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

Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs.
branches/devel_omp/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1599 by mciznick, Fri Jul 29 19:03:36 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	<	// gather the information for atomtype IDs (atids):
63	<	identsLocal = info_->getIdentArray();
64	<	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	<
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();
93	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
94	<	nGroupsInRow_ = cgCommIntRow->getSize();
95	<	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_);
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.resize(nAtomsInRow_);
108	<	identsCol.resize(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);
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);
120	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
97	>	#ifdef IS_MPI
98
99	<	groupListRow_.clear();
100	<	groupListRow_.resize(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	<	}
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++) {
138	<	int aid = AtomColToGlobal[j];
139	<	if (globalGroupMembership[aid] == gid)
140	<	groupListCol_[i].push_back(j);
141	<	}
142	<	}
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	<	skipsForRowAtom.clear();
109	<	skipsForRowAtom.resize(nAtomsInRow_);
110	<	for (int i = 0; i < nAtomsInRow_; i++) {
111	<	int iglob = AtomRowToGlobal[i];
112	<	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	<	}
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	<	toposForRowAtom.clear();
115	<	toposForRowAtom.resize(nAtomsInRow_);
116	<	for (int i = 0; i < nAtomsInRow_; i++) {
117	<	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	<	}
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	<	#endif
120	<	groupList_.clear();
121	<	groupList_.resize(nGroups_);
122	<	for (int i = 0; i < nGroups_; i++) {
184	<	int gid = cgLocalToGlobal[i];
185	<	for (int j = 0; j < nLocal_; j++) {
186	<	int aid = AtomLocalToGlobal[j];
187	<	if (globalGroupMembership[aid] == gid) {
188	<	groupList_[i].push_back(j);
119	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
120	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
121	>	nGroupsInRow_ = cgPlanIntRow->getSize();
122	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
123
124	<	}
125	<	}
126	<	}
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	<	skipsForLocalAtom.clear();
135	<	skipsForLocalAtom.resize(nLocal_);
134	>	identsRow.resize(nAtomsInRow_);
135	>	identsCol.resize(nAtomsInCol_);
136
137	<	for (int i = 0; i < nLocal_; i++) {
138	<	int iglob = AtomLocalToGlobal[i];
199	<	for (int j = 0; j < nLocal_; j++) {
200	<	int jglob = AtomLocalToGlobal[j];
201	<	if (excludes.hasPair(iglob, jglob))
202	<	skipsForLocalAtom[i].push_back(j);
203	<	}
204	<	}
205	<	toposForLocalAtom.clear();
206	<	toposForLocalAtom.resize(nLocal_);
207	<	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	<	}
137	>	AtomPlanIntRow->gather(idents, identsRow);
138	>	AtomPlanIntColumn->gather(idents, identsCol);
139
140	<	}
141	<
142	<	void ForceMatrixDecomposition::createGtypeCutoffMap() {
140	>	// allocate memory for the parallel objects
141	>	atypesRow.resize(nAtomsInRow_);
142	>	atypesCol.resize(nAtomsInCol_);
143
144	<	RealType tol = 1e-6;
145	<	RealType rc;
146	<	int atid;
147	<	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
238	<	vector<RealType> atypeCutoff;
239	<	atypeCutoff.resize( atypes.size() );
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	<	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
150	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
243	<	atid = (*at)->getIdent();
244	<	atypeCutoff[atid] = rc;
245	<	}
149	>	pot_row.resize(nAtomsInRow_);
150	>	pot_col.resize(nAtomsInCol_);
151
152	<	vector<RealType> gTypeCutoffs;
152	>	AtomRowToGlobal.resize(nAtomsInRow_);
153	>	AtomColToGlobal.resize(nAtomsInCol_);
154	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156
157	<	// first we do a single loop over the cutoff groups to find the
158	<	// largest cutoff for any atypes present in this group.
159	<	#ifdef IS_MPI
160	<	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
161	<	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
162	<	vector<int> atomListRow = getAtomsInGroupRow(cg1);
163	<	for (vector<int>::iterator ia = atomListRow.begin();
164	<	ia != atomListRow.end(); ++ia) {
165	<	int atom1 = (*ia);
166	<	atid = identsRow[atom1];
167	<	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
168	<	groupCutoffRow[cg1] = atypeCutoff[atid];
169	<	}
170	<	}
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	<	bool gTypeFound = false;
174	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
175	<	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
176	<	groupRowToGtype[cg1] = gt;
268	<	gTypeFound = true;
269	<	}
270	<	}
271	<	if (!gTypeFound) {
272	<	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
273	<	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
274	<	}
275	<
276	<	}
277	<	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
278	<	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
279	<	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
280	<	for (vector<int>::iterator jb = atomListCol.begin();
281	<	jb != atomListCol.end(); ++jb) {
282	<	int atom2 = (*jb);
283	<	atid = identsCol[atom2];
284	<	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
285	<	groupCutoffCol[cg2] = atypeCutoff[atid];
286	<	}
287	<	}
288	<	bool gTypeFound = false;
289	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
290	<	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
291	<	groupColToGtype[cg2] = gt;
292	<	gTypeFound = true;
293	<	}
294	<	}
295	<	if (!gTypeFound) {
296	<	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
297	<	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
298	<	}
299	<	}
300	<	#else
301	<	vector<RealType> groupCutoff(nGroups_, 0.0);
302	<	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
303	<	groupCutoff[cg1] = 0.0;
304	<	vector<int> atomList = getAtomsInGroupRow(cg1);
305	<	for (vector<int>::iterator ia = atomList.begin();
306	<	ia != atomList.end(); ++ia) {
307	<	int atom1 = (*ia);
308	<	atid = identsLocal[atom1];
309	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
310	<	groupCutoff[cg1] = atypeCutoff[atid];
311	<	}
312	<	}
173	>	cgRowToGlobal.resize(nGroupsInRow_);
174	>	cgColToGlobal.resize(nGroupsInCol_);
175	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177
178	<	bool gTypeFound = false;
179	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
180	<	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
181	<	groupToGtype[cg1] = gt;
182	<	gTypeFound = true;
183	<	}
184	<	}
185	<	if (!gTypeFound) {
186	<	gTypeCutoffs.push_back( groupCutoff[cg1] );
187	<	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
188	<	}
189	<	}
190	<	#endif
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	<	// Now we find the maximum group cutoff value present in the simulation
194	>	massFactorsRow.resize(nAtomsInRow_);
195	>	massFactorsCol.resize(nAtomsInCol_);
196	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
197	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
198
199	<	vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
200	<	RealType groupMax = *groupMaxLoc;
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	<	#ifdef IS_MPI
213	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
214	<	#endif
215	<
216	<	RealType tradRcut = groupMax;
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	<	for (int i = 0; i < gTypeCutoffs.size();  i++) {
226	<	for (int j = 0; j < gTypeCutoffs.size();  j++) {
227	<
228	<	RealType thisRcut;
229	<	switch(cutoffPolicy_) {
230	<	case TRADITIONAL:
231	<	thisRcut = tradRcut;
232	<	case MIX:
233	<	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
348	<	case MAX:
349	<	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
350	<	default:
351	<	sprintf(painCave.errMsg,
352	<	"ForceMatrixDecomposition::createGtypeCutoffMap "
353	<	"hit an unknown cutoff policy!\n");
354	<	painCave.severity = OPENMD_ERROR;
355	<	painCave.isFatal = 1;
356	<	simError();
357	<	}
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	<	pair<int,int> key = make_pair(i,j);
236	<	gTypeCutoffMap[key].first = thisRcut;
235	>	for (int j = 0; j < nAtomsInCol_; j++)
236	>	{
237	>	int jglob = AtomColToGlobal[j];
238
239	<	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
239	>	if (excludes->hasPair(iglob, jglob))
240	>	excludesForAtom[i].push_back(j);
241
242	<	gTypeCutoffMap[key].second = thisRcut*thisRcut;
243	<
244	<	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
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
264	<	// sanity check
369	<
370	<	if (userChoseCutoff_) {
371	<	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
372	<	sprintf(painCave.errMsg,
373	<	"ForceMatrixDecomposition::createGtypeCutoffMap "
374	<	"user-specified rCut does not match computed group Cutoff\n");
375	<	painCave.severity = OPENMD_ERROR;
376	<	painCave.isFatal = 1;
377	<	simError();
378	<	}
379	<	}
380	<	}
381	<	}
382	<	}
264	>	#endif
265
266	+	// allocate memory for the parallel objects
267	+	atypesLocal.resize(nLocal_);
268
269	<	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
270	<	int i, j;
269	>	for (int i = 0; i < nLocal_; i++)
270	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
271
272	<	#ifdef IS_MPI
273	<	i = groupRowToGtype[cg1];
274	<	j = groupColToGtype[cg2];
275	<	#else
276	<	i = groupToGtype[cg1];
277	<	j = groupToGtype[cg2];
278	<	#endif
279	<
280	<	return gTypeCutoffMap[make_pair(i,j)];
281	<	}
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	+	excludesForAtom.clear();
288	+	excludesForAtom.resize(nLocal_);
289	+	toposForAtom.clear();
290	+	toposForAtom.resize(nLocal_);
291	+	topoDist.clear();
292	+	topoDist.resize(nLocal_);
293
294	<	void ForceMatrixDecomposition::zeroWorkArrays() {
294	>	for (int i = 0; i < nLocal_; i++)
295	>	{
296	>	int iglob = AtomLocalToGlobal[i];
297
298	<	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
299	<	longRangePot_[j] = 0.0;
300	<	}
298	>	for (int j = 0; j < nLocal_; j++)
299	>	{
300	>	int jglob = AtomLocalToGlobal[j];
301	>
302	>	if (excludes->hasPair(iglob, jglob))
303	>	excludesForAtom[i].push_back(j);
304	>
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	<	#ifdef IS_MPI
328	<	if (storageLayout_ & DataStorage::dslForce) {
329	<	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
330	<	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
331	<	}
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	<	if (storageLayout_ & DataStorage::dslTorque) {
413	<	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
414	<	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
415	<	}
416	<
417	<	fill(pot_row.begin(), pot_row.end(),
418	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
337	>	createGtypeCutoffMap();
338
339	<	fill(pot_col.begin(), pot_col.end(),
421	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422	<
423	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
339	>	}
340
341	<	if (storageLayout_ & DataStorage::dslParticlePot) {
426	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
427	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
428	<	}
341	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
342
343	<	if (storageLayout_ & DataStorage::dslDensity) {
344	<	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
345	<	fill(atomColData.density.begin(), atomColData.density.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::dslFunctional) {
436	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
437	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
438	<	}
349	>	map<int, RealType> atypeCutoff;
350
351	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
352	<	fill(atomRowData.functionalDerivative.begin(),
353	<	atomRowData.functionalDerivative.end(), 0.0);
354	<	fill(atomColData.functionalDerivative.begin(),
355	<	atomColData.functionalDerivative.end(), 0.0);
356	<	}
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	+	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
467	–
468	–	}
458
459	+	// Now we find the maximum group cutoff value present in the simulation
460
461	<	void ForceMatrixDecomposition::distributeData()  {
462	<	snap_ = sman_->getCurrentSnapshot();
473	<	storageLayout_ = sman_->getStorageLayout();
461	>	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
462	>
463		#ifdef IS_MPI
464	<
465	<	// gather up the atomic positions
477	<	AtomCommVectorRow->gather(snap_->atomData.position,
478	<	atomRowData.position);
479	<	AtomCommVectorColumn->gather(snap_->atomData.position,
480	<	atomColData.position);
481	<
482	<	// gather up the cutoff group positions
483	<	cgCommVectorRow->gather(snap_->cgData.position,
484	<	cgRowData.position);
485	<	cgCommVectorColumn->gather(snap_->cgData.position,
486	<	cgColData.position);
487	<
488	<	// if needed, gather the atomic rotation matrices
489	<	if (storageLayout_ & DataStorage::dslAmat) {
490	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
491	<	atomRowData.aMat);
492	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
493	<	atomColData.aMat);
494	<	}
495	<
496	<	// if needed, gather the atomic eletrostatic frames
497	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
498	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
499	<	atomRowData.electroFrame);
500	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
501	<	atomColData.electroFrame);
502	<	}
503	<	#endif
504	<	}
505	<
506	<	/* collects information obtained during the pre-pair loop onto local
507	<	* data structures.
508	<	*/
509	<	void ForceMatrixDecomposition::collectIntermediateData() {
510	<	snap_ = sman_->getCurrentSnapshot();
511	<	storageLayout_ = sman_->getStorageLayout();
512	<	#ifdef IS_MPI
513	<
514	<	if (storageLayout_ & DataStorage::dslDensity) {
515	<
516	<	AtomCommRealRow->scatter(atomRowData.density,
517	<	snap_->atomData.density);
518	<
519	<	int n = snap_->atomData.density.size();
520	<	vector<RealType> rho_tmp(n, 0.0);
521	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
522	<	for (int i = 0; i < n; i++)
523	<	snap_->atomData.density[i] += rho_tmp[i];
524	<	}
464	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
465	>	MPI::MAX);
466		#endif
526	–	}
467
468	<	/*
529	<	* redistributes information obtained during the pre-pair loop out to
530	<	* row and column-indexed data structures
531	<	*/
532	<	void ForceMatrixDecomposition::distributeIntermediateData() {
533	<	snap_ = sman_->getCurrentSnapshot();
534	<	storageLayout_ = sman_->getStorageLayout();
535	<	#ifdef IS_MPI
536	<	if (storageLayout_ & DataStorage::dslFunctional) {
537	<	AtomCommRealRow->gather(snap_->atomData.functional,
538	<	atomRowData.functional);
539	<	AtomCommRealColumn->gather(snap_->atomData.functional,
540	<	atomColData.functional);
541	<	}
542	<
543	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
544	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
545	<	atomRowData.functionalDerivative);
546	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
547	<	atomColData.functionalDerivative);
548	<	}
549	<	#endif
550	<	}
551	<
552	<
553	<	void ForceMatrixDecomposition::collectData() {
554	<	snap_ = sman_->getCurrentSnapshot();
555	<	storageLayout_ = sman_->getStorageLayout();
556	<	#ifdef IS_MPI
557	<	int n = snap_->atomData.force.size();
558	<	vector<Vector3d> frc_tmp(n, V3Zero);
559	<
560	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
561	<	for (int i = 0; i < n; i++) {
562	<	snap_->atomData.force[i] += frc_tmp[i];
563	<	frc_tmp[i] = 0.0;
564	<	}
565	<
566	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
567	<	for (int i = 0; i < n; i++)
568	<	snap_->atomData.force[i] += frc_tmp[i];
569	<
570	<
571	<	if (storageLayout_ & DataStorage::dslTorque) {
468	>	RealType tradRcut = groupMax;
469
470	<	int nt = snap_->atomData.force.size();
471	<	vector<Vector3d> trq_tmp(nt, V3Zero);
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	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
495	<	for (int i = 0; i < n; i++) {
496	<	snap_->atomData.torque[i] += trq_tmp[i];
497	<	trq_tmp[i] = 0.0;
498	<	}
499	<
500	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
583	<	for (int i = 0; i < n; i++)
584	<	snap_->atomData.torque[i] += trq_tmp[i];
585	<	}
586	<
587	<	nLocal_ = snap_->getNumberOfAtoms();
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	<	vector<potVec> pot_temp(nLocal_,
503	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
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	<	// scatter/gather pot_row into the members of my column
518	<
594	<	AtomCommPotRow->scatter(pot_row, pot_temp);
595	<
596	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
597	<	pot_local += pot_temp[ii];
598	<
599	<	fill(pot_temp.begin(), pot_temp.end(),
600	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
601	<
602	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
603	<
604	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
605	<	pot_local += pot_temp[ii];
606	<
607	<	#endif
608	<	}
609	<
610	<	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];
626	<	#endif
627	<	}
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){
539	<	#ifdef IS_MPI
540	<	return groupListCol_[cg2];
632	<	#else
633	<	return groupList_[cg2];
634	<	#endif
635	<	}
636	<
637	<	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
638	<	Vector3d d;
639	<
640	<	#ifdef IS_MPI
641	<	d = cgColData.position[cg2] - cgRowData.position[cg1];
642	<	#else
643	<	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
644	<	#endif
645	<
646	<	snap_->wrapVector(d);
647	<	return d;
648	<	}
538	>	void ForceMatrixDecomposition::zeroWorkArrays() {
539	>	pairwisePot = 0.0;
540	>	embeddingPot = 0.0;
541
650	–
651	–	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
652	–
653	–	Vector3d d;
654	–
542		#ifdef IS_MPI
543	<	d = cgRowData.position[cg1] - atomRowData.position[atom1];
544	<	#else
545	<	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
546	<	#endif
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	<	snap_->wrapVector(d);
550	<	return d;
551	<	}
552	<
553	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
666	<	Vector3d d;
667	<
668	<	#ifdef IS_MPI
669	<	d = cgColData.position[cg2] - atomColData.position[atom2];
670	<	#else
671	<	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
672	<	#endif
673	<
674	<	snap_->wrapVector(d);
675	<	return d;
676	<	}
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	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
556	<	#ifdef IS_MPI
680	<	return massFactorsRow[atom1];
681	<	#else
682	<	return massFactorsLocal[atom1];
683	<	#endif
684	<	}
685	<
686	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
687	<	#ifdef IS_MPI
688	<	return massFactorsCol[atom2];
689	<	#else
690	<	return massFactorsLocal[atom2];
691	<	#endif
692	<
693	<	}
694	<
695	<	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
696	<	Vector3d d;
697	<
698	<	#ifdef IS_MPI
699	<	d = atomColData.position[atom2] - atomRowData.position[atom1];
700	<	#else
701	<	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
702	<	#endif
703	<
704	<	snap_->wrapVector(d);
705	<	return d;
706	<	}
555	>	fill(pot_row.begin(), pot_row.end(),
556	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
557
558	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
559	<	#ifdef IS_MPI
710	<	return skipsForRowAtom[atom1];
711	<	#else
712	<	return skipsForLocalAtom[atom1];
713	<	#endif
714	<	}
558	>	fill(pot_col.begin(), pot_col.end(),
559	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
560
561	<	/**
562	<	* There are a number of reasons to skip a pair or a
563	<	* particle. Mostly we do this to exclude atoms who are involved in
564	<	* short range interactions (bonds, bends, torsions), but we also
565	<	* need to exclude some overcounted interactions that result from
566	<	* the parallel decomposition.
567	<	*/
723	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
724	<	int unique_id_1, unique_id_2;
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	<	#ifdef IS_MPI
570	<	// in MPI, we have to look up the unique IDs for each atom
571	<	unique_id_1 = AtomRowToGlobal[atom1];
572	<	unique_id_2 = AtomColToGlobal[atom2];
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	<	// this situation should only arise in MPI simulations
576	<	if (unique_id_1 == unique_id_2) return true;
577	<
578	<	// this prevents us from doing the pair on multiple processors
579	<	if (unique_id_1 < unique_id_2) {
580	<	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
581	<	} else {
738	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
739	<	}
740	<	#else
741	<	// in the normal loop, the atom numbers are unique
742	<	unique_id_1 = atom1;
743	<	unique_id_2 = atom2;
744	<	#endif
745	<
746	<	#ifdef IS_MPI
747	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748	<	i != skipsForRowAtom[atom1].end(); ++i) {
749	<	if ( (*i) == unique_id_2 ) return true;
750	<	}
751	<	#else
752	<	for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
753	<	i != skipsForLocalAtom[atom1].end(); ++i) {
754	<	if ( (*i) == unique_id_2 ) return true;
755	<	}
756	<	#endif
757	<	}
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	<	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
584	<
585	<	#ifdef IS_MPI
586	<	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
587	<	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
588	<	}
589	<	#else
766	<	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
767	<	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
768	<	}
769	<	#endif
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	<	// zero is default for unconnected (i.e. normal) pair interactions
592	<	return 0;
593	<	}
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
775	–	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
776	–	#ifdef IS_MPI
777	–	atomRowData.force[atom1] += fg;
778	–	#else
779	–	snap_->atomData.force[atom1] += fg;
599		#endif
600	<	}
600	>	// even in parallel, we need to zero out the local arrays:
601
602	<	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
603	<	#ifdef IS_MPI
604	<	atomColData.force[atom2] += fg;
605	<	#else
787	<	snap_->atomData.force[atom2] += fg;
788	<	#endif
789	<	}
602	>	if (storageLayout_ & DataStorage::dslParticlePot)
603	>	{
604	>	fill(snap_->atomData.particlePot.begin(), snap_->atomData.particlePot.end(), 0.0);
605	>	}
606
607	<	// filling interaction blocks with pointers
608	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
609	<	InteractionData idat;
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	+	}
625	+
626	+	void ForceMatrixDecomposition::distributeData() {
627	+	snap_ = sman_->getCurrentSnapshot();
628	+	storageLayout_ = sman_->getStorageLayout();
629		#ifdef IS_MPI
796	–
797	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
798	–	ff_->getAtomType(identsCol[atom2]) );
630
631	<
632	<	if (storageLayout_ & DataStorage::dslAmat) {
633	<	idat.A1 = &(atomRowData.aMat[atom1]);
634	<	idat.A2 = &(atomColData.aMat[atom2]);
635	<	}
805	<
806	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
807	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
808	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
809	<	}
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	<	if (storageLayout_ & DataStorage::dslTorque) {
812	<	idat.t1 = &(atomRowData.torque[atom1]);
813	<	idat.t2 = &(atomColData.torque[atom2]);
814	<	}
637	>	// gather up the cutoff group positions
638
639	<	if (storageLayout_ & DataStorage::dslDensity) {
640	<	idat.rho1 = &(atomRowData.density[atom1]);
641	<	idat.rho2 = &(atomColData.density[atom2]);
642	<	}
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	<	if (storageLayout_ & DataStorage::dslFunctional) {
646	<	idat.frho1 = &(atomRowData.functional[atom1]);
823	<	idat.frho2 = &(atomColData.functional[atom2]);
824	<	}
645	>	cgPlanVectorRow->gather(snap_->cgData.position,
646	>	cgRowData.position);
647
648	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
649	<	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
650	<	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
651	<	}
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	<	if (storageLayout_ & DataStorage::dslParticlePot) {
655	<	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
656	<	idat.particlePot2 = &(atomColData.particlePot[atom2]);
657	<	}
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	<	#else
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	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
671	<	ff_->getAtomType(identsLocal[atom2]) );
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	<	if (storageLayout_ & DataStorage::dslAmat) {
680	<	idat.A1 = &(snap_->atomData.aMat[atom1]);
843	<	idat.A2 = &(snap_->atomData.aMat[atom2]);
844	<	}
679	>	#endif
680	>	}
681
682	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
683	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
684	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
685	<	}
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
690	<	if (storageLayout_ & DataStorage::dslTorque) {
691	<	idat.t1 = &(snap_->atomData.torque[atom1]);
853	<	idat.t2 = &(snap_->atomData.torque[atom2]);
854	<	}
690	>	if (storageLayout_ & DataStorage::dslDensity)
691	>	{
692
693	<	if (storageLayout_ & DataStorage::dslDensity) {
694	<	idat.rho1 = &(snap_->atomData.density[atom1]);
858	<	idat.rho2 = &(snap_->atomData.density[atom2]);
859	<	}
693	>	AtomPlanRealRow->scatter(atomRowData.density,
694	>	snap_->atomData.density);
695
696	<	if (storageLayout_ & DataStorage::dslFunctional) {
697	<	idat.frho1 = &(snap_->atomData.functional[atom1]);
698	<	idat.frho2 = &(snap_->atomData.functional[atom2]);
699	<	}
700	<
701	<	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
867	<	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
868	<	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
869	<	}
870	<
871	<	if (storageLayout_ & DataStorage::dslParticlePot) {
872	<	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
873	<	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
874	<	}
875	<
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	<	return idat;
878	<	}
703	>	}
704
705	<
706	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
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	<	pot_row[atom1] += 0.5 *  *(idat.pot);
714	<	pot_col[atom2] += 0.5 *  *(idat.pot);
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	<	atomRowData.force[atom1] += *(idat.f1);
722	<	atomColData.force[atom2] -= *(idat.f1);
723	<	#else
724	<	longRangePot_ += *(idat.pot);
725	<
726	<	snap_->atomData.force[atom1] += *(idat.f1);
727	<	snap_->atomData.force[atom2] -= *(idat.f1);
721	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
722	>	{
723	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
724	>	atomRowData.functionalDerivative);
725	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
726	>	atomColData.functionalDerivative);
727	>	}
728		#endif
729	+	}
730
731	<	}
731	>	void ForceMatrixDecomposition::collectData() {
732	>	snap_ = sman_->getCurrentSnapshot();
733	>	storageLayout_ = sman_->getStorageLayout();
734	>	#ifdef IS_MPI
735	>	int n = snap_->atomData.force.size();
736	>	vector<Vector3d> frc_tmp(n, V3Zero);
737
738	+	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
739	+	for (int i = 0; i < n; i++)
740	+	{
741	+	snap_->atomData.force[i] += frc_tmp[i];
742	+	frc_tmp[i] = 0.0;
743	+	}
744
745	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
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	<	InteractionData idat;
752	<	#ifdef IS_MPI
902	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
903	<	ff_->getAtomType(identsCol[atom2]) );
751	>	if (storageLayout_ & DataStorage::dslTorque)
752	>	{
753
754	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
755	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
907	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
908	<	}
909	<	if (storageLayout_ & DataStorage::dslTorque) {
910	<	idat.t1 = &(atomRowData.torque[atom1]);
911	<	idat.t2 = &(atomColData.torque[atom2]);
912	<	}
913	<	#else
914	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
915	<	ff_->getAtomType(identsLocal[atom2]) );
754	>	int nt = snap_->atomData.torque.size();
755	>	vector<Vector3d> trq_tmp(nt, V3Zero);
756
757	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
758	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
759	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
760	<	}
761	<	if (storageLayout_ & DataStorage::dslTorque) {
762	<	idat.t1 = &(snap_->atomData.torque[atom1]);
923	<	idat.t2 = &(snap_->atomData.torque[atom2]);
924	<	}
925	<	#endif
926	<	}
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	<	/*
765	<	* buildNeighborList
766	<	*
767	<	* first element of pair is row-indexed CutoffGroup
768	<	* second element of pair is column-indexed CutoffGroup
769	<	*/
770	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
771	<
772	<	vector<pair<int, int> > neighborList;
773	<	groupCutoffs cuts;
774	<	#ifdef IS_MPI
775	<	cellListRow_.clear();
776	<	cellListCol_.clear();
764	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
765	>	for (int i = 0; i < nt; i++)
766	>	snap_->atomData.torque[i] += trq_tmp[i];
767	>	}
768	>
769	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
770	>	{
771	>
772	>	int ns = snap_->atomData.skippedCharge.size();
773	>	vector<RealType> skch_tmp(ns, 0.0);
774	>
775	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
776	>	for (int i = 0; i < ns; i++)
777	>	{
778	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
779	>	skch_tmp[i] = 0.0;
780	>	}
781	>
782	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
783	>	for (int i = 0; i < ns; i++)
784	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
785	>	}
786	>
787	>	nLocal_ = snap_->getNumberOfAtoms();
788	>
789	>	vector<potVec> pot_temp(nLocal_,
790	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
791	>
792	>	// scatter/gather pot_row into the members of my column
793	>
794	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
795	>
796	>	for (int ii = 0; ii < pot_temp.size(); ii++ )
797	>	pairwisePot += pot_temp[ii];
798	>
799	>	fill(pot_temp.begin(), pot_temp.end(),
800	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
801	>
802	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
803	>
804	>	for (int ii = 0; ii < pot_temp.size(); ii++ )
805	>	pairwisePot += pot_temp[ii];
806	>	#endif
807	>
808	>	//      cerr << "pairwisePot = " << pairwisePot << "\n";
809	>	}
810	>
811	>	int ForceMatrixDecomposition::getNAtomsInRow() {
812	>	#ifdef IS_MPI
813	>	return nAtomsInRow_;
814		#else
815	<	cellList_.clear();
815	>	return nLocal_;
816		#endif
817	+	}
818
819	<	RealType rList_ = (largestRcut_ + skinThickness_);
820	<	RealType rl2 = rList_ * rList_;
821	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
822	<	Mat3x3d Hmat = snap_->getHmat();
823	<	Vector3d Hx = Hmat.getColumn(0);
824	<	Vector3d Hy = Hmat.getColumn(1);
825	<	Vector3d Hz = Hmat.getColumn(2);
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	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
831	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
832	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
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	<	Mat3x3d invHmat = snap_->getInvHmat();
839	<	Vector3d rs, scaled, dr;
959	<	Vector3i whichCell;
960	<	int cellIndex;
838	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2) {
839	>	Vector3d d;
840
841		#ifdef IS_MPI
842	<	for (int i = 0; i < nGroupsInRow_; i++) {
843	<	rs = cgRowData.position[i];
844	<	// scaled positions relative to the box vectors
845	<	scaled = invHmat * rs;
846	<	// wrap the vector back into the unit box by subtracting integer box
847	<	// numbers
848	<	for (int j = 0; j < 3; j++)
849	<	scaled[j] -= roundMe(scaled[j]);
971	<
972	<	// find xyz-indices of cell that cutoffGroup is in.
973	<	whichCell.x() = nCells_.x() * scaled.x();
974	<	whichCell.y() = nCells_.y() * scaled.y();
975	<	whichCell.z() = nCells_.z() * scaled.z();
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	<	// find single index of this cell:
852	<	cellIndex = Vlinear(whichCell, nCells_);
853	<	// add this cutoff group to the list of groups in this cell;
980	<	cellListRow_[cellIndex].push_back(i);
981	<	}
851	>	snap_->wrapVector(d);
852	>	return d;
853	>	}
854
855	<	for (int i = 0; i < nGroupsInCol_; i++) {
856	<	rs = cgColData.position[i];
985	<	// scaled positions relative to the box vectors
986	<	scaled = invHmat * rs;
987	<	// wrap the vector back into the unit box by subtracting integer box
988	<	// numbers
989	<	for (int j = 0; j < 3; j++)
990	<	scaled[j] -= roundMe(scaled[j]);
855	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2) {
856	>	Vector3d d;
857
858	<	// find xyz-indices of cell that cutoffGroup is in.
859	<	whichCell.x() = nCells_.x() * scaled.x();
860	<	whichCell.y() = nCells_.y() * scaled.y();
861	<	whichCell.z() = nCells_.z() * scaled.z();
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	<	// find single index of this cell:
865	<	cellIndex = Vlinear(whichCell, nCells_);
866	<	// add this cutoff group to the list of groups in this cell;
867	<	cellListCol_[cellIndex].push_back(i);
868	<	}
864	>	snap_->wrapVector(d);
865	>	return d;
866	>	}
867	>
868	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1) {
869	>
870	>	Vector3d d;
871	>
872	>	#ifdef IS_MPI
873	>	d = cgRowData.position[cg1] - atomRowData.position[atom1];
874		#else
875	<	for (int i = 0; i < nGroups_; i++) {
876	<	rs = snap_->cgData.position[i];
1005	<	// scaled positions relative to the box vectors
1006	<	scaled = invHmat * rs;
1007	<	// wrap the vector back into the unit box by subtracting integer box
1008	<	// numbers
1009	<	for (int j = 0; j < 3; j++)
1010	<	scaled[j] -= roundMe(scaled[j]);
875	>	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
876	>	#endif
877
878	<	// find xyz-indices of cell that cutoffGroup is in.
879	<	whichCell.x() = nCells_.x() * scaled.x();
880	<	whichCell.y() = nCells_.y() * scaled.y();
1015	<	whichCell.z() = nCells_.z() * scaled.z();
878	>	snap_->wrapVector(d);
879	>	return d;
880	>	}
881
882	<	// find single index of this cell:
883	<	cellIndex = Vlinear(whichCell, nCells_);
884	<	// add this cutoff group to the list of groups in this cell;
885	<	cellList_[cellIndex].push_back(i);
886	<	}
882	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2) {
883	>	Vector3d d;
884	>
885	>	#ifdef IS_MPI
886	>	d = cgColData.position[cg2] - atomColData.position[atom2];
887	>	#else
888	>	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
889		#endif
890
891	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
892	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
893	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1027	<	Vector3i m1v(m1x, m1y, m1z);
1028	<	int m1 = Vlinear(m1v, nCells_);
891	>	snap_->wrapVector(d);
892	>	return d;
893	>	}
894
895	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
896	<	os != cellOffsets_.end(); ++os) {
897	<
898	<	Vector3i m2v = m1v + (*os);
899	<
900	<	if (m2v.x() >= nCells_.x()) {
901	<	m2v.x() = 0;
1037	<	} else if (m2v.x() < 0) {
1038	<	m2v.x() = nCells_.x() - 1;
1039	<	}
1040	<
1041	<	if (m2v.y() >= nCells_.y()) {
1042	<	m2v.y() = 0;
1043	<	} else if (m2v.y() < 0) {
1044	<	m2v.y() = nCells_.y() - 1;
1045	<	}
1046	<
1047	<	if (m2v.z() >= nCells_.z()) {
1048	<	m2v.z() = 0;
1049	<	} else if (m2v.z() < 0) {
1050	<	m2v.z() = nCells_.z() - 1;
1051	<	}
1052	<
1053	<	int m2 = Vlinear (m2v, nCells_);
895	>	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
896	>	#ifdef IS_MPI
897	>	return massFactorsRow[atom1];
898	>	#else
899	>	return massFactors[atom1];
900	>	#endif
901	>	}
902
903	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
904		#ifdef IS_MPI
905	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
906	<	j1 != cellListRow_[m1].end(); ++j1) {
907	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
908	<	j2 != cellListCol_[m2].end(); ++j2) {
1060	<
1061	<	// Always do this if we're in different cells or if
1062	<	// we're in the same cell and the global index of the
1063	<	// j2 cutoff group is less than the j1 cutoff group
905	>	return massFactorsCol[atom2];
906	>	#else
907	>	return massFactors[atom2];
908	>	#endif
909
910	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
911	<	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
912	<	snap_->wrapVector(dr);
913	<	cuts = getGroupCutoffs( (*j1), (*j2) );
914	<	if (dr.lengthSquare() < cuts.third) {
915	<	neighborList.push_back(make_pair((*j1), (*j2)));
916	<	}
1072	<	}
1073	<	}
1074	<	}
910	>	}
911	>
912	>	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2) {
913	>	Vector3d d;
914	>
915	>	#ifdef IS_MPI
916	>	d = atomColData.position[atom2] - atomRowData.position[atom1];
917		#else
918	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
919	<	j1 != cellList_[m1].end(); ++j1) {
1078	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1079	<	j2 != cellList_[m2].end(); ++j2) {
1080	<
1081	<	// Always do this if we're in different cells or if
1082	<	// we're in the same cell and the global index of the
1083	<	// j2 cutoff group is less than the j1 cutoff group
918	>	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
919	>	#endif
920
921	<	if (m2 != m1 || (*j2) < (*j1)) {
922	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
923	<	snap_->wrapVector(dr);
924	<	cuts = getGroupCutoffs( (*j1), (*j2) );
925	<	if (dr.lengthSquare() < cuts.third) {
926	<	neighborList.push_back(make_pair((*j1), (*j2)));
927	<	}
928	<	}
929	<	}
930	<	}
921	>	snap_->wrapVector(d);
922	>	return d;
923	>	}
924	>
925	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
926	>	return excludesForAtom[atom1];
927	>	}
928	>
929	>	/**
930	>	* We need to exclude some overcounted interactions that result from
931	>	* the parallel decomposition.
932	>	*/
933	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
934	>	int unique_id_1, unique_id_2;
935	>
936	>	//      cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
937	>	#ifdef IS_MPI
938	>	// in MPI, we have to look up the unique IDs for each atom
939	>	unique_id_1 = AtomRowToGlobal[atom1];
940	>	unique_id_2 = AtomColToGlobal[atom2];
941	>
942	>	cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
943	>	// this situation should only arise in MPI simulations
944	>	if (unique_id_1 == unique_id_2) return true;
945	>
946	>	// this prevents us from doing the pair on multiple processors
947	>	if (unique_id_1 < unique_id_2)
948	>	{
949	>	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
950	>	} else
951	>	{
952	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
953	>	}
954	>	#endif
955	>	return false;
956	>	}
957	>
958	>	/**
959	>	* We need to handle the interactions for atoms who are involved in
960	>	* the same rigid body as well as some short range interactions
961	>	* (bonds, bends, torsions) differently from other interactions.
962	>	* We'll still visit the pairwise routines, but with a flag that
963	>	* tells those routines to exclude the pair from direct long range
964	>	* interactions.  Some indirect interactions (notably reaction
965	>	* field) must still be handled for these pairs.
966	>	*/
967	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
968	>	int unique_id_2;
969	>	#ifdef IS_MPI
970	>	// in MPI, we have to look up the unique IDs for the row atom.
971	>	unique_id_2 = AtomColToGlobal[atom2];
972	>	#else
973	>	// in the normal loop, the atom numbers are unique
974	>	unique_id_2 = atom2;
975	>	#endif
976	>
977	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin(); i != excludesForAtom[atom1].end(); ++i)
978	>	{
979	>	if ((*i) == unique_id_2)
980	>	return true;
981	>	}
982	>
983	>	return false;
984	>	}
985	>
986	>	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg) {
987	>	#ifdef IS_MPI
988	>	atomRowData.force[atom1] += fg;
989	>	#else
990	>	snap_->atomData.force[atom1] += fg;
991	>	#endif
992	>	}
993	>
994	>	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg) {
995	>	#ifdef IS_MPI
996	>	atomColData.force[atom2] += fg;
997	>	#else
998	>	snap_->atomData.force[atom2] += fg;
999		#endif
1000	<	}
1097	<	}
1098	<	}
1099	<	}
1000	>	}
1001
1002	<	// save the local cutoff group positions for the check that is
1003	<	// done on each loop:
1103	<	saved_CG_positions_.clear();
1104	<	for (int i = 0; i < nGroups_; i++)
1105	<	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	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1117	>	#ifdef IS_MPI
1118	>	pot_row[atom1] += 0.5 * *(idat.pot);
1119	>	pot_col[atom2] += 0.5 * *(idat.pot);
1120	>
1121	>	atomRowData.force[atom1] += *(idat.f1);
1122	>	atomColData.force[atom2] -= *(idat.f1);
1123	>	#else
1124	>	pairwisePot += *(idat.pot);
1125	>
1126	>	snap_->atomData.force[atom1] += *(idat.f1);
1127	>	snap_->atomData.force[atom2] -= *(idat.f1);
1128	>	#endif
1129	>
1130	>	}
1131	>
1132	>	void ForceMatrixDecomposition::reorderGroupCutoffs(vector<int> &order) {
1133	>	vector<int> tmp = vector<int> (groupToGtype.size());
1134	>
1135	>	for (int i = 0; i < groupToGtype.size(); ++i)
1136	>	{
1137	>	tmp[i] = groupToGtype[i];
1138	>	}
1139	>
1140	>	for (int i = 0; i < groupToGtype.size(); ++i)
1141	>	{
1142	>	groupToGtype[i] = tmp[order[i]];
1143	>	}
1144	>	}
1145	>
1146	>	void ForceMatrixDecomposition::reorderPosition(vector<int> &order) {
1147	>	Snapshot* snap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1148	>	DataStorage* cgConfig = &(snap_->cgData);
1149	>	vector<Vector3d> tmp = vector<Vector3d> (nGroups_);
1150	>
1151	>	for (int i = 0; i < nGroups_; ++i)
1152	>	{
1153	>	tmp[i] = snap_->cgData.position[i];
1154	>	}
1155	>
1156	>	vector<int> mapPos = vector<int> (nGroups_);
1157	>	for (int i = 0; i < nGroups_; ++i)
1158	>	{
1159	>	snap_->cgData.position[i] = tmp[order[i]];
1160	>	mapPos[order[i]] = i;
1161	>	}
1162	>
1163	>	SimInfo::MoleculeIterator mi;
1164	>	Molecule* mol;
1165	>	Molecule::CutoffGroupIterator ci;
1166	>	CutoffGroup* cg;
1167	>
1168	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1169	>	{
1170	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1171	>	{
1172	>	cg->setLocalIndex(mapPos[cg->getLocalIndex()]);
1173	>	}
1174	>	}
1175	>
1176	>	/*      if (info_->getNCutoffGroups() > 0)
1177	>	{
1178	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1179	>	{
1180	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1181	>	{
1182	>	printf("gbI:%d locI:%d x:%f y:%f z:%f\n", cg->getGlobalIndex(), cg->getLocalIndex(),
1183	>	cgConfig->position[cg->getLocalIndex()].x(), cgConfig->position[cg->getLocalIndex()].y(),
1184	>	cgConfig->position[cg->getLocalIndex()].z());
1185	>	}
1186	>	}
1187	>	} else
1188	>	{
1189	>	// center of mass of the group is the same as position of the atom
1190	>	// if cutoff group does not exist
1191	>	printf("ERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
1192	>	//                     cgConfig->position = config->position;
1193	>	}*/
1194	>	}
1195	>
1196	>	void ForceMatrixDecomposition::reorderGroupList(vector<int> &order) {
1197	>	vector<vector<int> > tmp = vector<vector<int> > (groupList_.size());
1198	>
1199	>	for (int i = 0; i < groupList_.size(); ++i)
1200	>	{
1201	>	tmp[i] = groupList_[i];
1202	>	}
1203	>
1204	>	for (int i = 0; i < groupList_.size(); ++i)
1205	>	{
1206	>	groupList_[i] = tmp[order[i]];
1207	>	}
1208	>	}
1209	>
1210	>	void ForceMatrixDecomposition::reorderMemory(vector<vector<CutoffGroup *> > &H_c_l) {
1211	>	int n = 0;
1212	>	//      printf("Reorder memory time:%f!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
1213	>	//                      info_->getSnapshotManager()->getCurrentSnapshot()->getTime());
1214	>
1215	>	/* record the reordered atom indices */
1216	>	vector<int> k = vector<int> (nGroups_);
1217	>
1218	>	for (int c = 0; c < H_c_l.size(); ++c)
1219	>	{
1220	>	for (vector<CutoffGroup *>::iterator cg = H_c_l[c].begin(); cg != H_c_l[c].end(); ++cg)
1221	>	{
1222	>	int i = (*cg)->getGlobalIndex();
1223	>	k[n] = i;
1224	>	++n;
1225	>	}
1226	>	}
1227	>
1228	>	//      reorderGroupCutoffs(k);
1229	>	//      reorderGroupList(k);
1230	>	reorderPosition(k);
1231	>	}
1232	>
1233	>	vector<vector<CutoffGroup *> > ForceMatrixDecomposition::buildLayerBasedNeighborList() {
1234	>	//      printf("buildLayerBasedNeighborList; nGroups:%d\n", nGroups_);
1235	>	// Na = nGroups_
1236	>	/* cell occupancy counter */
1237	>	//      vector<int> k_c;
1238	>	/* c_i - has cell containing atom i (size Na) */
1239	>	vector<int> c = vector<int> (nGroups_);
1240	>	/* l_i - layer containing atom i (size Na) */
1241	>	//      vector<int> l;
1242	>
1243	>	RealType rList_ = (largestRcut_ + skinThickness_);
1244	>	Snapshot* snap_ = sman_->getCurrentSnapshot();
1245	>	Mat3x3d Hmat = snap_->getHmat();
1246	>	Vector3d Hx = Hmat.getColumn(0);
1247	>	Vector3d Hy = Hmat.getColumn(1);
1248	>	Vector3d Hz = Hmat.getColumn(2);
1249	>
1250	>	nCells_.x() = (int) (Hx.length()) / rList_;
1251	>	nCells_.y() = (int) (Hy.length()) / rList_;
1252	>	nCells_.z() = (int) (Hz.length()) / rList_;
1253	>
1254	>	Mat3x3d invHmat = snap_->getInvHmat();
1255	>	Vector3d rs, scaled, dr;
1256	>	Vector3i whichCell;
1257	>	int cellIndex;
1258	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1259	>
1260	>	//      k_c = vector<int> (nCtot, 0);
1261	>
1262	>	SimInfo::MoleculeIterator mi;
1263	>	Molecule* mol;
1264	>	Molecule::CutoffGroupIterator ci;
1265	>	CutoffGroup* cg;
1266	>
1267	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1268	>	{
1269	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1270	>	{
1271	>	rs = snap_->cgData.position[cg->getLocalIndex()];
1272	>
1273	>	// scaled positions relative to the box vectors
1274	>	scaled = invHmat * rs;
1275	>
1276	>	// wrap the vector back into the unit box by subtracting integer box
1277	>	// numbers
1278	>	for (int j = 0; j < 3; j++)
1279	>	{
1280	>	scaled[j] -= roundMe(scaled[j]);
1281	>	scaled[j] += 0.5;
1282	>	}
1283	>
1284	>	// find xyz-indices of cell that cutoffGroup is in.
1285	>	whichCell.x() = nCells_.x() * scaled.x();
1286	>	whichCell.y() = nCells_.y() * scaled.y();
1287	>	whichCell.z() = nCells_.z() * scaled.z();
1288	>
1289	>	//                      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(),
1290	>	//                                      whichCell.z());
1291	>
1292	>	// find single index of this cell:
1293	>	cellIndex = Vlinear(whichCell, nCells_);
1294	>
1295	>	c[cg->getGlobalIndex()] = cellIndex;
1296	>	}
1297	>	}
1298	>
1299	>	//      int k_c_curr;
1300	>	//      int k_c_max = 0;
1301	>	/* the cell-layer occupancy matrix */
1302	>	vector<vector<CutoffGroup *> > H_c_l = vector<vector<CutoffGroup *> > (nCtot);
1303	>
1304	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1305	>	{
1306	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1307	>
1308	>	{
1309	>	//                      k_c_curr = ++k_c[c[cg1->getGlobalIndex()]];
1310	>	//                      l.push_back(k_c_curr);
1311	>	//
1312	>	//                      /* determines the number of layers in use */
1313	>	//                      if (k_c_max < k_c_curr)
1314	>	//                      {
1315	>	//                              k_c_max = k_c_curr;
1316	>	//                      }
1317	>	H_c_l[c[cg->getGlobalIndex()]].push_back(/*l[*/cg/*]*/);
1318	>	}
1319	>	}
1320	>
1321	>	/* Frequency of reordering the memory */
1322	>	if (neighborListReorderFreq != 0)
1323	>	{
1324	>	if (reorderFreqCounter == neighborListReorderFreq)
1325	>	{
1326	>	//printf("neighborListReorderFreq:%d\n", neighborListReorderFreq);
1327	>	reorderMemory(H_c_l);
1328	>	reorderFreqCounter = 1;
1329	>	} else
1330	>	{
1331	>	reorderFreqCounter++;
1332	>	}
1333	>	}
1334	>
1335	>	int m;
1336	>	/* the neighbor matrix */
1337	>	vector<vector<CutoffGroup *> > neighborMatW = vector<vector<CutoffGroup *> > (nGroups_);
1338	>
1339	>	groupCutoffs cuts;
1340	>	CutoffGroup *cg1;
1341	>
1342	>	/* loops over objects(atoms, rigidBodies, cutoffGroups, etc.) */
1343	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1344	>	{
1345	>	for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
1346	>	{
1347	>	/* c' */
1348	>	int c1 = c[cg1->getGlobalIndex()];
1349	>	Vector3i c1v = idxToV(c1, nCells_);
1350	>
1351	>	/* loops over the neighboring cells c'' */
1352	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1353	>	{
1354	>	Vector3i c2v = c1v + (*os);
1355	>
1356	>	if (c2v.x() >= nCells_.x())
1357	>	{
1358	>	c2v.x() = 0;
1359	>	} else if (c2v.x() < 0)
1360	>	{
1361	>	c2v.x() = nCells_.x() - 1;
1362	>	}
1363	>
1364	>	if (c2v.y() >= nCells_.y())
1365	>	{
1366	>	c2v.y() = 0;
1367	>	} else if (c2v.y() < 0)
1368	>	{
1369	>	c2v.y() = nCells_.y() - 1;
1370	>	}
1371	>
1372	>	if (c2v.z() >= nCells_.z())
1373	>	{
1374	>	c2v.z() = 0;
1375	>	} else if (c2v.z() < 0)
1376	>	{
1377	>	c2v.z() = nCells_.z() - 1;
1378	>	}
1379	>
1380	>	int c2 = Vlinear(c2v, nCells_);
1381	>	/* loops over layers l to access the neighbor atoms */
1382	>	for (vector<CutoffGroup *>::iterator cg2 = H_c_l[c2].begin(); cg2 != H_c_l[c2].end(); ++cg2)
1383	>	{
1384	>	//                              if i'' = 0 then break // doesn't apply to vector implementation of matrix
1385	>	//                              if(i != *j)
1386	>	if (c2 != c1 || (*cg2)->getGlobalIndex() < cg1->getGlobalIndex())
1387	>	{
1388	>	dr = snap_->cgData.position[(*cg2)->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
1389	>	snap_->wrapVector(dr);
1390	>	cuts = getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex());
1391	>	if (dr.lengthSquare() < cuts.third)
1392	>	{
1393	>	/* transposed version of Rapaport W mat, to occupy successive memory locations on CPU */
1394	>	neighborMatW[cg1->getGlobalIndex()].push_back((*cg2));
1395	>	}
1396	>	}
1397	>	}
1398	>	}
1399	>	}
1400	>	}
1401	>
1402	>	// save the local cutoff group positions for the check that is
1403	>	// done on each loop:
1404	>	saved_CG_positions_.clear();
1405	>	for (int i = 0; i < nGroups_; i++)
1406	>	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1407	>
1408	>	return neighborMatW;
1409	>	}
1410	>
1411	>	/*
1412	>	* buildNeighborList
1413	>	*
1414	>	* first element of pair is row-indexed CutoffGroup
1415	>	* second element of pair is column-indexed CutoffGroup
1416	>	*/
1417	>	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1418	>
1419	>	vector<pair<int, int> > neighborList;
1420	>	groupCutoffs cuts;
1421	>	bool doAllPairs = false;
1422	>
1423	>	#ifdef IS_MPI
1424	>	cellListRow_.clear();
1425	>	cellListCol_.clear();
1426	>	#else
1427	>	cellList_.clear();
1428	>	#endif
1429	>
1430	>	RealType rList_ = (largestRcut_ + skinThickness_);
1431	>	RealType rl2 = rList_ * rList_;
1432	>	Snapshot* snap_ = sman_->getCurrentSnapshot();
1433	>	Mat3x3d Hmat = snap_->getHmat();
1434	>	Vector3d Hx = Hmat.getColumn(0);
1435	>	Vector3d Hy = Hmat.getColumn(1);
1436	>	Vector3d Hz = Hmat.getColumn(2);
1437	>
1438	>	nCells_.x() = (int) (Hx.length()) / rList_;
1439	>	nCells_.y() = (int) (Hy.length()) / rList_;
1440	>	nCells_.z() = (int) (Hz.length()) / rList_;
1441	>
1442	>	// handle small boxes where the cell offsets can end up repeating cells
1443	>
1444	>	if (nCells_.x() < 3)
1445	>	doAllPairs = true;
1446	>	if (nCells_.y() < 3)
1447	>	doAllPairs = true;
1448	>	if (nCells_.z() < 3)
1449	>	doAllPairs = true;
1450	>
1451	>	Mat3x3d invHmat = snap_->getInvHmat();
1452	>	Vector3d rs, scaled, dr;
1453	>	Vector3i whichCell;
1454	>	int cellIndex;
1455	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1456	>
1457	>	#ifdef IS_MPI
1458	>	cellListRow_.resize(nCtot);
1459	>	cellListCol_.resize(nCtot);
1460	>	#else
1461	>	cellList_.resize(nCtot);
1462	>	#endif
1463	>
1464	>	if (!doAllPairs)
1465	>	{
1466	>	#ifdef IS_MPI
1467	>
1468	>	for (int i = 0; i < nGroupsInRow_; i++)
1469	>	{
1470	>	rs = cgRowData.position[i];
1471	>
1472	>	// scaled positions relative to the box vectors
1473	>	scaled = invHmat * rs;
1474	>
1475	>	// wrap the vector back into the unit box by subtracting integer box
1476	>	// numbers
1477	>	for (int j = 0; j < 3; j++)
1478	>	{
1479	>	scaled[j] -= roundMe(scaled[j]);
1480	>	scaled[j] += 0.5;
1481	>	}
1482	>
1483	>	// find xyz-indices of cell that cutoffGroup is in.
1484	>	whichCell.x() = nCells_.x() * scaled.x();
1485	>	whichCell.y() = nCells_.y() * scaled.y();
1486	>	whichCell.z() = nCells_.z() * scaled.z();
1487	>
1488	>	// find single index of this cell:
1489	>	cellIndex = Vlinear(whichCell, nCells_);
1490	>
1491	>	// add this cutoff group to the list of groups in this cell;
1492	>	cellListRow_[cellIndex].push_back(i);
1493	>	}
1494	>	for (int i = 0; i < nGroupsInCol_; i++)
1495	>	{
1496	>	rs = cgColData.position[i];
1497	>
1498	>	// scaled positions relative to the box vectors
1499	>	scaled = invHmat * rs;
1500	>
1501	>	// wrap the vector back into the unit box by subtracting integer box
1502	>	// numbers
1503	>	for (int j = 0; j < 3; j++)
1504	>	{
1505	>	scaled[j] -= roundMe(scaled[j]);
1506	>	scaled[j] += 0.5;
1507	>	}
1508	>
1509	>	// find xyz-indices of cell that cutoffGroup is in.
1510	>	whichCell.x() = nCells_.x() * scaled.x();
1511	>	whichCell.y() = nCells_.y() * scaled.y();
1512	>	whichCell.z() = nCells_.z() * scaled.z();
1513	>
1514	>	// find single index of this cell:
1515	>	cellIndex = Vlinear(whichCell, nCells_);
1516	>
1517	>	// add this cutoff group to the list of groups in this cell;
1518	>	cellListCol_[cellIndex].push_back(i);
1519	>	}
1520	>	#else
1521	>	for (int i = 0; i < nGroups_; i++)
1522	>	{
1523	>	rs = snap_->cgData.position[i];
1524	>
1525	>	// scaled positions relative to the box vectors
1526	>	scaled = invHmat * rs;
1527	>
1528	>	// wrap the vector back into the unit box by subtracting integer box
1529	>	// numbers
1530	>	for (int j = 0; j < 3; j++)
1531	>	{
1532	>	scaled[j] -= roundMe(scaled[j]);
1533	>	scaled[j] += 0.5;
1534	>	}
1535	>
1536	>	// find xyz-indices of cell that cutoffGroup is in.
1537	>	whichCell.x() = nCells_.x() * scaled.x();
1538	>	whichCell.y() = nCells_.y() * scaled.y();
1539	>	whichCell.z() = nCells_.z() * scaled.z();
1540	>
1541	>	// find single index of this cell:
1542	>	cellIndex = Vlinear(whichCell, nCells_);
1543	>
1544	>	// add this cutoff group to the list of groups in this cell;
1545	>	cellList_[cellIndex].push_back(i);
1546	>	}
1547	>	#endif
1548	>
1549	>	for (int m1z = 0; m1z < nCells_.z(); m1z++)
1550	>	{
1551	>	for (int m1y = 0; m1y < nCells_.y(); m1y++)
1552	>	{
1553	>	for (int m1x = 0; m1x < nCells_.x(); m1x++)
1554	>	{
1555	>	Vector3i m1v(m1x, m1y, m1z);
1556	>	int m1 = Vlinear(m1v, nCells_);
1557	>
1558	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1559	>	{
1560	>
1561	>	Vector3i m2v = m1v + (*os);
1562	>
1563	>	if (m2v.x() >= nCells_.x())
1564	>	{
1565	>	m2v.x() = 0;
1566	>	} else if (m2v.x() < 0)
1567	>	{
1568	>	m2v.x() = nCells_.x() - 1;
1569	>	}
1570	>
1571	>	if (m2v.y() >= nCells_.y())
1572	>	{
1573	>	m2v.y() = 0;
1574	>	} else if (m2v.y() < 0)
1575	>	{
1576	>	m2v.y() = nCells_.y() - 1;
1577	>	}
1578	>
1579	>	if (m2v.z() >= nCells_.z())
1580	>	{
1581	>	m2v.z() = 0;
1582	>	} else if (m2v.z() < 0)
1583	>	{
1584	>	m2v.z() = nCells_.z() - 1;
1585	>	}
1586	>
1587	>	int m2 = Vlinear(m2v, nCells_);
1588	>
1589	>	#ifdef IS_MPI
1590	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1591	>	j1 != cellListRow_[m1].end(); ++j1)
1592	>	{
1593	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1594	>	j2 != cellListCol_[m2].end(); ++j2)
1595	>	{
1596	>
1597	>	// In parallel, we need to visit *all* pairs of row &
1598	>	// column indicies and will truncate later on.
1599	>	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1600	>	snap_->wrapVector(dr);
1601	>	cuts = getGroupCutoffs( (*j1), (*j2) );
1602	>	if (dr.lengthSquare() < cuts.third)
1603	>	{
1604	>	neighborList.push_back(make_pair((*j1), (*j2)));
1605	>	}
1606	>	}
1607	>	}
1608	>	#else
1609	>
1610	>	for (vector<int>::iterator j1 = cellList_[m1].begin(); j1 != cellList_[m1].end(); ++j1)
1611	>	{
1612	>	for (vector<int>::iterator j2 = cellList_[m2].begin(); j2 != cellList_[m2].end(); ++j2)
1613	>	{
1614	>
1615	>	// Always do this if we're in different cells or if
1616	>	// we're in the same cell and the global index of the
1617	>	// j2 cutoff group is less than the j1 cutoff group
1618	>
1619	>	if (m2 != m1 || (*j2) < (*j1))
1620	>	{
1621	>	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1622	>	snap_->wrapVector(dr);
1623	>	cuts = getGroupCutoffs((*j1), (*j2));
1624	>	if (dr.lengthSquare() < cuts.third)
1625	>	{
1626	>	neighborList.push_back(make_pair((*j1), (*j2)));
1627	>	}
1628	>	}
1629	>	}
1630	>	}
1631	>	#endif
1632	>	}
1633	>	}
1634	>	}
1635	>	}
1636	>	} else
1637	>	{
1638	>	// branch to do all cutoff group pairs
1639	>	#ifdef IS_MPI
1640	>	for (int j1 = 0; j1 < nGroupsInRow_; j1++)
1641	>	{
1642	>	for (int j2 = 0; j2 < nGroupsInCol_; j2++)
1643	>	{
1644	>	dr = cgColData.position[j2] - cgRowData.position[j1];
1645	>	snap_->wrapVector(dr);
1646	>	cuts = getGroupCutoffs( j1, j2 );
1647	>	if (dr.lengthSquare() < cuts.third)
1648	>	{
1649	>	neighborList.push_back(make_pair(j1, j2));
1650	>	}
1651	>	}
1652	>	}
1653	>	#else
1654	>	for (int j1 = 0; j1 < nGroups_ - 1; j1++)
1655	>	{
1656	>	for (int j2 = j1 + 1; j2 < nGroups_; j2++)
1657	>	{
1658	>	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1659	>	snap_->wrapVector(dr);
1660	>	cuts = getGroupCutoffs(j1, j2);
1661	>	if (dr.lengthSquare() < cuts.third)
1662	>	{
1663	>	neighborList.push_back(make_pair(j1, j2));
1664	>	}
1665	>	}
1666	>	}
1667	>	#endif
1668	>	}
1669	>
1670	>	// save the local cutoff group positions for the check that is
1671	>	// done on each loop:
1672	>	saved_CG_positions_.clear();
1673	>	for (int i = 0; i < nGroups_; i++)
1674	>	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1675	>
1676	>	return neighborList;
1677	>	}
1678		} //end namespace OpenMD

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