ViewVC Help

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

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

Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
branches/devel_omp/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1598 by mciznick, Wed Jul 27 14:26:53 2011 UTC

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

Diff Legend

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