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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1592 by gezelter, Tue Jul 12 20:33:14 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 2057 by gezelter, Tue Mar 3 15:22:26 2015 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
#	Line 47 | Line 48 | namespace OpenMD {
48		using namespace std;
49		namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	+
53	+	// Row and colum scans must visit all surrounding cells
54	+	cellOffsets_.clear();
55	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
56	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
57	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
58	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
65	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
66	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
67	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
74	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
75	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
76	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
82	+	}
83	+
84	+
85		/**
86		* distributeInitialData is essentially a copy of the older fortran
87		* SimulationSetup
88		*/
54	–
89		void ForceMatrixDecomposition::distributeInitialData() {
90		snap_ = sman_->getCurrentSnapshot();
91		storageLayout_ = sman_->getStorageLayout();
92		ff_ = info_->getForceField();
93		nLocal_ = snap_->getNumberOfAtoms();
94	<
94	>
95		nGroups_ = info_->getNLocalCutoffGroups();
96		// gather the information for atomtype IDs (atids):
97		idents = info_->getIdentArray();
98	+	regions = info_->getRegions();
99		AtomLocalToGlobal = info_->getGlobalAtomIndices();
100		cgLocalToGlobal = info_->getGlobalGroupIndices();
101		vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
#	Line 71 | Line 106 | namespace OpenMD {
106		PairList* oneTwo = info_->getOneTwoInteractions();
107		PairList* oneThree = info_->getOneThreeInteractions();
108		PairList* oneFour = info_->getOneFourInteractions();
109	<
109	>
110	>	if (needVelocities_)
111	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
112	>	DataStorage::dslVelocity);
113	>	else
114	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
115	>
116		#ifdef IS_MPI
117
118	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
119	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
79	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
80	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
81	<	AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
118	>	MPI_Comm row = rowComm.getComm();
119	>	MPI_Comm col = colComm.getComm();
120
121	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
122	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
123	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
124	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
125	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
121	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
122	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
123	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
124	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
125	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
126
127	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
128	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
129	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
130	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
127	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
128	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
129	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
130	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
131	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
132
133	<	nAtomsInRow_ = AtomCommIntRow->getSize();
134	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
135	<	nGroupsInRow_ = cgCommIntRow->getSize();
136	<	nGroupsInCol_ = cgCommIntColumn->getSize();
133	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
134	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
135	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
136	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
137
138	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
139	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
140	+	nGroupsInRow_ = cgPlanIntRow->getSize();
141	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
142	+
143		// Modify the data storage objects with the correct layouts and sizes:
144		atomRowData.resize(nAtomsInRow_);
145		atomRowData.setStorageLayout(storageLayout_);
#	Line 104 | Line 148 | namespace OpenMD {
148		cgRowData.resize(nGroupsInRow_);
149		cgRowData.setStorageLayout(DataStorage::dslPosition);
150		cgColData.resize(nGroupsInCol_);
151	<	cgColData.setStorageLayout(DataStorage::dslPosition);
152	<
151	>	if (needVelocities_)
152	>	// we only need column velocities if we need them.
153	>	cgColData.setStorageLayout(DataStorage::dslPosition |
154	>	DataStorage::dslVelocity);
155	>	else
156	>	cgColData.setStorageLayout(DataStorage::dslPosition);
157	>
158		identsRow.resize(nAtomsInRow_);
159		identsCol.resize(nAtomsInCol_);
160
161	<	AtomCommIntRow->gather(idents, identsRow);
162	<	AtomCommIntColumn->gather(idents, identsCol);
161	>	AtomPlanIntRow->gather(idents, identsRow);
162	>	AtomPlanIntColumn->gather(idents, identsCol);
163	>
164	>	regionsRow.resize(nAtomsInRow_);
165	>	regionsCol.resize(nAtomsInCol_);
166
167	+	AtomPlanIntRow->gather(regions, regionsRow);
168	+	AtomPlanIntColumn->gather(regions, regionsCol);
169	+
170		// allocate memory for the parallel objects
171		atypesRow.resize(nAtomsInRow_);
172		atypesCol.resize(nAtomsInCol_);
#	Line 124 | Line 179 | namespace OpenMD {
179		pot_row.resize(nAtomsInRow_);
180		pot_col.resize(nAtomsInCol_);
181
182	+	expot_row.resize(nAtomsInRow_);
183	+	expot_col.resize(nAtomsInCol_);
184	+
185		AtomRowToGlobal.resize(nAtomsInRow_);
186		AtomColToGlobal.resize(nAtomsInCol_);
187	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
188	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
189	<
187	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
188	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
189	>
190		cgRowToGlobal.resize(nGroupsInRow_);
191		cgColToGlobal.resize(nGroupsInCol_);
192	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
193	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
192	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
193	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
194
195		massFactorsRow.resize(nAtomsInRow_);
196		massFactorsCol.resize(nAtomsInCol_);
197	<	AtomCommRealRow->gather(massFactors, massFactorsRow);
198	<	AtomCommRealColumn->gather(massFactors, massFactorsCol);
197	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
198	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
199
200		groupListRow_.clear();
201		groupListRow_.resize(nGroupsInRow_);
#	Line 193 | Line 251 | namespace OpenMD {
251		}
252		}
253
254	<	#endif
197	<
198	<	// allocate memory for the parallel objects
199	<	atypesLocal.resize(nLocal_);
200	<
201	<	for (int i = 0; i < nLocal_; i++)
202	<	atypesLocal[i] = ff_->getAtomType(idents[i]);
203	<
204	<	groupList_.clear();
205	<	groupList_.resize(nGroups_);
206	<	for (int i = 0; i < nGroups_; i++) {
207	<	int gid = cgLocalToGlobal[i];
208	<	for (int j = 0; j < nLocal_; j++) {
209	<	int aid = AtomLocalToGlobal[j];
210	<	if (globalGroupMembership[aid] == gid) {
211	<	groupList_[i].push_back(j);
212	<	}
213	<	}
214	<	}
215	<
254	>	#else
255		excludesForAtom.clear();
256		excludesForAtom.resize(nLocal_);
257		toposForAtom.clear();
#	Line 245 | Line 284 | namespace OpenMD {
284		}
285		}
286		}
287	<
249	<	createGtypeCutoffMap();
287	>	#endif
288
289	+	// allocate memory for the parallel objects
290	+	atypesLocal.resize(nLocal_);
291	+
292	+	for (int i = 0; i < nLocal_; i++)
293	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
294	+
295	+	groupList_.clear();
296	+	groupList_.resize(nGroups_);
297	+	for (int i = 0; i < nGroups_; i++) {
298	+	int gid = cgLocalToGlobal[i];
299	+	for (int j = 0; j < nLocal_; j++) {
300	+	int aid = AtomLocalToGlobal[j];
301	+	if (globalGroupMembership[aid] == gid) {
302	+	groupList_[i].push_back(j);
303	+	}
304	+	}
305	+	}
306		}
252	–
253	–	void ForceMatrixDecomposition::createGtypeCutoffMap() {
307
255	–	RealType tol = 1e-6;
256	–	largestRcut_ = 0.0;
257	–	RealType rc;
258	–	int atid;
259	–	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
260	–
261	–	map<int, RealType> atypeCutoff;
262	–
263	–	for (set<AtomType*>::iterator at = atypes.begin();
264	–	at != atypes.end(); ++at){
265	–	atid = (*at)->getIdent();
266	–	if (userChoseCutoff_)
267	–	atypeCutoff[atid] = userCutoff_;
268	–	else
269	–	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
270	–	}
271	–
272	–	vector<RealType> gTypeCutoffs;
273	–	// first we do a single loop over the cutoff groups to find the
274	–	// largest cutoff for any atypes present in this group.
275	–	#ifdef IS_MPI
276	–	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
277	–	groupRowToGtype.resize(nGroupsInRow_);
278	–	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
279	–	vector<int> atomListRow = getAtomsInGroupRow(cg1);
280	–	for (vector<int>::iterator ia = atomListRow.begin();
281	–	ia != atomListRow.end(); ++ia) {
282	–	int atom1 = (*ia);
283	–	atid = identsRow[atom1];
284	–	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
285	–	groupCutoffRow[cg1] = atypeCutoff[atid];
286	–	}
287	–	}
288	–
289	–	bool gTypeFound = false;
290	–	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
291	–	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
292	–	groupRowToGtype[cg1] = gt;
293	–	gTypeFound = true;
294	–	}
295	–	}
296	–	if (!gTypeFound) {
297	–	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
298	–	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
299	–	}
300	–
301	–	}
302	–	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
303	–	groupColToGtype.resize(nGroupsInCol_);
304	–	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
305	–	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
306	–	for (vector<int>::iterator jb = atomListCol.begin();
307	–	jb != atomListCol.end(); ++jb) {
308	–	int atom2 = (*jb);
309	–	atid = identsCol[atom2];
310	–	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
311	–	groupCutoffCol[cg2] = atypeCutoff[atid];
312	–	}
313	–	}
314	–	bool gTypeFound = false;
315	–	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
316	–	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
317	–	groupColToGtype[cg2] = gt;
318	–	gTypeFound = true;
319	–	}
320	–	}
321	–	if (!gTypeFound) {
322	–	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
323	–	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
324	–	}
325	–	}
326	–	#else
327	–
328	–	vector<RealType> groupCutoff(nGroups_, 0.0);
329	–	groupToGtype.resize(nGroups_);
330	–	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
331	–	groupCutoff[cg1] = 0.0;
332	–	vector<int> atomList = getAtomsInGroupRow(cg1);
333	–	for (vector<int>::iterator ia = atomList.begin();
334	–	ia != atomList.end(); ++ia) {
335	–	int atom1 = (*ia);
336	–	atid = idents[atom1];
337	–	if (atypeCutoff[atid] > groupCutoff[cg1])
338	–	groupCutoff[cg1] = atypeCutoff[atid];
339	–	}
340	–
341	–	bool gTypeFound = false;
342	–	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
343	–	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
344	–	groupToGtype[cg1] = gt;
345	–	gTypeFound = true;
346	–	}
347	–	}
348	–	if (!gTypeFound) {
349	–	gTypeCutoffs.push_back( groupCutoff[cg1] );
350	–	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
351	–	}
352	–	}
353	–	#endif
354	–
355	–	// Now we find the maximum group cutoff value present in the simulation
356	–
357	–	RealType groupMax = *max_element(gTypeCutoffs.begin(),
358	–	gTypeCutoffs.end());
359	–
360	–	#ifdef IS_MPI
361	–	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
362	–	MPI::MAX);
363	–	#endif
364	–
365	–	RealType tradRcut = groupMax;
366	–
367	–	for (int i = 0; i < gTypeCutoffs.size();  i++) {
368	–	for (int j = 0; j < gTypeCutoffs.size();  j++) {
369	–	RealType thisRcut;
370	–	switch(cutoffPolicy_) {
371	–	case TRADITIONAL:
372	–	thisRcut = tradRcut;
373	–	break;
374	–	case MIX:
375	–	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
376	–	break;
377	–	case MAX:
378	–	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
379	–	break;
380	–	default:
381	–	sprintf(painCave.errMsg,
382	–	"ForceMatrixDecomposition::createGtypeCutoffMap "
383	–	"hit an unknown cutoff policy!\n");
384	–	painCave.severity = OPENMD_ERROR;
385	–	painCave.isFatal = 1;
386	–	simError();
387	–	break;
388	–	}
389	–
390	–	pair<int,int> key = make_pair(i,j);
391	–	gTypeCutoffMap[key].first = thisRcut;
392	–	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
393	–	gTypeCutoffMap[key].second = thisRcut*thisRcut;
394	–	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
395	–	// sanity check
396	–
397	–	if (userChoseCutoff_) {
398	–	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
399	–	sprintf(painCave.errMsg,
400	–	"ForceMatrixDecomposition::createGtypeCutoffMap "
401	–	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
402	–	painCave.severity = OPENMD_ERROR;
403	–	painCave.isFatal = 1;
404	–	simError();
405	–	}
406	–	}
407	–	}
408	–	}
409	–	}
410	–
411	–
412	–	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
413	–	int i, j;
414	–	#ifdef IS_MPI
415	–	i = groupRowToGtype[cg1];
416	–	j = groupColToGtype[cg2];
417	–	#else
418	–	i = groupToGtype[cg1];
419	–	j = groupToGtype[cg2];
420	–	#endif
421	–	return gTypeCutoffMap[make_pair(i,j)];
422	–	}
423	–
308		int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
309	<	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
309	>	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
310		if (toposForAtom[atom1][j] == atom2)
311		return topoDist[atom1][j];
312	<	}
312	>	}
313		return 0;
314		}
315
316		void ForceMatrixDecomposition::zeroWorkArrays() {
317		pairwisePot = 0.0;
318		embeddingPot = 0.0;
319	+	excludedPot = 0.0;
320	+	excludedSelfPot = 0.0;
321
322		#ifdef IS_MPI
323		if (storageLayout_ & DataStorage::dslForce) {
#	Line 450 | Line 336 | namespace OpenMD {
336		fill(pot_col.begin(), pot_col.end(),
337		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
338
339	+	fill(expot_row.begin(), expot_row.end(),
340	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
341	+
342	+	fill(expot_col.begin(), expot_col.end(),
343	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
344	+
345		if (storageLayout_ & DataStorage::dslParticlePot) {
346		fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
347		0.0);
#	Line 481 | Line 373 | namespace OpenMD {
373		atomRowData.skippedCharge.end(), 0.0);
374		fill(atomColData.skippedCharge.begin(),
375		atomColData.skippedCharge.end(), 0.0);
376	+	}
377	+
378	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
379	+	fill(atomRowData.flucQFrc.begin(),
380	+	atomRowData.flucQFrc.end(), 0.0);
381	+	fill(atomColData.flucQFrc.begin(),
382	+	atomColData.flucQFrc.end(), 0.0);
383	+	}
384	+
385	+	if (storageLayout_ & DataStorage::dslElectricField) {
386	+	fill(atomRowData.electricField.begin(),
387	+	atomRowData.electricField.end(), V3Zero);
388	+	fill(atomColData.electricField.begin(),
389	+	atomColData.electricField.end(), V3Zero);
390		}
391
392	+	if (storageLayout_ & DataStorage::dslSitePotential) {
393	+	fill(atomRowData.sitePotential.begin(),
394	+	atomRowData.sitePotential.end(), 0.0);
395	+	fill(atomColData.sitePotential.begin(),
396	+	atomColData.sitePotential.end(), 0.0);
397	+	}
398	+
399		#endif
400		// even in parallel, we need to zero out the local arrays:
401
#	Line 495 | Line 408 | namespace OpenMD {
408		fill(snap_->atomData.density.begin(),
409		snap_->atomData.density.end(), 0.0);
410		}
411	+
412		if (storageLayout_ & DataStorage::dslFunctional) {
413		fill(snap_->atomData.functional.begin(),
414		snap_->atomData.functional.end(), 0.0);
415		}
416	+
417		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
418		fill(snap_->atomData.functionalDerivative.begin(),
419		snap_->atomData.functionalDerivative.end(), 0.0);
420		}
421	+
422		if (storageLayout_ & DataStorage::dslSkippedCharge) {
423		fill(snap_->atomData.skippedCharge.begin(),
424		snap_->atomData.skippedCharge.end(), 0.0);
425		}
426	<
426	>
427	>	if (storageLayout_ & DataStorage::dslElectricField) {
428	>	fill(snap_->atomData.electricField.begin(),
429	>	snap_->atomData.electricField.end(), V3Zero);
430	>	}
431	>	if (storageLayout_ & DataStorage::dslSitePotential) {
432	>	fill(snap_->atomData.sitePotential.begin(),
433	>	snap_->atomData.sitePotential.end(), 0.0);
434	>	}
435		}
436
437
438		void ForceMatrixDecomposition::distributeData()  {
439		snap_ = sman_->getCurrentSnapshot();
440		storageLayout_ = sman_->getStorageLayout();
441	+
442	+	bool needsCG = true;
443	+	if(info_->getNCutoffGroups() != info_->getNAtoms())
444	+	needsCG = false;
445	+
446		#ifdef IS_MPI
447
448		// gather up the atomic positions
449	<	AtomCommVectorRow->gather(snap_->atomData.position,
449	>	AtomPlanVectorRow->gather(snap_->atomData.position,
450		atomRowData.position);
451	<	AtomCommVectorColumn->gather(snap_->atomData.position,
451	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
452		atomColData.position);
453
454		// gather up the cutoff group positions
455	<	cgCommVectorRow->gather(snap_->cgData.position,
456	<	cgRowData.position);
457	<	cgCommVectorColumn->gather(snap_->cgData.position,
458	<	cgColData.position);
455	>
456	>	if (needsCG) {
457	>	cgPlanVectorRow->gather(snap_->cgData.position,
458	>	cgRowData.position);
459	>
460	>	cgPlanVectorColumn->gather(snap_->cgData.position,
461	>	cgColData.position);
462	>	}
463	>
464	>
465	>	if (needVelocities_) {
466	>	// gather up the atomic velocities
467	>	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
468	>	atomColData.velocity);
469	>
470	>	if (needsCG) {
471	>	cgPlanVectorColumn->gather(snap_->cgData.velocity,
472	>	cgColData.velocity);
473	>	}
474	>	}
475	>
476
477		// if needed, gather the atomic rotation matrices
478		if (storageLayout_ & DataStorage::dslAmat) {
479	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
479	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
480		atomRowData.aMat);
481	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
481	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
482		atomColData.aMat);
483		}
484	<
485	<	// if needed, gather the atomic eletrostatic frames
486	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
487	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
488	<	atomRowData.electroFrame);
489	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
490	<	atomColData.electroFrame);
484	>
485	>	// if needed, gather the atomic eletrostatic information
486	>	if (storageLayout_ & DataStorage::dslDipole) {
487	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
488	>	atomRowData.dipole);
489	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
490	>	atomColData.dipole);
491		}
492
493	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
494	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
495	+	atomRowData.quadrupole);
496	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
497	+	atomColData.quadrupole);
498	+	}
499	+
500	+	// if needed, gather the atomic fluctuating charge values
501	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
502	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
503	+	atomRowData.flucQPos);
504	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
505	+	atomColData.flucQPos);
506	+	}
507	+
508		#endif
509		}
510
#	Line 557 | Line 518 | namespace OpenMD {
518
519		if (storageLayout_ & DataStorage::dslDensity) {
520
521	<	AtomCommRealRow->scatter(atomRowData.density,
521	>	AtomPlanRealRow->scatter(atomRowData.density,
522		snap_->atomData.density);
523
524		int n = snap_->atomData.density.size();
525		vector<RealType> rho_tmp(n, 0.0);
526	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
526	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
527		for (int i = 0; i < n; i++)
528		snap_->atomData.density[i] += rho_tmp[i];
529		}
530	+
531	+	// this isn't necessary if we don't have polarizable atoms, but
532	+	// we'll leave it here for now.
533	+	if (storageLayout_ & DataStorage::dslElectricField) {
534	+
535	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
536	+	snap_->atomData.electricField);
537	+
538	+	int n = snap_->atomData.electricField.size();
539	+	vector<Vector3d> field_tmp(n, V3Zero);
540	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
541	+	field_tmp);
542	+	for (int i = 0; i < n; i++)
543	+	snap_->atomData.electricField[i] += field_tmp[i];
544	+	}
545		#endif
546		}
547
#	Line 578 | Line 554 | namespace OpenMD {
554		storageLayout_ = sman_->getStorageLayout();
555		#ifdef IS_MPI
556		if (storageLayout_ & DataStorage::dslFunctional) {
557	<	AtomCommRealRow->gather(snap_->atomData.functional,
557	>	AtomPlanRealRow->gather(snap_->atomData.functional,
558		atomRowData.functional);
559	<	AtomCommRealColumn->gather(snap_->atomData.functional,
559	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
560		atomColData.functional);
561		}
562
563		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
564	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
564	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
565		atomRowData.functionalDerivative);
566	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
566	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
567		atomColData.functionalDerivative);
568		}
569		#endif
#	Line 601 | Line 577 | namespace OpenMD {
577		int n = snap_->atomData.force.size();
578		vector<Vector3d> frc_tmp(n, V3Zero);
579
580	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
580	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
581		for (int i = 0; i < n; i++) {
582		snap_->atomData.force[i] += frc_tmp[i];
583		frc_tmp[i] = 0.0;
584		}
585
586	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
587	<	for (int i = 0; i < n; i++)
586	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
587	>	for (int i = 0; i < n; i++) {
588		snap_->atomData.force[i] += frc_tmp[i];
589	+	}
590
591		if (storageLayout_ & DataStorage::dslTorque) {
592
593		int nt = snap_->atomData.torque.size();
594		vector<Vector3d> trq_tmp(nt, V3Zero);
595
596	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
596	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
597		for (int i = 0; i < nt; i++) {
598		snap_->atomData.torque[i] += trq_tmp[i];
599		trq_tmp[i] = 0.0;
600		}
601
602	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
602	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
603		for (int i = 0; i < nt; i++)
604		snap_->atomData.torque[i] += trq_tmp[i];
605		}
#	Line 632 | Line 609 | namespace OpenMD {
609		int ns = snap_->atomData.skippedCharge.size();
610		vector<RealType> skch_tmp(ns, 0.0);
611
612	<	AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
612	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
613		for (int i = 0; i < ns; i++) {
614		snap_->atomData.skippedCharge[i] += skch_tmp[i];
615		skch_tmp[i] = 0.0;
616		}
617
618	<	AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
619	<	for (int i = 0; i < ns; i++)
618	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
619	>	for (int i = 0; i < ns; i++)
620		snap_->atomData.skippedCharge[i] += skch_tmp[i];
621	+
622		}
623
624	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
625	+
626	+	int nq = snap_->atomData.flucQFrc.size();
627	+	vector<RealType> fqfrc_tmp(nq, 0.0);
628	+
629	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
630	+	for (int i = 0; i < nq; i++) {
631	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
632	+	fqfrc_tmp[i] = 0.0;
633	+	}
634	+
635	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
636	+	for (int i = 0; i < nq; i++)
637	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
638	+
639	+	}
640	+
641	+	if (storageLayout_ & DataStorage::dslElectricField) {
642	+
643	+	int nef = snap_->atomData.electricField.size();
644	+	vector<Vector3d> efield_tmp(nef, V3Zero);
645	+
646	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
647	+	for (int i = 0; i < nef; i++) {
648	+	snap_->atomData.electricField[i] += efield_tmp[i];
649	+	efield_tmp[i] = 0.0;
650	+	}
651	+
652	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
653	+	for (int i = 0; i < nef; i++)
654	+	snap_->atomData.electricField[i] += efield_tmp[i];
655	+	}
656	+
657	+	if (storageLayout_ & DataStorage::dslSitePotential) {
658	+
659	+	int nsp = snap_->atomData.sitePotential.size();
660	+	vector<RealType> sp_tmp(nsp, 0.0);
661	+
662	+	AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
663	+	for (int i = 0; i < nsp; i++) {
664	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
665	+	sp_tmp[i] = 0.0;
666	+	}
667	+
668	+	AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
669	+	for (int i = 0; i < nsp; i++)
670	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
671	+	}
672	+
673		nLocal_ = snap_->getNumberOfAtoms();
674
675		vector<potVec> pot_temp(nLocal_,
676		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
677	+	vector<potVec> expot_temp(nLocal_,
678	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
679
680		// scatter/gather pot_row into the members of my column
681
682	<	AtomCommPotRow->scatter(pot_row, pot_temp);
682	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
683	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
684
685	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
685	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
686		pairwisePot += pot_temp[ii];
687	<
687	>
688	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
689	>	excludedPot += expot_temp[ii];
690	>
691	>	if (storageLayout_ & DataStorage::dslParticlePot) {
692	>	// This is the pairwise contribution to the particle pot.  The
693	>	// embedding contribution is added in each of the low level
694	>	// non-bonded routines.  In single processor, this is done in
695	>	// unpackInteractionData, not in collectData.
696	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
697	>	for (int i = 0; i < nLocal_; i++) {
698	>	// factor of two is because the total potential terms are divided
699	>	// by 2 in parallel due to row/ column scatter
700	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
701	>	}
702	>	}
703	>	}
704	>
705		fill(pot_temp.begin(), pot_temp.end(),
706		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
707	+	fill(expot_temp.begin(), expot_temp.end(),
708	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
709
710	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
710	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
711	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
712
713		for (int ii = 0;  ii < pot_temp.size(); ii++ )
714		pairwisePot += pot_temp[ii];
715	+
716	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
717	+	excludedPot += expot_temp[ii];
718	+
719	+	if (storageLayout_ & DataStorage::dslParticlePot) {
720	+	// This is the pairwise contribution to the particle pot.  The
721	+	// embedding contribution is added in each of the low level
722	+	// non-bonded routines.  In single processor, this is done in
723	+	// unpackInteractionData, not in collectData.
724	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
725	+	for (int i = 0; i < nLocal_; i++) {
726	+	// factor of two is because the total potential terms are divided
727	+	// by 2 in parallel due to row/ column scatter
728	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
729	+	}
730	+	}
731	+	}
732	+
733	+	if (storageLayout_ & DataStorage::dslParticlePot) {
734	+	int npp = snap_->atomData.particlePot.size();
735	+	vector<RealType> ppot_temp(npp, 0.0);
736	+
737	+	// This is the direct or embedding contribution to the particle
738	+	// pot.
739	+
740	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
741	+	for (int i = 0; i < npp; i++) {
742	+	snap_->atomData.particlePot[i] += ppot_temp[i];
743	+	}
744	+
745	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
746	+
747	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
748	+	for (int i = 0; i < npp; i++) {
749	+	snap_->atomData.particlePot[i] += ppot_temp[i];
750	+	}
751	+	}
752	+
753	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
754	+	RealType ploc1 = pairwisePot[ii];
755	+	RealType ploc2 = 0.0;
756	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
757	+	pairwisePot[ii] = ploc2;
758	+	}
759	+
760	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
761	+	RealType ploc1 = excludedPot[ii];
762	+	RealType ploc2 = 0.0;
763	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
764	+	excludedPot[ii] = ploc2;
765	+	}
766	+
767	+	// Here be dragons.
768	+	MPI_Comm col = colComm.getComm();
769	+
770	+	MPI_Allreduce(MPI_IN_PLACE,
771	+	&snap_->frameData.conductiveHeatFlux[0], 3,
772	+	MPI_REALTYPE, MPI_SUM, col);
773	+
774	+
775		#endif
776
777		}
778
779	<	int ForceMatrixDecomposition::getNAtomsInRow() {
779	>	/**
780	>	* Collects information obtained during the post-pair (and embedding
781	>	* functional) loops onto local data structures.
782	>	*/
783	>	void ForceMatrixDecomposition::collectSelfData() {
784	>	snap_ = sman_->getCurrentSnapshot();
785	>	storageLayout_ = sman_->getStorageLayout();
786	>
787		#ifdef IS_MPI
788	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
789	+	RealType ploc1 = embeddingPot[ii];
790	+	RealType ploc2 = 0.0;
791	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
792	+	embeddingPot[ii] = ploc2;
793	+	}
794	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
795	+	RealType ploc1 = excludedSelfPot[ii];
796	+	RealType ploc2 = 0.0;
797	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
798	+	excludedSelfPot[ii] = ploc2;
799	+	}
800	+	#endif
801	+
802	+	}
803	+
804	+
805	+
806	+	int& ForceMatrixDecomposition::getNAtomsInRow() {
807	+	#ifdef IS_MPI
808		return nAtomsInRow_;
809		#else
810		return nLocal_;
#	Line 677 | Line 814 | namespace OpenMD {
814		/**
815		* returns the list of atoms belonging to this group.
816		*/
817	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
817	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
818		#ifdef IS_MPI
819		return groupListRow_[cg1];
820		#else
#	Line 685 | Line 822 | namespace OpenMD {
822		#endif
823		}
824
825	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
825	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
826		#ifdef IS_MPI
827		return groupListCol_[cg2];
828		#else
#	Line 702 | Line 839 | namespace OpenMD {
839		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
840		#endif
841
842	<	snap_->wrapVector(d);
842	>	if (usePeriodicBoundaryConditions_) {
843	>	snap_->wrapVector(d);
844	>	}
845		return d;
846		}
847
848	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
849	+	#ifdef IS_MPI
850	+	return cgColData.velocity[cg2];
851	+	#else
852	+	return snap_->cgData.velocity[cg2];
853	+	#endif
854	+	}
855
856	+	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
857	+	#ifdef IS_MPI
858	+	return atomColData.velocity[atom2];
859	+	#else
860	+	return snap_->atomData.velocity[atom2];
861	+	#endif
862	+	}
863	+
864	+
865		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
866
867		Vector3d d;
#	Line 716 | Line 871 | namespace OpenMD {
871		#else
872		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
873		#endif
874	<
875	<	snap_->wrapVector(d);
874	>	if (usePeriodicBoundaryConditions_) {
875	>	snap_->wrapVector(d);
876	>	}
877		return d;
878		}
879
#	Line 729 | Line 885 | namespace OpenMD {
885		#else
886		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
887		#endif
888	<
889	<	snap_->wrapVector(d);
888	>	if (usePeriodicBoundaryConditions_) {
889	>	snap_->wrapVector(d);
890	>	}
891		return d;
892		}
893
894	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
894	>	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
895		#ifdef IS_MPI
896		return massFactorsRow[atom1];
897		#else
#	Line 742 | Line 899 | namespace OpenMD {
899		#endif
900		}
901
902	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
902	>	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
903		#ifdef IS_MPI
904		return massFactorsCol[atom2];
905		#else
#	Line 759 | Line 916 | namespace OpenMD {
916		#else
917		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
918		#endif
919	<
920	<	snap_->wrapVector(d);
919	>	if (usePeriodicBoundaryConditions_) {
920	>	snap_->wrapVector(d);
921	>	}
922		return d;
923		}
924
925	<	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
925	>	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
926		return excludesForAtom[atom1];
927		}
928
#	Line 772 | Line 930 | namespace OpenMD {
930		* We need to exclude some overcounted interactions that result from
931		* the parallel decomposition.
932		*/
933	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
933	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
934		int unique_id_1, unique_id_2;
935	<
935	>
936		#ifdef IS_MPI
937		// in MPI, we have to look up the unique IDs for each atom
938		unique_id_1 = AtomRowToGlobal[atom1];
939		unique_id_2 = AtomColToGlobal[atom2];
940	+	// group1 = cgRowToGlobal[cg1];
941	+	// group2 = cgColToGlobal[cg2];
942	+	#else
943	+	unique_id_1 = AtomLocalToGlobal[atom1];
944	+	unique_id_2 = AtomLocalToGlobal[atom2];
945	+	int group1 = cgLocalToGlobal[cg1];
946	+	int group2 = cgLocalToGlobal[cg2];
947	+	#endif
948
783	–	// this situation should only arise in MPI simulations
949		if (unique_id_1 == unique_id_2) return true;
950	<
950	>
951	>	#ifdef IS_MPI
952		// this prevents us from doing the pair on multiple processors
953		if (unique_id_1 < unique_id_2) {
954		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
955		} else {
956	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
956	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
957		}
958	+	#endif
959	+
960	+	#ifndef IS_MPI
961	+	if (group1 == group2) {
962	+	if (unique_id_1 < unique_id_2) return true;
963	+	}
964		#endif
965	+
966		return false;
967		}
968
#	Line 803 | Line 976 | namespace OpenMD {
976		* field) must still be handled for these pairs.
977		*/
978		bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
979	<	int unique_id_2;
979	>
980	>	// excludesForAtom was constructed to use row/column indices in the MPI
981	>	// version, and to use local IDs in the non-MPI version:
982
808	–	#ifdef IS_MPI
809	–	// in MPI, we have to look up the unique IDs for the row atom.
810	–	unique_id_2 = AtomColToGlobal[atom2];
811	–	#else
812	–	// in the normal loop, the atom numbers are unique
813	–	unique_id_2 = atom2;
814	–	#endif
815	–
983		for (vector<int>::iterator i = excludesForAtom[atom1].begin();
984		i != excludesForAtom[atom1].end(); ++i) {
985	<	if ( (*i) == unique_id_2 ) return true;
985	>	if ( (*i) == atom2 ) return true;
986		}
987
988		return false;
#	Line 840 | Line 1007 | namespace OpenMD {
1007
1008		// filling interaction blocks with pointers
1009		void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1010	<	int atom1, int atom2) {
1010	>	int atom1, int atom2,
1011	>	bool newAtom1) {
1012
1013		idat.excluded = excludeAtomPair(atom1, atom2);
1014	<
1014	>
1015	>	if (newAtom1) {
1016	>
1017		#ifdef IS_MPI
1018	<	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1019	<	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1020	<	//                         ff_->getAtomType(identsCol[atom2]) );
1021	<
1018	>	idat.atid1 = identsRow[atom1];
1019	>	idat.atid2 = identsCol[atom2];
1020	>
1021	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1022	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1023	>	} else {
1024	>	idat.sameRegion = false;
1025	>	}
1026	>
1027	>	if (storageLayout_ & DataStorage::dslAmat) {
1028	>	idat.A1 = &(atomRowData.aMat[atom1]);
1029	>	idat.A2 = &(atomColData.aMat[atom2]);
1030	>	}
1031	>
1032	>	if (storageLayout_ & DataStorage::dslTorque) {
1033	>	idat.t1 = &(atomRowData.torque[atom1]);
1034	>	idat.t2 = &(atomColData.torque[atom2]);
1035	>	}
1036	>
1037	>	if (storageLayout_ & DataStorage::dslDipole) {
1038	>	idat.dipole1 = &(atomRowData.dipole[atom1]);
1039	>	idat.dipole2 = &(atomColData.dipole[atom2]);
1040	>	}
1041	>
1042	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1043	>	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1044	>	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1045	>	}
1046	>
1047	>	if (storageLayout_ & DataStorage::dslDensity) {
1048	>	idat.rho1 = &(atomRowData.density[atom1]);
1049	>	idat.rho2 = &(atomColData.density[atom2]);
1050	>	}
1051	>
1052	>	if (storageLayout_ & DataStorage::dslFunctional) {
1053	>	idat.frho1 = &(atomRowData.functional[atom1]);
1054	>	idat.frho2 = &(atomColData.functional[atom2]);
1055	>	}
1056	>
1057	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1058	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1059	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1060	>	}
1061	>
1062	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1063	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1064	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1065	>	}
1066	>
1067	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1068	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1069	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1070	>	}
1071	>
1072	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1073	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1074	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1075	>	}
1076	>
1077	>	#else
1078	>
1079	>	idat.atid1 = idents[atom1];
1080	>	idat.atid2 = idents[atom2];
1081	>
1082	>	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1083	>	idat.sameRegion = (regions[atom1] == regions[atom2]);
1084	>	} else {
1085	>	idat.sameRegion = false;
1086	>	}
1087	>
1088	>	if (storageLayout_ & DataStorage::dslAmat) {
1089	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1090	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1091	>	}
1092	>
1093	>	if (storageLayout_ & DataStorage::dslTorque) {
1094	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1095	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1096	>	}
1097	>
1098	>	if (storageLayout_ & DataStorage::dslDipole) {
1099	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1100	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1101	>	}
1102	>
1103	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1104	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1105	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1106	>	}
1107	>
1108	>	if (storageLayout_ & DataStorage::dslDensity) {
1109	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1110	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1111	>	}
1112	>
1113	>	if (storageLayout_ & DataStorage::dslFunctional) {
1114	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1115	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1116	>	}
1117	>
1118	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1119	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1120	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1121	>	}
1122	>
1123	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1124	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1125	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1126	>	}
1127	>
1128	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1129	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1130	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1131	>	}
1132	>
1133	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1134	>	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1135	>	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1136	>	}
1137	>	#endif
1138	>
1139	>	} else {
1140	>	// atom1 is not new, so don't bother updating properties of that atom:
1141	>	#ifdef IS_MPI
1142	>	idat.atid2 = identsCol[atom2];
1143	>
1144	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1145	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1146	>	} else {
1147	>	idat.sameRegion = false;
1148	>	}
1149	>
1150		if (storageLayout_ & DataStorage::dslAmat) {
853	–	idat.A1 = &(atomRowData.aMat[atom1]);
1151		idat.A2 = &(atomColData.aMat[atom2]);
1152		}
1153
857	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
858	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
859	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
860	–	}
861	–
1154		if (storageLayout_ & DataStorage::dslTorque) {
863	–	idat.t1 = &(atomRowData.torque[atom1]);
1155		idat.t2 = &(atomColData.torque[atom2]);
1156		}
1157
1158	+	if (storageLayout_ & DataStorage::dslDipole) {
1159	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1160	+	}
1161	+
1162	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1163	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1164	+	}
1165	+
1166		if (storageLayout_ & DataStorage::dslDensity) {
868	–	idat.rho1 = &(atomRowData.density[atom1]);
1167		idat.rho2 = &(atomColData.density[atom2]);
1168		}
1169
1170		if (storageLayout_ & DataStorage::dslFunctional) {
873	–	idat.frho1 = &(atomRowData.functional[atom1]);
1171		idat.frho2 = &(atomColData.functional[atom2]);
1172		}
1173
1174		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
878	–	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1175		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1176		}
1177
1178		if (storageLayout_ & DataStorage::dslParticlePot) {
883	–	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1179		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1180		}
1181
1182		if (storageLayout_ & DataStorage::dslSkippedCharge) {
888	–	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1183		idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1184		}
1185
1186	<	#else
1186	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1187	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1188	>	}
1189
1190	<	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1191	<	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
896	<	//                         ff_->getAtomType(idents[atom2]) );
1190	>	#else
1191	>	idat.atid2 = idents[atom2];
1192
1193	+	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1194	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1195	+	} else {
1196	+	idat.sameRegion = false;
1197	+	}
1198	+
1199		if (storageLayout_ & DataStorage::dslAmat) {
899	–	idat.A1 = &(snap_->atomData.aMat[atom1]);
1200		idat.A2 = &(snap_->atomData.aMat[atom2]);
1201		}
1202
903	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
904	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
905	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
906	–	}
907	–
1203		if (storageLayout_ & DataStorage::dslTorque) {
909	–	idat.t1 = &(snap_->atomData.torque[atom1]);
1204		idat.t2 = &(snap_->atomData.torque[atom2]);
1205		}
1206
1207	+	if (storageLayout_ & DataStorage::dslDipole) {
1208	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1209	+	}
1210	+
1211	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1212	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1213	+	}
1214	+
1215		if (storageLayout_ & DataStorage::dslDensity) {
914	–	idat.rho1 = &(snap_->atomData.density[atom1]);
1216		idat.rho2 = &(snap_->atomData.density[atom2]);
1217		}
1218
1219		if (storageLayout_ & DataStorage::dslFunctional) {
919	–	idat.frho1 = &(snap_->atomData.functional[atom1]);
1220		idat.frho2 = &(snap_->atomData.functional[atom2]);
1221		}
1222
1223		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
924	–	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1224		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1225		}
1226
1227		if (storageLayout_ & DataStorage::dslParticlePot) {
929	–	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1228		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1229		}
1230
1231		if (storageLayout_ & DataStorage::dslSkippedCharge) {
934	–	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1232		idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1233		}
1234	+
1235	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1236	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1237	+	}
1238	+
1239		#endif
1240	+	}
1241		}
939	–
1242
1243	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1243	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat,
1244	>	int atom1, int atom2) {
1245		#ifdef IS_MPI
1246	<	pot_row[atom1] += 0.5 *  *(idat.pot);
1247	<	pot_col[atom2] += 0.5 *  *(idat.pot);
1246	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1247	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1248	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1249	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1250
1251		atomRowData.force[atom1] += *(idat.f1);
1252		atomColData.force[atom2] -= *(idat.f1);
1253	+
1254	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1255	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1256	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1257	+	}
1258	+
1259	+	if (storageLayout_ & DataStorage::dslElectricField) {
1260	+	atomRowData.electricField[atom1] += *(idat.eField1);
1261	+	atomColData.electricField[atom2] += *(idat.eField2);
1262	+	}
1263	+
1264	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1265	+	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1266	+	atomColData.sitePotential[atom2] += *(idat.sPot2);
1267	+	}
1268	+
1269		#else
1270		pairwisePot += *(idat.pot);
1271	+	excludedPot += *(idat.excludedPot);
1272
1273		snap_->atomData.force[atom1] += *(idat.f1);
1274		snap_->atomData.force[atom2] -= *(idat.f1);
1275	+
1276	+	if (idat.doParticlePot) {
1277	+	// This is the pairwise contribution to the particle pot.  The
1278	+	// embedding contribution is added in each of the low level
1279	+	// non-bonded routines.  In parallel, this calculation is done
1280	+	// in collectData, not in unpackInteractionData.
1281	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1282	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1283	+	}
1284	+
1285	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1286	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1287	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1288	+	}
1289	+
1290	+	if (storageLayout_ & DataStorage::dslElectricField) {
1291	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1292	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1293	+	}
1294	+
1295	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1296	+	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1297	+	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1298	+	}
1299	+
1300		#endif
1301
1302		}
#	Line 957 | Line 1304 | namespace OpenMD {
1304		/*
1305		* buildNeighborList
1306		*
1307	<	* first element of pair is row-indexed CutoffGroup
1308	<	* second element of pair is column-indexed CutoffGroup
1307	>	* Constructs the Verlet neighbor list for a force-matrix
1308	>	* decomposition.  In this case, each processor is responsible for
1309	>	* row-site interactions with column-sites.
1310	>	*
1311	>	* neighborList is returned as a packed array of neighboring
1312	>	* column-ordered CutoffGroups.  The starting position in
1313	>	* neighborList for each row-ordered CutoffGroup is given by the
1314	>	* returned vector point.
1315		*/
1316	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1317	<
1318	<	vector<pair<int, int> > neighborList;
1319	<	groupCutoffs cuts;
1316	>	void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
1317	>	vector<int>& point) {
1318	>	neighborList.clear();
1319	>	point.clear();
1320	>	int len = 0;
1321	>
1322		bool doAllPairs = false;
1323
1324	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1325	+	Mat3x3d box;
1326	+	Mat3x3d invBox;
1327	+
1328	+	Vector3d rs, scaled, dr;
1329	+	Vector3i whichCell;
1330	+	int cellIndex;
1331	+
1332		#ifdef IS_MPI
1333		cellListRow_.clear();
1334		cellListCol_.clear();
1335	+	point.resize(nGroupsInRow_+1);
1336		#else
1337		cellList_.clear();
1338	+	point.resize(nGroups_+1);
1339		#endif
1340	+
1341	+	if (!usePeriodicBoundaryConditions_) {
1342	+	box = snap_->getBoundingBox();
1343	+	invBox = snap_->getInvBoundingBox();
1344	+	} else {
1345	+	box = snap_->getHmat();
1346	+	invBox = snap_->getInvHmat();
1347	+	}
1348	+
1349	+	Vector3d A = box.getColumn(0);
1350	+	Vector3d B = box.getColumn(1);
1351	+	Vector3d C = box.getColumn(2);
1352
1353	<	RealType rList_ = (largestRcut_ + skinThickness_);
1354	<	RealType rl2 = rList_ * rList_;
1355	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
1356	<	Mat3x3d Hmat = snap_->getHmat();
980	<	Vector3d Hx = Hmat.getColumn(0);
981	<	Vector3d Hy = Hmat.getColumn(1);
982	<	Vector3d Hz = Hmat.getColumn(2);
1353	>	// Required for triclinic cells
1354	>	Vector3d AxB = cross(A, B);
1355	>	Vector3d BxC = cross(B, C);
1356	>	Vector3d CxA = cross(C, A);
1357
1358	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
1359	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
1360	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
1358	>	// unit vectors perpendicular to the faces of the triclinic cell:
1359	>	AxB.normalize();
1360	>	BxC.normalize();
1361	>	CxA.normalize();
1362
1363	<	// handle small boxes where the cell offsets can end up repeating cells
1363	>	// A set of perpendicular lengths in triclinic cells:
1364	>	RealType Wa = abs(dot(A, BxC));
1365	>	RealType Wb = abs(dot(B, CxA));
1366	>	RealType Wc = abs(dot(C, AxB));
1367
1368	+	nCells_.x() = int( Wa / rList_ );
1369	+	nCells_.y() = int( Wb / rList_ );
1370	+	nCells_.z() = int( Wc / rList_ );
1371	+
1372	+	// handle small boxes where the cell offsets can end up repeating cells
1373		if (nCells_.x() < 3) doAllPairs = true;
1374		if (nCells_.y() < 3) doAllPairs = true;
1375		if (nCells_.z() < 3) doAllPairs = true;
1376	<
994	<	Mat3x3d invHmat = snap_->getInvHmat();
995	<	Vector3d rs, scaled, dr;
996	<	Vector3i whichCell;
997	<	int cellIndex;
1376	>
1377		int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1378	<
1378	>
1379		#ifdef IS_MPI
1380		cellListRow_.resize(nCtot);
1381		cellListCol_.resize(nCtot);
1382		#else
1383		cellList_.resize(nCtot);
1384		#endif
1385	<
1385	>
1386		if (!doAllPairs) {
1387	+
1388		#ifdef IS_MPI
1389	<
1389	>
1390		for (int i = 0; i < nGroupsInRow_; i++) {
1391		rs = cgRowData.position[i];
1392
1393		// scaled positions relative to the box vectors
1394	<	scaled = invHmat * rs;
1394	>	scaled = invBox * rs;
1395
1396		// wrap the vector back into the unit box by subtracting integer box
1397		// numbers
1398		for (int j = 0; j < 3; j++) {
1399		scaled[j] -= roundMe(scaled[j]);
1400		scaled[j] += 0.5;
1401	+	// Handle the special case when an object is exactly on the
1402	+	// boundary (a scaled coordinate of 1.0 is the same as
1403	+	// scaled coordinate of 0.0)
1404	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1405		}
1406
1407		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1031 | Line 1415 | namespace OpenMD {
1415		// add this cutoff group to the list of groups in this cell;
1416		cellListRow_[cellIndex].push_back(i);
1417		}
1034	–
1418		for (int i = 0; i < nGroupsInCol_; i++) {
1419		rs = cgColData.position[i];
1420
1421		// scaled positions relative to the box vectors
1422	<	scaled = invHmat * rs;
1422	>	scaled = invBox * rs;
1423
1424		// wrap the vector back into the unit box by subtracting integer box
1425		// numbers
1426		for (int j = 0; j < 3; j++) {
1427		scaled[j] -= roundMe(scaled[j]);
1428		scaled[j] += 0.5;
1429	+	// Handle the special case when an object is exactly on the
1430	+	// boundary (a scaled coordinate of 1.0 is the same as
1431	+	// scaled coordinate of 0.0)
1432	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1433		}
1434
1435		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1056 | Line 1443 | namespace OpenMD {
1443		// add this cutoff group to the list of groups in this cell;
1444		cellListCol_[cellIndex].push_back(i);
1445		}
1446	+
1447		#else
1448		for (int i = 0; i < nGroups_; i++) {
1449		rs = snap_->cgData.position[i];
1450
1451		// scaled positions relative to the box vectors
1452	<	scaled = invHmat * rs;
1452	>	scaled = invBox * rs;
1453
1454		// wrap the vector back into the unit box by subtracting integer box
1455		// numbers
1456		for (int j = 0; j < 3; j++) {
1457		scaled[j] -= roundMe(scaled[j]);
1458		scaled[j] += 0.5;
1459	+	// Handle the special case when an object is exactly on the
1460	+	// boundary (a scaled coordinate of 1.0 is the same as
1461	+	// scaled coordinate of 0.0)
1462	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1463		}
1464
1465		// find xyz-indices of cell that cutoffGroup is in.
1466	<	whichCell.x() = nCells_.x() * scaled.x();
1467	<	whichCell.y() = nCells_.y() * scaled.y();
1468	<	whichCell.z() = nCells_.z() * scaled.z();
1466	>	whichCell.x() = int(nCells_.x() * scaled.x());
1467	>	whichCell.y() = int(nCells_.y() * scaled.y());
1468	>	whichCell.z() = int(nCells_.z() * scaled.z());
1469
1470		// find single index of this cell:
1471	<	cellIndex = Vlinear(whichCell, nCells_);
1471	>	cellIndex = Vlinear(whichCell, nCells_);
1472
1473		// add this cutoff group to the list of groups in this cell;
1474		cellList_[cellIndex].push_back(i);
1475		}
1476	+
1477		#endif
1478
1086	–	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1087	–	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1088	–	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1089	–	Vector3i m1v(m1x, m1y, m1z);
1090	–	int m1 = Vlinear(m1v, nCells_);
1091	–
1092	–	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1093	–	os != cellOffsets_.end(); ++os) {
1094	–
1095	–	Vector3i m2v = m1v + (*os);
1096	–
1097	–	if (m2v.x() >= nCells_.x()) {
1098	–	m2v.x() = 0;
1099	–	} else if (m2v.x() < 0) {
1100	–	m2v.x() = nCells_.x() - 1;
1101	–	}
1102	–
1103	–	if (m2v.y() >= nCells_.y()) {
1104	–	m2v.y() = 0;
1105	–	} else if (m2v.y() < 0) {
1106	–	m2v.y() = nCells_.y() - 1;
1107	–	}
1108	–
1109	–	if (m2v.z() >= nCells_.z()) {
1110	–	m2v.z() = 0;
1111	–	} else if (m2v.z() < 0) {
1112	–	m2v.z() = nCells_.z() - 1;
1113	–	}
1114	–
1115	–	int m2 = Vlinear (m2v, nCells_);
1116	–
1479		#ifdef IS_MPI
1480	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1481	<	j1 != cellListRow_[m1].end(); ++j1) {
1120	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1121	<	j2 != cellListCol_[m2].end(); ++j2) {
1122	<
1123	<	// Always do this if we're in different cells or if
1124	<	// we're in the same cell and the global index of the
1125	<	// j2 cutoff group is less than the j1 cutoff group
1126	<
1127	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1128	<	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1129	<	snap_->wrapVector(dr);
1130	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1131	<	if (dr.lengthSquare() < cuts.third) {
1132	<	neighborList.push_back(make_pair((*j1), (*j2)));
1133	<	}
1134	<	}
1135	<	}
1136	<	}
1480	>	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1481	>	rs = cgRowData.position[j1];
1482		#else
1483	+
1484	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1485	+	rs = snap_->cgData.position[j1];
1486	+	#endif
1487	+	point[j1] = len;
1488	+
1489	+	// scaled positions relative to the box vectors
1490	+	scaled = invBox * rs;
1491	+
1492	+	// wrap the vector back into the unit box by subtracting integer box
1493	+	// numbers
1494	+	for (int j = 0; j < 3; j++) {
1495	+	scaled[j] -= roundMe(scaled[j]);
1496	+	scaled[j] += 0.5;
1497	+	// Handle the special case when an object is exactly on the
1498	+	// boundary (a scaled coordinate of 1.0 is the same as
1499	+	// scaled coordinate of 0.0)
1500	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1501	+	}
1502	+
1503	+	// find xyz-indices of cell that cutoffGroup is in.
1504	+	whichCell.x() = nCells_.x() * scaled.x();
1505	+	whichCell.y() = nCells_.y() * scaled.y();
1506	+	whichCell.z() = nCells_.z() * scaled.z();
1507	+
1508	+	// find single index of this cell:
1509	+	int m1 = Vlinear(whichCell, nCells_);
1510	+
1511	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1512	+	os != cellOffsets_.end(); ++os) {
1513
1514	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1515	<	j1 != cellList_[m1].end(); ++j1) {
1516	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1517	<	j2 != cellList_[m2].end(); ++j2) {
1518	<
1519	<	// Always do this if we're in different cells or if
1520	<	// we're in the same cell and the global index of the
1521	<	// j2 cutoff group is less than the j1 cutoff group
1522	<
1523	<	if (m2 != m1 || (*j2) < (*j1)) {
1524	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1525	<	snap_->wrapVector(dr);
1526	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1527	<	if (dr.lengthSquare() < cuts.third) {
1528	<	neighborList.push_back(make_pair((*j1), (*j2)));
1529	<	}
1530	<	}
1531	<	}
1514	>	Vector3i m2v = whichCell + (*os);
1515	>
1516	>	if (m2v.x() >= nCells_.x()) {
1517	>	m2v.x() = 0;
1518	>	} else if (m2v.x() < 0) {
1519	>	m2v.x() = nCells_.x() - 1;
1520	>	}
1521	>
1522	>	if (m2v.y() >= nCells_.y()) {
1523	>	m2v.y() = 0;
1524	>	} else if (m2v.y() < 0) {
1525	>	m2v.y() = nCells_.y() - 1;
1526	>	}
1527	>
1528	>	if (m2v.z() >= nCells_.z()) {
1529	>	m2v.z() = 0;
1530	>	} else if (m2v.z() < 0) {
1531	>	m2v.z() = nCells_.z() - 1;
1532	>	}
1533	>	int m2 = Vlinear (m2v, nCells_);
1534	>	#ifdef IS_MPI
1535	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1536	>	j2 != cellListCol_[m2].end(); ++j2) {
1537	>
1538	>	// In parallel, we need to visit *all* pairs of row
1539	>	// & column indicies and will divide labor in the
1540	>	// force evaluation later.
1541	>	dr = cgColData.position[(*j2)] - rs;
1542	>	if (usePeriodicBoundaryConditions_) {
1543	>	snap_->wrapVector(dr);
1544	>	}
1545	>	if (dr.lengthSquare() < rListSq_) {
1546	>	neighborList.push_back( (*j2) );
1547	>	++len;
1548	>	}
1549	>	}
1550	>	#else
1551	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1552	>	j2 != cellList_[m2].end(); ++j2) {
1553	>
1554	>	// Always do this if we're in different cells or if
1555	>	// we're in the same cell and the global index of
1556	>	// the j2 cutoff group is greater than or equal to
1557	>	// the j1 cutoff group.  Note that Rappaport's code
1558	>	// has a "less than" conditional here, but that
1559	>	// deals with atom-by-atom computation.  OpenMD
1560	>	// allows atoms within a single cutoff group to
1561	>	// interact with each other.
1562	>
1563	>	if ( (*j2) >= j1 ) {
1564	>
1565	>	dr = snap_->cgData.position[(*j2)] - rs;
1566	>	if (usePeriodicBoundaryConditions_) {
1567	>	snap_->wrapVector(dr);
1568		}
1569	<	#endif
1569	>	if ( dr.lengthSquare() < rListSq_) {
1570	>	neighborList.push_back( (*j2) );
1571	>	++len;
1572	>	}
1573		}
1574	<	}
1574	>	}
1575	>	#endif
1576		}
1577	<	}
1577	>	}
1578		} else {
1579		// branch to do all cutoff group pairs
1580		#ifdef IS_MPI
1581		for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1582	<	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1583	<	dr = cgColData.position[j2] - cgRowData.position[j1];
1584	<	snap_->wrapVector(dr);
1585	<	cuts = getGroupCutoffs( j1, j2 );
1586	<	if (dr.lengthSquare() < cuts.third) {
1587	<	neighborList.push_back(make_pair(j1, j2));
1582	>	point[j1] = len;
1583	>	rs = cgRowData.position[j1];
1584	>	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1585	>	dr = cgColData.position[j2] - rs;
1586	>	if (usePeriodicBoundaryConditions_) {
1587	>	snap_->wrapVector(dr);
1588		}
1589	+	if (dr.lengthSquare() < rListSq_) {
1590	+	neighborList.push_back( j2 );
1591	+	++len;
1592	+	}
1593		}
1594	<	}
1594	>	}
1595		#else
1596	<	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1597	<	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1598	<	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1599	<	snap_->wrapVector(dr);
1600	<	cuts = getGroupCutoffs( j1, j2 );
1601	<	if (dr.lengthSquare() < cuts.third) {
1602	<	neighborList.push_back(make_pair(j1, j2));
1596	>	// include all groups here.
1597	>	for (int j1 = 0; j1 < nGroups_; j1++) {
1598	>	point[j1] = len;
1599	>	rs = snap_->cgData.position[j1];
1600	>	// include self group interactions j2 == j1
1601	>	for (int j2 = j1; j2 < nGroups_; j2++) {
1602	>	dr = snap_->cgData.position[j2] - rs;
1603	>	if (usePeriodicBoundaryConditions_) {
1604	>	snap_->wrapVector(dr);
1605		}
1606	<	}
1607	<	}
1606	>	if (dr.lengthSquare() < rListSq_) {
1607	>	neighborList.push_back( j2 );
1608	>	++len;
1609	>	}
1610	>	}
1611	>	}
1612		#endif
1613		}
1614	<
1614	>
1615	>	#ifdef IS_MPI
1616	>	point[nGroupsInRow_] = len;
1617	>	#else
1618	>	point[nGroups_] = len;
1619	>	#endif
1620	>
1621		// save the local cutoff group positions for the check that is
1622		// done on each loop:
1623		saved_CG_positions_.clear();
1624	+	saved_CG_positions_.reserve(nGroups_);
1625		for (int i = 0; i < nGroups_; i++)
1626		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1195	–
1196	–	return neighborList;
1627		}
1628		} //end namespace OpenMD

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