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

Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1579 by gezelter, Thu Jun 9 20:26:29 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	<
55	<	void ForceMatrixDecomposition::distributeInitialData() {
56	<	snap_ = sman_->getCurrentSnapshot();
57	<	storageLayout_ = sman_->getStorageLayout();
58	<	ff_ = info_->getForceField();
59	<	nLocal_ = snap_->getNumberOfAtoms();
60	<
61	<	nGroups_ = info_->getNLocalCutoffGroups();
62	<	cerr << "in dId, nGroups = " << nGroups_ << "\n";
63	<	// gather the information for atomtype IDs (atids):
64	<	identsLocal = info_->getIdentArray();
65	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
66	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
67	<	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68	<	vector<RealType> massFactorsLocal = info_->getMassFactors();
69	<	PairList excludes = info_->getExcludedInteractions();
70	<	PairList oneTwo = info_->getOneTwoInteractions();
71	<	PairList oneThree = info_->getOneThreeInteractions();
72	<	PairList oneFour = info_->getOneFourInteractions();
73	<
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	<
58	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
59	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
60	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
61	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
62	<	AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
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	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
74	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
75	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
76	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
77	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
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	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
84	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
85	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
86	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
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	<	nAtomsInRow_ = AtomCommIntRow->getSize();
94	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
95	<	nGroupsInRow_ = cgCommIntRow->getSize();
96	<	nGroupsInCol_ = cgCommIntColumn->getSize();
90	>	massFactors = info_->getMassFactors();
91
92	<	// Modify the data storage objects with the correct layouts and sizes:
93	<	atomRowData.resize(nAtomsInRow_);
94	<	atomRowData.setStorageLayout(storageLayout_);
95	<	atomColData.resize(nAtomsInCol_);
102	<	atomColData.setStorageLayout(storageLayout_);
103	<	cgRowData.resize(nGroupsInRow_);
104	<	cgRowData.setStorageLayout(DataStorage::dslPosition);
105	<	cgColData.resize(nGroupsInCol_);
106	<	cgColData.setStorageLayout(DataStorage::dslPosition);
107	<
108	<	identsRow.resize(nAtomsInRow_);
109	<	identsCol.resize(nAtomsInCol_);
110	<
111	<	AtomCommIntRow->gather(identsLocal, identsRow);
112	<	AtomCommIntColumn->gather(identsLocal, identsCol);
113	<
114	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
115	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
116	<
117	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
118	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
92	>	PairList* excludes = info_->getExcludedInteractions();
93	>	PairList* oneTwo = info_->getOneTwoInteractions();
94	>	PairList* oneThree = info_->getOneThreeInteractions();
95	>	PairList* oneFour = info_->getOneFourInteractions();
96
97	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
121	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
97	>	#ifdef IS_MPI
98
99	<	groupListRow_.clear();
100	<	groupListRow_.resize(nGroupsInRow_);
125	<	for (int i = 0; i < nGroupsInRow_; i++) {
126	<	int gid = cgRowToGlobal[i];
127	<	for (int j = 0; j < nAtomsInRow_; j++) {
128	<	int aid = AtomRowToGlobal[j];
129	<	if (globalGroupMembership[aid] == gid)
130	<	groupListRow_[i].push_back(j);
131	<	}
132	<	}
99	>	MPI::Intracomm row = rowComm.getComm();
100	>	MPI::Intracomm col = colComm.getComm();
101
102	<	groupListCol_.clear();
103	<	groupListCol_.resize(nGroupsInCol_);
104	<	for (int i = 0; i < nGroupsInCol_; i++) {
105	<	int gid = cgColToGlobal[i];
106	<	for (int j = 0; j < nAtomsInCol_; j++) {
139	<	int aid = AtomColToGlobal[j];
140	<	if (globalGroupMembership[aid] == gid)
141	<	groupListCol_[i].push_back(j);
142	<	}
143	<	}
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	<	skipsForAtom.clear();
109	<	skipsForAtom.resize(nAtomsInRow_);
110	<	toposForAtom.clear();
111	<	toposForAtom.resize(nAtomsInRow_);
112	<	topoDist.clear();
150	<	topoDist.resize(nAtomsInRow_);
151	<	for (int i = 0; i < nAtomsInRow_; i++) {
152	<	int iglob = AtomRowToGlobal[i];
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	<	for (int j = 0; j < nAtomsInCol_; j++) {
115	<	int jglob = AtomColToGlobal[j];
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	<	if (excludes.hasPair(iglob, jglob))
120	<	skipsForAtom[i].push_back(j);
121	<
122	<	if (oneTwo.hasPair(iglob, jglob)) {
161	<	toposForAtom[i].push_back(j);
162	<	topoDist[i].push_back(1);
163	<	} else {
164	<	if (oneThree.hasPair(iglob, jglob)) {
165	<	toposForAtom[i].push_back(j);
166	<	topoDist[i].push_back(2);
167	<	} else {
168	<	if (oneFour.hasPair(iglob, jglob)) {
169	<	toposForAtom[i].push_back(j);
170	<	topoDist[i].push_back(3);
171	<	}
172	<	}
173	<	}
174	<	}
175	<	}
119	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
120	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
121	>	nGroupsInRow_ = cgPlanIntRow->getSize();
122	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
123
124	<	#endif
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	<	groupList_.clear();
135	<	groupList_.resize(nGroups_);
181	<	for (int i = 0; i < nGroups_; i++) {
182	<	int gid = cgLocalToGlobal[i];
183	<	for (int j = 0; j < nLocal_; j++) {
184	<	int aid = AtomLocalToGlobal[j];
185	<	if (globalGroupMembership[aid] == gid) {
186	<	groupList_[i].push_back(j);
187	<	}
188	<	}
189	<	}
134	>	identsRow.resize(nAtomsInRow_);
135	>	identsCol.resize(nAtomsInCol_);
136
137	<	skipsForAtom.clear();
138	<	skipsForAtom.resize(nLocal_);
193	<	toposForAtom.clear();
194	<	toposForAtom.resize(nLocal_);
195	<	topoDist.clear();
196	<	topoDist.resize(nLocal_);
137	>	AtomPlanIntRow->gather(idents, identsRow);
138	>	AtomPlanIntColumn->gather(idents, identsCol);
139
140	<	for (int i = 0; i < nLocal_; i++) {
141	<	int iglob = AtomLocalToGlobal[i];
140	>	// allocate memory for the parallel objects
141	>	atypesRow.resize(nAtomsInRow_);
142	>	atypesCol.resize(nAtomsInCol_);
143
144	<	for (int j = 0; j < nLocal_; j++) {
145	<	int jglob = AtomLocalToGlobal[j];
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	<	if (excludes.hasPair(iglob, jglob))
150	<	skipsForAtom[i].push_back(j);
206	<
207	<	if (oneTwo.hasPair(iglob, jglob)) {
208	<	toposForAtom[i].push_back(j);
209	<	topoDist[i].push_back(1);
210	<	} else {
211	<	if (oneThree.hasPair(iglob, jglob)) {
212	<	toposForAtom[i].push_back(j);
213	<	topoDist[i].push_back(2);
214	<	} else {
215	<	if (oneFour.hasPair(iglob, jglob)) {
216	<	toposForAtom[i].push_back(j);
217	<	topoDist[i].push_back(3);
218	<	}
219	<	}
220	<	}
221	<	}
222	<	}
223	<
224	<	createGtypeCutoffMap();
225	<	}
226	<
227	<	void ForceMatrixDecomposition::createGtypeCutoffMap() {
149	>	pot_row.resize(nAtomsInRow_);
150	>	pot_col.resize(nAtomsInCol_);
151
152	<	RealType tol = 1e-6;
153	<	RealType rc;
154	<	int atid;
155	<	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
233	<	vector<RealType> atypeCutoff;
234	<	atypeCutoff.resize( atypes.size() );
152	>	AtomRowToGlobal.resize(nAtomsInRow_);
153	>	AtomColToGlobal.resize(nAtomsInCol_);
154	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156
157	<	for (set<AtomType*>::iterator at = atypes.begin();
158	<	at != atypes.end(); ++at){
159	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
160	<	atid = (*at)->getIdent();
161	<	atypeCutoff[atid] = rc;
162	<	}
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	<	vector<RealType> gTypeCutoffs;
173	>	cgRowToGlobal.resize(nGroupsInRow_);
174	>	cgColToGlobal.resize(nGroupsInCol_);
175	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177
178	<	// first we do a single loop over the cutoff groups to find the
179	<	// largest cutoff for any atypes present in this group.
180	<	#ifdef IS_MPI
181	<	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
182	<	groupRowToGtype.resize(nGroupsInRow_);
183	<	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
184	<	vector<int> atomListRow = getAtomsInGroupRow(cg1);
185	<	for (vector<int>::iterator ia = atomListRow.begin();
186	<	ia != atomListRow.end(); ++ia) {
187	<	int atom1 = (*ia);
188	<	atid = identsRow[atom1];
189	<	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
190	<	groupCutoffRow[cg1] = atypeCutoff[atid];
191	<	}
192	<	}
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	<	bool gTypeFound = false;
195	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
196	<	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
197	<	groupRowToGtype[cg1] = gt;
265	<	gTypeFound = true;
266	<	}
267	<	}
268	<	if (!gTypeFound) {
269	<	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
270	<	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
271	<	}
272	<
273	<	}
274	<	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
275	<	groupColToGtype.resize(nGroupsInCol_);
276	<	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
277	<	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
278	<	for (vector<int>::iterator jb = atomListCol.begin();
279	<	jb != atomListCol.end(); ++jb) {
280	<	int atom2 = (*jb);
281	<	atid = identsCol[atom2];
282	<	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
283	<	groupCutoffCol[cg2] = atypeCutoff[atid];
284	<	}
285	<	}
286	<	bool gTypeFound = false;
287	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
288	<	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
289	<	groupColToGtype[cg2] = gt;
290	<	gTypeFound = true;
291	<	}
292	<	}
293	<	if (!gTypeFound) {
294	<	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
295	<	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
296	<	}
297	<	}
298	<	#else
194	>	massFactorsRow.resize(nAtomsInRow_);
195	>	massFactorsCol.resize(nAtomsInCol_);
196	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
197	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
198
199	<	vector<RealType> groupCutoff(nGroups_, 0.0);
200	<	groupToGtype.resize(nGroups_);
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	<	cerr << "nGroups = " << nGroups_ << "\n";
213	<	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
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	<	groupCutoff[cg1] = 0.0;
226	<	vector<int> atomList = getAtomsInGroupRow(cg1);
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	<	for (vector<int>::iterator ia = atomList.begin();
236	<	ia != atomList.end(); ++ia) {
237	<	int atom1 = (*ia);
312	<	atid = identsLocal[atom1];
313	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
314	<	groupCutoff[cg1] = atypeCutoff[atid];
315	<	}
316	<	}
235	>	for (int j = 0; j < nAtomsInCol_; j++)
236	>	{
237	>	int jglob = AtomColToGlobal[j];
238
239	<	bool gTypeFound = false;
240	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
320	<	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
321	<	groupToGtype[cg1] = gt;
322	<	gTypeFound = true;
323	<	}
324	<	}
325	<	if (!gTypeFound) {
326	<	gTypeCutoffs.push_back( groupCutoff[cg1] );
327	<	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
328	<	}
329	<	}
330	<	#endif
239	>	if (excludes->hasPair(iglob, jglob))
240	>	excludesForAtom[i].push_back(j);
241
242	<	cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
243	<	// Now we find the maximum group cutoff value present in the simulation
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
335	–	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
336	–
337	–	#ifdef IS_MPI
338	–	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
264		#endif
340	–
341	–	RealType tradRcut = groupMax;
265
266	<	for (int i = 0; i < gTypeCutoffs.size();  i++) {
267	<	for (int j = 0; j < gTypeCutoffs.size();  j++) {
345	<	RealType thisRcut;
346	<	switch(cutoffPolicy_) {
347	<	case TRADITIONAL:
348	<	thisRcut = tradRcut;
349	<	break;
350	<	case MIX:
351	<	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
352	<	break;
353	<	case MAX:
354	<	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
355	<	break;
356	<	default:
357	<	sprintf(painCave.errMsg,
358	<	"ForceMatrixDecomposition::createGtypeCutoffMap "
359	<	"hit an unknown cutoff policy!\n");
360	<	painCave.severity = OPENMD_ERROR;
361	<	painCave.isFatal = 1;
362	<	simError();
363	<	break;
364	<	}
266	>	// allocate memory for the parallel objects
267	>	atypesLocal.resize(nLocal_);
268
269	<	pair<int,int> key = make_pair(i,j);
270	<	gTypeCutoffMap[key].first = thisRcut;
269	>	for (int i = 0; i < nLocal_; i++)
270	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
271
272	<	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
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	<	gTypeCutoffMap[key].second = thisRcut*thisRcut;
288	<
289	<	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
287	>	excludesForAtom.clear();
288	>	excludesForAtom.resize(nLocal_);
289	>	toposForAtom.clear();
290	>	toposForAtom.resize(nLocal_);
291	>	topoDist.clear();
292	>	topoDist.resize(nLocal_);
293
294	<	// sanity check
295	<
296	<	if (userChoseCutoff_) {
378	<	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
379	<	sprintf(painCave.errMsg,
380	<	"ForceMatrixDecomposition::createGtypeCutoffMap "
381	<	"user-specified rCut does not match computed group Cutoff\n");
382	<	painCave.severity = OPENMD_ERROR;
383	<	painCave.isFatal = 1;
384	<	simError();
385	<	}
386	<	}
387	<	}
388	<	}
389	<	}
294	>	for (int i = 0; i < nLocal_; i++)
295	>	{
296	>	int iglob = AtomLocalToGlobal[i];
297
298	+	for (int j = 0; j < nLocal_; j++)
299	+	{
300	+	int jglob = AtomLocalToGlobal[j];
301
302	<	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
303	<	int i, j;
394	<	#ifdef IS_MPI
395	<	i = groupRowToGtype[cg1];
396	<	j = groupColToGtype[cg2];
397	<	#else
398	<	i = groupToGtype[cg1];
399	<	j = groupToGtype[cg2];
400	<	#endif
401	<	return gTypeCutoffMap[make_pair(i,j)];
402	<	}
302	>	if (excludes->hasPair(iglob, jglob))
303	>	excludesForAtom[i].push_back(j);
304
305	<	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
306	<	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
307	<	if (toposForAtom[atom1][j] == atom2)
308	<	return topoDist[atom1][j];
309	<	}
310	<	return 0;
311	<	}
312	<
313	<	void ForceMatrixDecomposition::zeroWorkArrays() {
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	<	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
328	<	longRangePot_[j] = 0.0;
329	<	}
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	<	#ifdef IS_MPI
419	<	if (storageLayout_ & DataStorage::dslForce) {
420	<	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
421	<	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
422	<	}
337	>	createGtypeCutoffMap();
338
339	<	if (storageLayout_ & DataStorage::dslTorque) {
425	<	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
426	<	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
427	<	}
428	<
429	<	fill(pot_row.begin(), pot_row.end(),
430	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
339	>	}
340
341	<	fill(pot_col.begin(), pot_col.end(),
433	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434	<
435	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
341	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
342
343	<	if (storageLayout_ & DataStorage::dslParticlePot) {
344	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
345	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
346	<	}
343	>	RealType tol = 1e-6;
344	>	largestRcut_ = 0.0;
345	>	RealType rc;
346	>	int atid;
347	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
348
349	<	if (storageLayout_ & DataStorage::dslDensity) {
443	<	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
444	<	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
445	<	}
349	>	map<int, RealType> atypeCutoff;
350
351	<	if (storageLayout_ & DataStorage::dslFunctional) {
352	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
353	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
354	<	}
351	>	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::dslFunctionalDerivative) {
361	<	fill(atomRowData.functionalDerivative.begin(),
362	<	atomRowData.functionalDerivative.end(), 0.0);
363	<	fill(atomColData.functionalDerivative.begin(),
364	<	atomColData.functionalDerivative.end(), 0.0);
365	<	}
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	<	if (storageLayout_ & DataStorage::dslParticlePot) {
429	<	fill(snap_->atomData.particlePot.begin(),
430	<	snap_->atomData.particlePot.end(), 0.0);
431	<	}
432	<
433	<	if (storageLayout_ & DataStorage::dslDensity) {
434	<	fill(snap_->atomData.density.begin(),
435	<	snap_->atomData.density.end(), 0.0);
436	<	}
437	<	if (storageLayout_ & DataStorage::dslFunctional) {
438	<	fill(snap_->atomData.functional.begin(),
439	<	snap_->atomData.functional.end(), 0.0);
440	<	}
441	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
442	<	fill(snap_->atomData.functionalDerivative.begin(),
443	<	snap_->atomData.functionalDerivative.end(), 0.0);
444	<	}
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	>	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
479	–
480	–	}
458
459	+	// Now we find the maximum group cutoff value present in the simulation
460
461	<	void ForceMatrixDecomposition::distributeData()  {
462	<	snap_ = sman_->getCurrentSnapshot();
485	<	storageLayout_ = sman_->getStorageLayout();
461	>	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
462	>
463		#ifdef IS_MPI
464	<
465	<	// gather up the atomic positions
489	<	AtomCommVectorRow->gather(snap_->atomData.position,
490	<	atomRowData.position);
491	<	AtomCommVectorColumn->gather(snap_->atomData.position,
492	<	atomColData.position);
493	<
494	<	// gather up the cutoff group positions
495	<	cgCommVectorRow->gather(snap_->cgData.position,
496	<	cgRowData.position);
497	<	cgCommVectorColumn->gather(snap_->cgData.position,
498	<	cgColData.position);
499	<
500	<	// if needed, gather the atomic rotation matrices
501	<	if (storageLayout_ & DataStorage::dslAmat) {
502	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
503	<	atomRowData.aMat);
504	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
505	<	atomColData.aMat);
506	<	}
507	<
508	<	// if needed, gather the atomic eletrostatic frames
509	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
510	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
511	<	atomRowData.electroFrame);
512	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
513	<	atomColData.electroFrame);
514	<	}
515	<	#endif
516	<	}
517	<
518	<	/* collects information obtained during the pre-pair loop onto local
519	<	* data structures.
520	<	*/
521	<	void ForceMatrixDecomposition::collectIntermediateData() {
522	<	snap_ = sman_->getCurrentSnapshot();
523	<	storageLayout_ = sman_->getStorageLayout();
524	<	#ifdef IS_MPI
525	<
526	<	if (storageLayout_ & DataStorage::dslDensity) {
527	<
528	<	AtomCommRealRow->scatter(atomRowData.density,
529	<	snap_->atomData.density);
530	<
531	<	int n = snap_->atomData.density.size();
532	<	vector<RealType> rho_tmp(n, 0.0);
533	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
534	<	for (int i = 0; i < n; i++)
535	<	snap_->atomData.density[i] += rho_tmp[i];
536	<	}
537	<	#endif
538	<	}
539	<
540	<	/*
541	<	* redistributes information obtained during the pre-pair loop out to
542	<	* row and column-indexed data structures
543	<	*/
544	<	void ForceMatrixDecomposition::distributeIntermediateData() {
545	<	snap_ = sman_->getCurrentSnapshot();
546	<	storageLayout_ = sman_->getStorageLayout();
547	<	#ifdef IS_MPI
548	<	if (storageLayout_ & DataStorage::dslFunctional) {
549	<	AtomCommRealRow->gather(snap_->atomData.functional,
550	<	atomRowData.functional);
551	<	AtomCommRealColumn->gather(snap_->atomData.functional,
552	<	atomColData.functional);
553	<	}
554	<
555	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
556	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
557	<	atomRowData.functionalDerivative);
558	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
559	<	atomColData.functionalDerivative);
560	<	}
464	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
465	>	MPI::MAX);
466		#endif
562	–	}
563	–
564	–
565	–	void ForceMatrixDecomposition::collectData() {
566	–	snap_ = sman_->getCurrentSnapshot();
567	–	storageLayout_ = sman_->getStorageLayout();
568	–	#ifdef IS_MPI
569	–	int n = snap_->atomData.force.size();
570	–	vector<Vector3d> frc_tmp(n, V3Zero);
571	–
572	–	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
573	–	for (int i = 0; i < n; i++) {
574	–	snap_->atomData.force[i] += frc_tmp[i];
575	–	frc_tmp[i] = 0.0;
576	–	}
577	–
578	–	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
579	–	for (int i = 0; i < n; i++)
580	–	snap_->atomData.force[i] += frc_tmp[i];
581	–
582	–
583	–	if (storageLayout_ & DataStorage::dslTorque) {
467
468	<	int nt = snap_->atomData.force.size();
586	<	vector<Vector3d> trq_tmp(nt, V3Zero);
468	>	RealType tradRcut = groupMax;
469
470	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
471	<	for (int i = 0; i < n; i++) {
472	<	snap_->atomData.torque[i] += trq_tmp[i];
473	<	trq_tmp[i] = 0.0;
474	<	}
475	<
476	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
477	<	for (int i = 0; i < n; i++)
478	<	snap_->atomData.torque[i] += trq_tmp[i];
479	<	}
480	<
481	<	nLocal_ = snap_->getNumberOfAtoms();
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	<	vector<potVec> pot_temp(nLocal_,
495	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
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	<	// scatter/gather pot_row into the members of my column
503	<
504	<	AtomCommPotRow->scatter(pot_row, pot_temp);
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	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
518	<	pot_local += pot_temp[ii];
610	<
611	<	fill(pot_temp.begin(), pot_temp.end(),
612	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
613	<
614	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
615	<
616	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
617	<	pot_local += pot_temp[ii];
618	<
619	<	#endif
620	<	}
621	<
622	<	int ForceMatrixDecomposition::getNAtomsInRow() {
517	>	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
518	>	int i, j;
519		#ifdef IS_MPI
520	<	return nAtomsInRow_;
520	>	i = groupRowToGtype[cg1];
521	>	j = groupColToGtype[cg2];
522		#else
523	<	return nLocal_;
524	<	#endif
525	<	}
523	>	i = groupToGtype[cg1];
524	>	j = groupToGtype[cg2];
525	>	#endif
526	>	return gTypeCutoffMap[make_pair(i, j)];
527	>	}
528
529	<	/**
530	<	* returns the list of atoms belonging to this group.
531	<	*/
532	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
533	<	#ifdef IS_MPI
534	<	return groupListRow_[cg1];
535	<	#else
536	<	return groupList_[cg1];
638	<	#endif
639	<	}
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	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
538	>	void ForceMatrixDecomposition::zeroWorkArrays() {
539	>	pairwisePot = 0.0;
540	>	embeddingPot = 0.0;
541	>
542		#ifdef IS_MPI
543	<	return groupListCol_[cg2];
544	<	#else
545	<	return groupList_[cg2];
546	<	#endif
547	<	}
648	<
649	<	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
650	<	Vector3d d;
651	<
652	<	#ifdef IS_MPI
653	<	d = cgColData.position[cg2] - cgRowData.position[cg1];
654	<	#else
655	<	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
656	<	#endif
657	<
658	<	snap_->wrapVector(d);
659	<	return d;
660	<	}
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	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
555	>	fill(pot_row.begin(), pot_row.end(),
556	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
557
558	<	Vector3d d;
559	<
667	<	#ifdef IS_MPI
668	<	d = cgRowData.position[cg1] - atomRowData.position[atom1];
669	<	#else
670	<	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
671	<	#endif
558	>	fill(pot_col.begin(), pot_col.end(),
559	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
560
561	<	snap_->wrapVector(d);
562	<	return d;
563	<	}
564	<
565	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
566	<	Vector3d d;
567	<
680	<	#ifdef IS_MPI
681	<	d = cgColData.position[cg2] - atomColData.position[atom2];
682	<	#else
683	<	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
684	<	#endif
685	<
686	<	snap_->wrapVector(d);
687	<	return d;
688	<	}
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	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
570	<	#ifdef IS_MPI
571	<	return massFactorsRow[atom1];
572	<	#else
573	<	return massFactorsLocal[atom1];
695	<	#endif
696	<	}
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	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
576	<	#ifdef IS_MPI
577	<	return massFactorsCol[atom2];
578	<	#else
579	<	return massFactorsLocal[atom2];
580	<	#endif
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	<	}
584	<
585	<	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
586	<	Vector3d d;
587	<
588	<	#ifdef IS_MPI
589	<	d = atomColData.position[atom2] - atomRowData.position[atom1];
590	<	#else
591	<	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
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	<	snap_->wrapVector(d);
603	<	return d;
604	<	}
602	>	if (storageLayout_ & DataStorage::dslParticlePot)
603	>	{
604	>	fill(snap_->atomData.particlePot.begin(), snap_->atomData.particlePot.end(), 0.0);
605	>	}
606
607	<	vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
608	<	return skipsForAtom[atom1];
609	<	}
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	<	/**
725	<	* There are a number of reasons to skip a pair or a
726	<	* particle. Mostly we do this to exclude atoms who are involved in
727	<	* short range interactions (bonds, bends, torsions), but we also
728	<	* need to exclude some overcounted interactions that result from
729	<	* the parallel decomposition.
730	<	*/
731	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
732	<	int unique_id_1, unique_id_2;
624	>	}
625
626	+	void ForceMatrixDecomposition::distributeData() {
627	+	snap_ = sman_->getCurrentSnapshot();
628	+	storageLayout_ = sman_->getStorageLayout();
629		#ifdef IS_MPI
735	–	// in MPI, we have to look up the unique IDs for each atom
736	–	unique_id_1 = AtomRowToGlobal[atom1];
737	–	unique_id_2 = AtomColToGlobal[atom2];
630
631	<	// this situation should only arise in MPI simulations
632	<	if (unique_id_1 == unique_id_2) return true;
633	<
634	<	// this prevents us from doing the pair on multiple processors
635	<	if (unique_id_1 < unique_id_2) {
744	<	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
745	<	} else {
746	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
747	<	}
748	<	#else
749	<	// in the normal loop, the atom numbers are unique
750	<	unique_id_1 = atom1;
751	<	unique_id_2 = atom2;
752	<	#endif
753	<
754	<	for (vector<int>::iterator i = skipsForAtom[atom1].begin();
755	<	i != skipsForAtom[atom1].end(); ++i) {
756	<	if ( (*i) == unique_id_2 ) return true;
757	<	}
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	<	}
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	<	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
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
689	<	atomRowData.force[atom1] += fg;
690	<	#else
691	<	snap_->atomData.force[atom1] += fg;
689	>
690	>	if (storageLayout_ & DataStorage::dslDensity)
691	>	{
692	>
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	<	}
703	>	}
704
705	<	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
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	<	atomColData.force[atom2] += fg;
714	<	#else
715	<	snap_->atomData.force[atom2] += fg;
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	>	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	<	}
729	>	}
730
731	<	// filling interaction blocks with pointers
732	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
733	<	InteractionData idat;
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	<	#ifdef IS_MPI
739	<
740	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
741	<	ff_->getAtomType(identsCol[atom2]) );
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	<
746	<	if (storageLayout_ & DataStorage::dslAmat) {
747	<	idat.A1 = &(atomRowData.aMat[atom1]);
748	<	idat.A2 = &(atomColData.aMat[atom2]);
749	<	}
792	<
793	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
794	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
795	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
796	<	}
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	<	idat.t1 = &(atomRowData.torque[atom1]);
800	<	idat.t2 = &(atomColData.torque[atom2]);
801	<	}
751	>	if (storageLayout_ & DataStorage::dslTorque)
752	>	{
753
754	<	if (storageLayout_ & DataStorage::dslDensity) {
755	<	idat.rho1 = &(atomRowData.density[atom1]);
805	<	idat.rho2 = &(atomColData.density[atom2]);
806	<	}
754	>	int nt = snap_->atomData.torque.size();
755	>	vector<Vector3d> trq_tmp(nt, V3Zero);
756
757	<	if (storageLayout_ & DataStorage::dslFunctional) {
758	<	idat.frho1 = &(atomRowData.functional[atom1]);
759	<	idat.frho2 = &(atomColData.functional[atom2]);
760	<	}
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	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
765	<	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
766	<	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
767	<	}
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::dslParticlePot) {
770	<	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
820	<	idat.particlePot2 = &(atomColData.particlePot[atom2]);
821	<	}
769	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
770	>	{
771
772	<	#else
772	>	int ns = snap_->atomData.skippedCharge.size();
773	>	vector<RealType> skch_tmp(ns, 0.0);
774
775	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
776	<	ff_->getAtomType(identsLocal[atom2]) );
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	<	if (storageLayout_ & DataStorage::dslAmat) {
783	<	idat.A1 = &(snap_->atomData.aMat[atom1]);
784	<	idat.A2 = &(snap_->atomData.aMat[atom2]);
785	<	}
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	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
834	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
835	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
836	<	}
787	>	nLocal_ = snap_->getNumberOfAtoms();
788
789	<	if (storageLayout_ & DataStorage::dslTorque) {
790	<	idat.t1 = &(snap_->atomData.torque[atom1]);
840	<	idat.t2 = &(snap_->atomData.torque[atom2]);
841	<	}
789	>	vector<potVec> pot_temp(nLocal_,
790	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
791
792	<	if (storageLayout_ & DataStorage::dslDensity) {
844	<	idat.rho1 = &(snap_->atomData.density[atom1]);
845	<	idat.rho2 = &(snap_->atomData.density[atom2]);
846	<	}
792	>	// scatter/gather pot_row into the members of my column
793
794	<	if (storageLayout_ & DataStorage::dslFunctional) {
849	<	idat.frho1 = &(snap_->atomData.functional[atom1]);
850	<	idat.frho2 = &(snap_->atomData.functional[atom2]);
851	<	}
794	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
795
796	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
797	<	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
855	<	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
856	<	}
796	>	for (int ii = 0; ii < pot_temp.size(); ii++ )
797	>	pairwisePot += pot_temp[ii];
798
799	<	if (storageLayout_ & DataStorage::dslParticlePot) {
800	<	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
860	<	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
861	<	}
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
864	–	return idat;
865	–	}
807
808	<
809	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
869	<	#ifdef IS_MPI
870	<	pot_row[atom1] += 0.5 *  *(idat.pot);
871	<	pot_col[atom2] += 0.5 *  *(idat.pot);
808	>	//      cerr << "pairwisePot = " << pairwisePot << "\n";
809	>	}
810
811	<	atomRowData.force[atom1] += *(idat.f1);
812	<	atomColData.force[atom2] -= *(idat.f1);
811	>	int ForceMatrixDecomposition::getNAtomsInRow() {
812	>	#ifdef IS_MPI
813	>	return nAtomsInRow_;
814		#else
815	<	longRangePot_ += *(idat.pot);
877	<
878	<	snap_->atomData.force[atom1] += *(idat.f1);
879	<	snap_->atomData.force[atom2] -= *(idat.f1);
815	>	return nLocal_;
816		#endif
817	+	}
818
819	<	}
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	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
838	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2) {
839	>	Vector3d d;
840
887	–	InteractionData idat;
841		#ifdef IS_MPI
842	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
843	<	ff_->getAtomType(identsCol[atom2]) );
844	<
845	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
846	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
847	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
848	<	}
849	<	if (storageLayout_ & DataStorage::dslTorque) {
897	<	idat.t1 = &(atomRowData.torque[atom1]);
898	<	idat.t2 = &(atomColData.torque[atom2]);
899	<	}
900	<	#else
901	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
902	<	ff_->getAtomType(identsLocal[atom2]) );
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	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
852	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
853	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
907	<	}
908	<	if (storageLayout_ & DataStorage::dslTorque) {
909	<	idat.t1 = &(snap_->atomData.torque[atom1]);
910	<	idat.t2 = &(snap_->atomData.torque[atom2]);
911	<	}
912	<	#endif
913	<	}
851	>	snap_->wrapVector(d);
852	>	return d;
853	>	}
854
855	<	/*
856	<	* buildNeighborList
857	<	*
858	<	* first element of pair is row-indexed CutoffGroup
859	<	* second element of pair is column-indexed CutoffGroup
860	<	*/
861	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
862	<
863	<	vector<pair<int, int> > neighborList;
864	<	groupCutoffs cuts;
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	<	cellListRow_.clear();
927	<	cellListCol_.clear();
873	>	d = cgRowData.position[cg1] - atomRowData.position[atom1];
874		#else
875	<	cellList_.clear();
875	>	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
876		#endif
877
878	<	RealType rList_ = (largestRcut_ + skinThickness_);
879	<	RealType rl2 = rList_ * rList_;
880	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
935	<	Mat3x3d Hmat = snap_->getHmat();
936	<	Vector3d Hx = Hmat.getColumn(0);
937	<	Vector3d Hy = Hmat.getColumn(1);
938	<	Vector3d Hz = Hmat.getColumn(2);
878	>	snap_->wrapVector(d);
879	>	return d;
880	>	}
881
882	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
883	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
942	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
882	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2) {
883	>	Vector3d d;
884
885	<	Mat3x3d invHmat = snap_->getInvHmat();
886	<	Vector3d rs, scaled, dr;
887	<	Vector3i whichCell;
888	<	int cellIndex;
889	<	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
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	<	cellListRow_.resize(nCtot);
952	<	cellListCol_.resize(nCtot);
897	>	return massFactorsRow[atom1];
898		#else
899	<	cellList_.resize(nCtot);
899	>	return massFactors[atom1];
900		#endif
901	+	}
902
903	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
904		#ifdef IS_MPI
905	<	for (int i = 0; i < nGroupsInRow_; i++) {
906	<	rs = cgRowData.position[i];
907	<	// scaled positions relative to the box vectors
908	<	scaled = invHmat * rs;
962	<	// wrap the vector back into the unit box by subtracting integer box
963	<	// numbers
964	<	for (int j = 0; j < 3; j++)
965	<	scaled[j] -= roundMe(scaled[j]);
966	<
967	<	// find xyz-indices of cell that cutoffGroup is in.
968	<	whichCell.x() = nCells_.x() * scaled.x();
969	<	whichCell.y() = nCells_.y() * scaled.y();
970	<	whichCell.z() = nCells_.z() * scaled.z();
905	>	return massFactorsCol[atom2];
906	>	#else
907	>	return massFactors[atom2];
908	>	#endif
909
910	<	// find single index of this cell:
973	<	cellIndex = Vlinear(whichCell, nCells_);
974	<	// add this cutoff group to the list of groups in this cell;
975	<	cellListRow_[cellIndex].push_back(i);
976	<	}
910	>	}
911
912	<	for (int i = 0; i < nGroupsInCol_; i++) {
913	<	rs = cgColData.position[i];
980	<	// scaled positions relative to the box vectors
981	<	scaled = invHmat * rs;
982	<	// wrap the vector back into the unit box by subtracting integer box
983	<	// numbers
984	<	for (int j = 0; j < 3; j++)
985	<	scaled[j] -= roundMe(scaled[j]);
912	>	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2) {
913	>	Vector3d d;
914
915	<	// find xyz-indices of cell that cutoffGroup is in.
916	<	whichCell.x() = nCells_.x() * scaled.x();
989	<	whichCell.y() = nCells_.y() * scaled.y();
990	<	whichCell.z() = nCells_.z() * scaled.z();
991	<
992	<	// find single index of this cell:
993	<	cellIndex = Vlinear(whichCell, nCells_);
994	<	// add this cutoff group to the list of groups in this cell;
995	<	cellListCol_[cellIndex].push_back(i);
996	<	}
915	>	#ifdef IS_MPI
916	>	d = atomColData.position[atom2] - atomRowData.position[atom1];
917		#else
918	<	for (int i = 0; i < nGroups_; i++) {
919	<	rs = snap_->cgData.position[i];
1000	<	// scaled positions relative to the box vectors
1001	<	scaled = invHmat * rs;
1002	<	// wrap the vector back into the unit box by subtracting integer box
1003	<	// numbers
1004	<	for (int j = 0; j < 3; j++)
1005	<	scaled[j] -= roundMe(scaled[j]);
918	>	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
919	>	#endif
920
921	<	// find xyz-indices of cell that cutoffGroup is in.
922	<	whichCell.x() = nCells_.x() * scaled.x();
923	<	whichCell.y() = nCells_.y() * scaled.y();
1010	<	whichCell.z() = nCells_.z() * scaled.z();
921	>	snap_->wrapVector(d);
922	>	return d;
923	>	}
924
925	<	// find single index of this cell:
926	<	cellIndex = Vlinear(whichCell, nCells_);
927	<	// add this cutoff group to the list of groups in this cell;
1015	<	cellList_[cellIndex].push_back(i);
1016	<	}
1017	<	#endif
925	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
926	>	return excludesForAtom[atom1];
927	>	}
928
929	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
930	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
931	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
932	<	Vector3i m1v(m1x, m1y, m1z);
933	<	int m1 = Vlinear(m1v, nCells_);
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	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
937	<	os != cellOffsets_.end(); ++os) {
938	<
939	<	Vector3i m2v = m1v + (*os);
940	<
1030	<	if (m2v.x() >= nCells_.x()) {
1031	<	m2v.x() = 0;
1032	<	} else if (m2v.x() < 0) {
1033	<	m2v.x() = nCells_.x() - 1;
1034	<	}
1035	<
1036	<	if (m2v.y() >= nCells_.y()) {
1037	<	m2v.y() = 0;
1038	<	} else if (m2v.y() < 0) {
1039	<	m2v.y() = nCells_.y() - 1;
1040	<	}
1041	<
1042	<	if (m2v.z() >= nCells_.z()) {
1043	<	m2v.z() = 0;
1044	<	} else if (m2v.z() < 0) {
1045	<	m2v.z() = nCells_.z() - 1;
1046	<	}
1047	<
1048	<	int m2 = Vlinear (m2v, nCells_);
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	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
971	<	j1 != cellListRow_[m1].end(); ++j1) {
972	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
973	<	j2 != cellListCol_[m2].end(); ++j2) {
974	<
975	<	// Always do this if we're in different cells or if
1057	<	// we're in the same cell and the global index of the
1058	<	// j2 cutoff group is less than the j1 cutoff group
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	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
978	<	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
979	<	snap_->wrapVector(dr);
980	<	cuts = getGroupCutoffs( (*j1), (*j2) );
981	<	if (dr.lengthSquare() < cuts.third) {
982	<	neighborList.push_back(make_pair((*j1), (*j2)));
983	<	}
984	<	}
985	<	}
986	<	}
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	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
991	<	j1 != cellList_[m1].end(); ++j1) {
992	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1074	<	j2 != cellList_[m2].end(); ++j2) {
1075	<
1076	<	// Always do this if we're in different cells or if
1077	<	// we're in the same cell and the global index of the
1078	<	// j2 cutoff group is less than the j1 cutoff group
990	>	snap_->atomData.force[atom1] += fg;
991	>	#endif
992	>	}
993
994	<	if (m2 != m1 || (*j2) < (*j1)) {
995	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
996	<	snap_->wrapVector(dr);
997	<	cuts = getGroupCutoffs( (*j1), (*j2) );
998	<	if (dr.lengthSquare() < cuts.third) {
1085	<	neighborList.push_back(make_pair((*j1), (*j2)));
1086	<	}
1087	<	}
1088	<	}
1089	<	}
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	<	}
1092	<	}
1093	<	}
1094	<	}
1000	>	}
1001
1002	<	// save the local cutoff group positions for the check that is
1003	<	// done on each loop:
1098	<	saved_CG_positions_.clear();
1099	<	for (int i = 0; i < nGroups_; i++)
1100	<	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1002	>	// filling interaction blocks with pointers
1003	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, int atom1, int atom2) {
1004
1005	<	return neighborList;
1006	<	}
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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