360	>
1361	>	SimInfo::MoleculeIterator mi;
1362	>	Molecule* mol;
1363	>	Molecule::CutoffGroupIterator ci;
1364	>	CutoffGroup* cg;
1365	>
1366	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1367	>	{
1368	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1369	>	{
1370	>	rs = snap_->cgData.position[cg->getLocalIndex()];
1371	>
1372	>	// scaled positions relative to the box vectors
1373	>	scaled = invHmat * rs;
1374	>
1375	>	// wrap the vector back into the unit box by subtracting integer box
1376	>	// numbers
1377	>	for (int j = 0; j < 3; j++)
1378	>	{
1379	>	scaled[j] -= roundMe(scaled[j]);
1380	>	scaled[j] += 0.5;
1381	>	}
1382	>
1383	>	// find xyz-indices of cell that cutoffGroup is in.
1384	>	whichCell.x() = nCells_.x() * scaled.x();
1385	>	whichCell.y() = nCells_.y() * scaled.y();
1386	>	whichCell.z() = nCells_.z() * scaled.z();
1387	>
1388	>	//                      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(),
1389	>	//                                      whichCell.z());
1390	>
1391	>	// find single index of this cell:
1392	>	cellIndex = Vlinear(whichCell, nCells_);
1393	>
1394	>	c[cg->getGlobalIndex()] = cellIndex;
1395	>	}
1396	>	}
1397	>
1398	>	//      int k_c_curr;
1399	>	//      int k_c_max = 0;
1400	>	/* the cell-layer occupancy matrix */
1401	>	vector<vector<CutoffGroup *> > H_c_l = vector<vector<CutoffGroup *> > (nCtot);
1402	>
1403	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1404	>	{
1405	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1406	>
1407	>	{
1408	>	//                      k_c_curr = ++k_c[c[cg1->getGlobalIndex()]];
1409	>	//                      l.push_back(k_c_curr);
1410	>	//
1411	>	//                      /* determines the number of layers in use */
1412	>	//                      if (k_c_max < k_c_curr)
1413	>	//                      {
1414	>	//                              k_c_max = k_c_curr;
1415	>	//                      }
1416	>	H_c_l[c[cg->getGlobalIndex()]].push_back(/*l[*/cg/*]*/);
1417	>	}
1418	>	}
1419	>
1420	>	/* Frequency of reordering the memory */
1421	>	if (neighborListReorderFreq != 0)
1422	>	{
1423	>	if (reorderFreqCounter == neighborListReorderFreq)
1424	>	{
1425	>	reorderMemory(H_c_l);
1426	>	reorderFreqCounter = 1;
1427	>	} else
1428	>	{
1429	>	reorderFreqCounter++;
1430	>	}
1431	>	}
1432	>
1433	>	int m;
1434	>	/* The neighbor matrix */
1435	>	vector<vector<CutoffGroup *> > neighborMatW = vector<vector<CutoffGroup *> > (nGroups_);
1436	>
1437	>	groupCutoffs cuts;
1438	>	CutoffGroup *cg1;
1439	>
1440	>	/* Loops over objects(atoms, rigidBodies, cutoffGroups, etc.) */
1441	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1442	>	{
1443	>	for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
1444	>	{
1445	>	/* c' */
1446	>	int c1 = c[cg1->getGlobalIndex()];
1447	>	Vector3i c1v = idxToV(c1, nCells_);
1448	>
1449	>	/* loops over the neighboring cells c'' */
1450	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1451	>	{
1452	>	Vector3i c2v = c1v + (*os);
1453	>
1454	>	if (c2v.x() >= nCells_.x())
1455	>	{
1456	>	c2v.x() = 0;
1457	>	} else if (c2v.x() < 0)
1458	>	{
1459	>	c2v.x() = nCells_.x() - 1;
1460	>	}
1461	>
1462	>	if (c2v.y() >= nCells_.y())
1463	>	{
1464	>	c2v.y() = 0;
1465	>	} else if (c2v.y() < 0)
1466	>	{
1467	>	c2v.y() = nCells_.y() - 1;
1468	>	}
1469	>
1470	>	if (c2v.z() >= nCells_.z())
1471	>	{
1472	>	c2v.z() = 0;
1473	>	} else if (c2v.z() < 0)
1474	>	{
1475	>	c2v.z() = nCells_.z() - 1;
1476	>	}
1477	>
1478	>	int c2 = Vlinear(c2v, nCells_);
1479	>	/* Loops over layers l to access the neighbor atoms */
1480	>	for (vector<CutoffGroup *>::iterator cg2 = H_c_l[c2].begin(); cg2 != H_c_l[c2].end(); ++cg2)
1481	>	{
1482	>	//                              if i'' = 0 then break // doesn't apply to vector implementation of the matrix
1483	>	//                              if(i != *j)
1484	>	if (c2 != c1 || (*cg2)->getGlobalIndex() < cg1->getGlobalIndex())
1485	>	{
1486	>	dr = snap_->cgData.position[(*cg2)->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
1487	>	snap_->wrapVector(dr);
1488	>	cuts = getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex());
1489	>	if (dr.lengthSquare() < cuts.third)
1490	>	{
1491	>	/* Transposed version of Rapaport W mat, to occupy successive memory locations on CPU */
1492	>	neighborMatW[cg1->getGlobalIndex()].push_back((*cg2));
1493	>	}
1494	>	}
1495	>	}
1496	>	}
1497	>	}
1498	>	}
1499	>
1500	>	// save the local cutoff group positions for the check that is
1501	>	// done on each loop:
1502	>	saved_CG_positions_.clear();
1503	>	for (int i = 0; i < nGroups_; i++)
1504	>	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1505	>
1506	>	return neighborMatW;
1507	>	}
1508	>
1509	>	/*
1510	>	* buildNeighborList
1511	>	*
1512	>	* first element of pair is row-indexed CutoffGroup
1513	>	* second element of pair is column-indexed CutoffGroup
1514	>	*/
1515	>	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1516	>
1517	>	vector<pair<int, int> > neighborList;
1518	>	groupCutoffs cuts;
1519	>	bool doAllPairs = false;
1520	>
1521	>	#ifdef IS_MPI
1522	>	cellListRow_.clear();
1523	>	cellListCol_.clear();
1524	>	#else
1525	>	cellList_.clear();
1526	>	#endif
1527	>
1528	>	RealType rList_ = (largestRcut_ + skinThickness_);
1529	>	RealType rl2 = rList_ * rList_;
1530	>	Snapshot* snap_ = sman_->getCurrentSnapshot();
1531	>	Mat3x3d Hmat = snap_->getHmat();
1532	>	Vector3d Hx = Hmat.getColumn(0);
1533	>	Vector3d Hy = Hmat.getColumn(1);
1534	>	Vector3d Hz = Hmat.getColumn(2);
1535	>
1536	>	nCells_.x() = (int) (Hx.length()) / rList_;
1537	>	nCells_.y() = (int) (Hy.length()) / rList_;
1538	>	nCells_.z() = (int) (Hz.length()) / rList_;
1539	>
1540	>	// handle small boxes where the cell offsets can end up repeating cells
1541	>
1542	>	if (nCells_.x() < 3)
1543	>	doAllPairs = true;
1544	>	if (nCells_.y() < 3)
1545	>	doAllPairs = true;
1546	>	if (nCells_.z() < 3)
1547	>	doAllPairs = true;
1548	>
1549	>	Mat3x3d invHmat = snap_->getInvHmat();
1550	>	Vector3d rs, scaled, dr;
1551	>	Vector3i whichCell;
1552	>	int cellIndex;
1553	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1554	>
1555	>	#ifdef IS_MPI
1556	>	cellListRow_.resize(nCtot);
1557	>	cellListCol_.resize(nCtot);
1558	>	#else
1559	>	cellList_.resize(nCtot);
1560	>	#endif
1561	>
1562	>	if (!doAllPairs)
1563	>	{
1564	>	#ifdef IS_MPI
1565	>
1566	>	for (int i = 0; i < nGroupsInRow_; i++)
1567	>	{
1568	>	rs = cgRowData.position[i];
1569	>
1570	>	// scaled positions relative to the box vectors
1571	>	scaled = invHmat * rs;
1572	>
1573	>	// wrap the vector back into the unit box by subtracting integer box
1574	>	// numbers
1575	>	for (int j = 0; j < 3; j++)
1576	>	{
1577	>	scaled[j] -= roundMe(scaled[j]);
1578	>	scaled[j] += 0.5;
1579	>	}
1580	>
1581	>	// find xyz-indices of cell that cutoffGroup is in.
1582	>	whichCell.x() = nCells_.x() * scaled.x();
1583	>	whichCell.y() = nCells_.y() * scaled.y();
1584	>	whichCell.z() = nCells_.z() * scaled.z();
1585	>
1586	>	// find single index of this cell:
1587	>	cellIndex = Vlinear(whichCell, nCells_);
1588	>
1589	>	// add this cutoff group to the list of groups in this cell;
1590	>	cellListRow_[cellIndex].push_back(i);
1591	>	}
1592	>	for (int i = 0; i < nGroupsInCol_; i++)
1593	>	{
1594	>	rs = cgColData.position[i];
1595	>
1596	>	// scaled positions relative to the box vectors
1597	>	scaled = invHmat * rs;
1598	>
1599	>	// wrap the vector back into the unit box by subtracting integer box
1600	>	// numbers
1601	>	for (int j = 0; j < 3; j++)
1602	>	{
1603	>	scaled[j] -= roundMe(scaled[j]);
1604	>	scaled[j] += 0.5;
1605	>	}
1606	>
1607	>	// find xyz-indices of cell that cutoffGroup is in.
1608	>	whichCell.x() = nCells_.x() * scaled.x();
1609	>	whichCell.y() = nCells_.y() * scaled.y();
1610	>	whichCell.z() = nCells_.z() * scaled.z();
1611	>
1612	>	// find single index of this cell:
1613	>	cellIndex = Vlinear(whichCell, nCells_);
1614	>
1615	>	// add this cutoff group to the list of groups in this cell;
1616	>	cellListCol_[cellIndex].push_back(i);
1617	>	}
1618	>	#else
1619	>	for (int i = 0; i < nGroups_; i++)
1620	>	{
1621	>	rs = snap_->cgData.position[i];
1622	>
1623	>	// scaled positions relative to the box vectors
1624	>	scaled = invHmat * rs;
1625	>
1626	>	// wrap the vector back into the unit box by subtracting integer box
1627	>	// numbers
1628	>	for (int j = 0; j < 3; j++)
1629	>	{
1630	>	scaled[j] -= roundMe(scaled[j]);
1631	>	scaled[j] += 0.5;
1632	>	}
1633	>
1634	>	// find xyz-indices of cell that cutoffGroup is in.
1635	>	whichCell.x() = nCells_.x() * scaled.x();
1636	>	whichCell.y() = nCells_.y() * scaled.y();
1637	>	whichCell.z() = nCells_.z() * scaled.z();
1638	>
1639	>	// find single index of this cell:
1640	>	cellIndex = Vlinear(whichCell, nCells_);
1641	>
1642	>	// add this cutoff group to the list of groups in this cell;
1643	>	cellList_[cellIndex].push_back(i);
1644	>	}
1645	>	#endif
1646	>
1647	>	for (int m1z = 0; m1z < nCells_.z(); m1z++)
1648	>	{
1649	>	for (int m1y = 0; m1y < nCells_.y(); m1y++)
1650	>	{
1651	>	for (int m1x = 0; m1x < nCells_.x(); m1x++)
1652	>	{
1653	>	Vector3i m1v(m1x, m1y, m1z);
1654	>	int m1 = Vlinear(m1v, nCells_);
1655	>
1656	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1657	>	{
1658	>
1659	>	Vector3i m2v = m1v + (*os);
1660	>
1661	>	if (m2v.x() >= nCells_.x())
1662	>	{
1663	>	m2v.x() = 0;
1664	>	} else if (m2v.x() < 0)
1665	>	{
1666	>	m2v.x() = nCells_.x() - 1;
1667	>	}
1668	>
1669	>	if (m2v.y() >= nCells_.y())
1670	>	{
1671	>	m2v.y() = 0;
1672	>	} else if (m2v.y() < 0)
1673	>	{
1674	>	m2v.y() = nCells_.y() - 1;
1675	>	}
1676	>
1677	>	if (m2v.z() >= nCells_.z())
1678	>	{
1679	>	m2v.z() = 0;
1680	>	} else if (m2v.z() < 0)
1681	>	{
1682	>	m2v.z() = nCells_.z() - 1;
1683	>	}
1684	>
1685	>	int m2 = Vlinear(m2v, nCells_);
1686	>
1687	>	#ifdef IS_MPI
1688	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1689	>	j1 != cellListRow_[m1].end(); ++j1)
1690	>	{
1691	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1692	>	j2 != cellListCol_[m2].end(); ++j2)
1693	>	{
1694	>
1695	>	// In parallel, we need to visit *all* pairs of row &
1696	>	// column indicies and will truncate later on.
1697	>	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1698	>	snap_->wrapVector(dr);
1699	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1700	>	if (dr.lengthSquare() < cuts.third)
1701	>	{
1702	>	neighborList.push_back(make_pair((*j1), (*j2)));
1703	>	}
1704	>	}
1705	>	}
1706	>	#else
1707	>
1708	>	for (vector<int>::iterator j1 = cellList_[m1].begin(); j1 != cellList_[m1].end(); ++j1)
1709	>	{
1710	>	for (vector<int>::iterator j2 = cellList_[m2].begin(); j2 != cellList_[m2].end(); ++j2)
1711	>	{
1712	>
1713	>	// Always do this if we're in different cells or if
1714	>	// we're in the same cell and the global index of the
1715	>	// j2 cutoff group is less than the j1 cutoff group
1716	>
1717	>	if (m2 != m1 || (*j2) < (*j1))
1718	>	{
1719	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1720	>	snap_->wrapVector(dr);
1721	>	cuts = getGroupCutoffs((*j1), (*j2));
1722	>	if (dr.lengthSquare() < cuts.third)
1723	>	{
1724	>	neighborList.push_back(make_pair((*j1), (*j2)));
1725	>	}
1726	>	}
1727	>	}
1728	>	}
1729	>	#endif
1730	>	}
1731	>	}
1732	>	}
1733	>	}
1734	>	} else
1735	>	{
1736	>	// branch to do all cutoff group pairs
1737	>	#ifdef IS_MPI
1738	>	for (int j1 = 0; j1 < nGroupsInRow_; j1++)
1739	>	{
1740	>	for (int j2 = 0; j2 < nGroupsInCol_; j2++)
1741	>	{
1742	>	dr = cgColData.position[j2] - cgRowData.position[j1];
1743	>	snap_->wrapVector(dr);
1744	>	cuts = getGroupCutoffs( j1, j2 );
1745	>	if (dr.lengthSquare() < cuts.third)
1746	>	{
1747	>	neighborList.push_back(make_pair(j1, j2));
1748	>	}
1749	>	}
1750	>	}
1751	>	#else
1752	>	for (int j1 = 0; j1 < nGroups_ - 1; j1++)
1753	>	{
1754	>	for (int j2 = j1 + 1; j2 < nGroups_; j2++)
1755	>	{
1756	>	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1757	>	snap_->wrapVector(dr);
1758	>	cuts = getGroupCutoffs(j1, j2);
1759	>	if (dr.lengthSquare() < cuts.third)
1760	>	{
1761	>	neighborList.push_back(make_pair(j1, j2));
1762	>	}
1763	>	}
1764	>	}
1765	>	#endif
1766	>	}
1767	>
1768	>	// save the local cutoff group positions for the check that is
1769	>	// done on each loop:
1770	>	saved_CG_positions_.clear();
1771	>	for (int i = 0; i < nGroups_; i++)
1772	>	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1773	>
1774	>	return neighborList;
1775	>	}
1776		} //end namespace OpenMD

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