[ViewVC] Diff of: OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp

Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1590 by gezelter, Mon Jul 11 01:39:49 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1893 by gezelter, Wed Jun 19 17:19:07 2013 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	+	// In a parallel computation, row and colum scans must visit all
54	+	// surrounding cells (not just the 14 upper triangular blocks that
55	+	// are used when the processor can see all pairs)
56	+	#ifdef IS_MPI
57	+	cellOffsets_.clear();
58	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
66	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	+	#endif
86	+	}
87	+
88	+
89		/**
90		* distributeInitialData is essentially a copy of the older fortran
91		* SimulationSetup
92		*/
54	–
93		void ForceMatrixDecomposition::distributeInitialData() {
94		snap_ = sman_->getCurrentSnapshot();
95		storageLayout_ = sman_->getStorageLayout();
96		ff_ = info_->getForceField();
97		nLocal_ = snap_->getNumberOfAtoms();
98	<
98	>
99		nGroups_ = info_->getNLocalCutoffGroups();
100		// gather the information for atomtype IDs (atids):
101		idents = info_->getIdentArray();
#	Line 71 \| Line 109 \| namespace OpenMD {
109		PairList* oneTwo = info_->getOneTwoInteractions();
110		PairList* oneThree = info_->getOneThreeInteractions();
111		PairList* oneFour = info_->getOneFourInteractions();
112	<
112	>
113	>	if (needVelocities_)
114	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition \|
115	>	DataStorage::dslVelocity);
116	>	else
117	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118	>
119		#ifdef IS_MPI
120
121	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
122	<	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_);
121	>	MPI::Intracomm row = rowComm.getComm();
122	>	MPI::Intracomm col = colComm.getComm();
123
124	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
125	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
126	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
127	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
128	<	AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
124	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
125	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
126	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
127	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
128	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
129
130	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
131	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
132	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
133	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
130	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
131	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
132	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
133	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
134	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
135
136	<	nAtomsInRow_ = AtomCommIntRow->getSize();
137	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
138	<	nGroupsInRow_ = cgCommIntRow->getSize();
139	<	nGroupsInCol_ = cgCommIntColumn->getSize();
136	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
137	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
138	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
139	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
140
141	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
142	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
143	+	nGroupsInRow_ = cgPlanIntRow->getSize();
144	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
145	+
146		// Modify the data storage objects with the correct layouts and sizes:
147		atomRowData.resize(nAtomsInRow_);
148		atomRowData.setStorageLayout(storageLayout_);
#	Line 104 \| Line 151 \| namespace OpenMD {
151		cgRowData.resize(nGroupsInRow_);
152		cgRowData.setStorageLayout(DataStorage::dslPosition);
153		cgColData.resize(nGroupsInCol_);
154	<	cgColData.setStorageLayout(DataStorage::dslPosition);
155	<
154	>	if (needVelocities_)
155	>	// we only need column velocities if we need them.
156	>	cgColData.setStorageLayout(DataStorage::dslPosition \|
157	>	DataStorage::dslVelocity);
158	>	else
159	>	cgColData.setStorageLayout(DataStorage::dslPosition);
160	>
161		identsRow.resize(nAtomsInRow_);
162		identsCol.resize(nAtomsInCol_);
163
164	<	AtomCommIntRow->gather(idents, identsRow);
165	<	AtomCommIntColumn->gather(idents, identsCol);
164	>	AtomPlanIntRow->gather(idents, identsRow);
165	>	AtomPlanIntColumn->gather(idents, identsCol);
166
167		// allocate memory for the parallel objects
168	+	atypesRow.resize(nAtomsInRow_);
169	+	atypesCol.resize(nAtomsInCol_);
170	+
171	+	for (int i = 0; i < nAtomsInRow_; i++)
172	+	atypesRow[i] = ff_->getAtomType(identsRow[i]);
173	+	for (int i = 0; i < nAtomsInCol_; i++)
174	+	atypesCol[i] = ff_->getAtomType(identsCol[i]);
175	+
176	+	pot_row.resize(nAtomsInRow_);
177	+	pot_col.resize(nAtomsInCol_);
178	+
179	+	expot_row.resize(nAtomsInRow_);
180	+	expot_col.resize(nAtomsInCol_);
181	+
182		AtomRowToGlobal.resize(nAtomsInRow_);
183		AtomColToGlobal.resize(nAtomsInCol_);
184	+	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
185	+	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
186	+
187		cgRowToGlobal.resize(nGroupsInRow_);
188		cgColToGlobal.resize(nGroupsInCol_);
189	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
190	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
191	+
192		massFactorsRow.resize(nAtomsInRow_);
193		massFactorsCol.resize(nAtomsInCol_);
194	<	pot_row.resize(nAtomsInRow_);
195	<	pot_col.resize(nAtomsInCol_);
194	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
195	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
196
125	–	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
126	–	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
127	–
128	–	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
129	–	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
130	–
131	–	AtomCommRealRow->gather(massFactors, massFactorsRow);
132	–	AtomCommRealColumn->gather(massFactors, massFactorsCol);
133	–
197		groupListRow_.clear();
198		groupListRow_.resize(nGroupsInRow_);
199		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 185 \| Line 248 \| namespace OpenMD {
248		}
249		}
250
251	<	#endif
189	<
190	<	groupList_.clear();
191	<	groupList_.resize(nGroups_);
192	<	for (int i = 0; i < nGroups_; i++) {
193	<	int gid = cgLocalToGlobal[i];
194	<	for (int j = 0; j < nLocal_; j++) {
195	<	int aid = AtomLocalToGlobal[j];
196	<	if (globalGroupMembership[aid] == gid) {
197	<	groupList_[i].push_back(j);
198	<	}
199	<	}
200	<	}
201	<
251	>	#else
252		excludesForAtom.clear();
253		excludesForAtom.resize(nLocal_);
254		toposForAtom.clear();
#	Line 231 \| Line 281 \| namespace OpenMD {
281		}
282		}
283		}
284	<
284	>	#endif
285	>
286	>	// allocate memory for the parallel objects
287	>	atypesLocal.resize(nLocal_);
288	>
289	>	for (int i = 0; i < nLocal_; i++)
290	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
291	>
292	>	groupList_.clear();
293	>	groupList_.resize(nGroups_);
294	>	for (int i = 0; i < nGroups_; i++) {
295	>	int gid = cgLocalToGlobal[i];
296	>	for (int j = 0; j < nLocal_; j++) {
297	>	int aid = AtomLocalToGlobal[j];
298	>	if (globalGroupMembership[aid] == gid) {
299	>	groupList_[i].push_back(j);
300	>	}
301	>	}
302	>	}
303	>
304	>
305		createGtypeCutoffMap();
306
307		}
#	Line 239 \| Line 309 \| namespace OpenMD {
309		void ForceMatrixDecomposition::createGtypeCutoffMap() {
310
311		RealType tol = 1e-6;
312	<	RealType rc;
312	>	largestRcut_ = 0.0;
313		int atid;
314		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315	+
316		map<int, RealType> atypeCutoff;
317
318		for (set<AtomType*>::iterator at = atypes.begin();
#	Line 249 \| Line 320 \| namespace OpenMD {
320		atid = (*at)->getIdent();
321		if (userChoseCutoff_)
322		atypeCutoff[atid] = userCutoff_;
323	<	else
323	>	else
324		atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
325		}
326	<
326	>
327		vector<RealType> gTypeCutoffs;
328		// first we do a single loop over the cutoff groups to find the
329		// largest cutoff for any atypes present in this group.
#	Line 312 \| Line 383 \| namespace OpenMD {
383		vector<RealType> groupCutoff(nGroups_, 0.0);
384		groupToGtype.resize(nGroups_);
385		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
315	–
386		groupCutoff[cg1] = 0.0;
387		vector<int> atomList = getAtomsInGroupRow(cg1);
318	–
388		for (vector<int>::iterator ia = atomList.begin();
389		ia != atomList.end(); ++ia) {
390		int atom1 = (*ia);
391		atid = idents[atom1];
392	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
392	>	if (atypeCutoff[atid] > groupCutoff[cg1])
393		groupCutoff[cg1] = atypeCutoff[atid];
325	–	}
394		}
395	<
395	>
396		bool gTypeFound = false;
397	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
397	>	for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
398		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
399		groupToGtype[cg1] = gt;
400		gTypeFound = true;
401		}
402		}
403	<	if (!gTypeFound) {
403	>	if (!gTypeFound) {
404		gTypeCutoffs.push_back( groupCutoff[cg1] );
405		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
406		}
#	Line 351 \| Line 419 \| namespace OpenMD {
419
420		RealType tradRcut = groupMax;
421
422	<	for (int i = 0; i < gTypeCutoffs.size(); i++) {
423	<	for (int j = 0; j < gTypeCutoffs.size(); j++) {
422	>	for (unsigned int i = 0; i < gTypeCutoffs.size(); i++) {
423	>	for (unsigned int j = 0; j < gTypeCutoffs.size(); j++) {
424		RealType thisRcut;
425		switch(cutoffPolicy_) {
426		case TRADITIONAL:
#	Line 376 \| Line 444 \| namespace OpenMD {
444
445		pair<int,int> key = make_pair(i,j);
446		gTypeCutoffMap[key].first = thisRcut;
379	–
447		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
381	–
448		gTypeCutoffMap[key].second = thisRcut*thisRcut;
383	–
449		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
385	–
450		// sanity check
451
452		if (userChoseCutoff_) {
#	Line 399 \| Line 463 \| namespace OpenMD {
463		}
464		}
465
402	–
466		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467		int i, j;
468		#ifdef IS_MPI
#	Line 413 \| Line 476 \| namespace OpenMD {
476		}
477
478		int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
479	<	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
479	>	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
480		if (toposForAtom[atom1][j] == atom2)
481		return topoDist[atom1][j];
482	<	}
482	>	}
483		return 0;
484		}
485
486		void ForceMatrixDecomposition::zeroWorkArrays() {
487		pairwisePot = 0.0;
488		embeddingPot = 0.0;
489	+	excludedPot = 0.0;
490	+	excludedSelfPot = 0.0;
491
492		#ifdef IS_MPI
493		if (storageLayout_ & DataStorage::dslForce) {
#	Line 441 \| Line 506 \| namespace OpenMD {
506		fill(pot_col.begin(), pot_col.end(),
507		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
508
509	+	fill(expot_row.begin(), expot_row.end(),
510	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
511	+
512	+	fill(expot_col.begin(), expot_col.end(),
513	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
514	+
515		if (storageLayout_ & DataStorage::dslParticlePot) {
516		fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
517		0.0);
#	Line 474 \| Line 545 \| namespace OpenMD {
545		atomColData.skippedCharge.end(), 0.0);
546		}
547
548	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
549	+	fill(atomRowData.flucQFrc.begin(),
550	+	atomRowData.flucQFrc.end(), 0.0);
551	+	fill(atomColData.flucQFrc.begin(),
552	+	atomColData.flucQFrc.end(), 0.0);
553	+	}
554	+
555	+	if (storageLayout_ & DataStorage::dslElectricField) {
556	+	fill(atomRowData.electricField.begin(),
557	+	atomRowData.electricField.end(), V3Zero);
558	+	fill(atomColData.electricField.begin(),
559	+	atomColData.electricField.end(), V3Zero);
560	+	}
561	+
562		#endif
563		// even in parallel, we need to zero out the local arrays:
564
#	Line 486 \| Line 571 \| namespace OpenMD {
571		fill(snap_->atomData.density.begin(),
572		snap_->atomData.density.end(), 0.0);
573		}
574	+
575		if (storageLayout_ & DataStorage::dslFunctional) {
576		fill(snap_->atomData.functional.begin(),
577		snap_->atomData.functional.end(), 0.0);
578		}
579	+
580		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
581		fill(snap_->atomData.functionalDerivative.begin(),
582		snap_->atomData.functionalDerivative.end(), 0.0);
583		}
584	+
585		if (storageLayout_ & DataStorage::dslSkippedCharge) {
586		fill(snap_->atomData.skippedCharge.begin(),
587		snap_->atomData.skippedCharge.end(), 0.0);
588		}
589	<
589	>
590	>	if (storageLayout_ & DataStorage::dslElectricField) {
591	>	fill(snap_->atomData.electricField.begin(),
592	>	snap_->atomData.electricField.end(), V3Zero);
593	>	}
594		}
595
596
#	Line 508 \| Line 600 \| namespace OpenMD {
600		#ifdef IS_MPI
601
602		// gather up the atomic positions
603	<	AtomCommVectorRow->gather(snap_->atomData.position,
603	>	AtomPlanVectorRow->gather(snap_->atomData.position,
604		atomRowData.position);
605	<	AtomCommVectorColumn->gather(snap_->atomData.position,
605	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
606		atomColData.position);
607
608		// gather up the cutoff group positions
609	<	cgCommVectorRow->gather(snap_->cgData.position,
609	>
610	>	cgPlanVectorRow->gather(snap_->cgData.position,
611		cgRowData.position);
612	<	cgCommVectorColumn->gather(snap_->cgData.position,
612	>
613	>	cgPlanVectorColumn->gather(snap_->cgData.position,
614		cgColData.position);
615	+
616	+
617	+
618	+	if (needVelocities_) {
619	+	// gather up the atomic velocities
620	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
621	+	atomColData.velocity);
622	+
623	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
624	+	cgColData.velocity);
625	+	}
626	+
627
628		// if needed, gather the atomic rotation matrices
629		if (storageLayout_ & DataStorage::dslAmat) {
630	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
630	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
631		atomRowData.aMat);
632	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
632	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
633		atomColData.aMat);
634		}
635	<
636	<	// if needed, gather the atomic eletrostatic frames
637	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
638	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
639	<	atomRowData.electroFrame);
640	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
641	<	atomColData.electroFrame);
635	>
636	>	// if needed, gather the atomic eletrostatic information
637	>	if (storageLayout_ & DataStorage::dslDipole) {
638	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
639	>	atomRowData.dipole);
640	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
641	>	atomColData.dipole);
642		}
643
644	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
645	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
646	+	atomRowData.quadrupole);
647	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
648	+	atomColData.quadrupole);
649	+	}
650	+
651	+	// if needed, gather the atomic fluctuating charge values
652	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
653	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
654	+	atomRowData.flucQPos);
655	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
656	+	atomColData.flucQPos);
657	+	}
658	+
659		#endif
660		}
661
#	Line 548 \| Line 669 \| namespace OpenMD {
669
670		if (storageLayout_ & DataStorage::dslDensity) {
671
672	<	AtomCommRealRow->scatter(atomRowData.density,
672	>	AtomPlanRealRow->scatter(atomRowData.density,
673		snap_->atomData.density);
674
675		int n = snap_->atomData.density.size();
676		vector<RealType> rho_tmp(n, 0.0);
677	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
677	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
678		for (int i = 0; i < n; i++)
679		snap_->atomData.density[i] += rho_tmp[i];
680		}
681	+
682	+	// this isn't necessary if we don't have polarizable atoms, but
683	+	// we'll leave it here for now.
684	+	if (storageLayout_ & DataStorage::dslElectricField) {
685	+
686	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
687	+	snap_->atomData.electricField);
688	+
689	+	int n = snap_->atomData.electricField.size();
690	+	vector<Vector3d> field_tmp(n, V3Zero);
691	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
692	+	field_tmp);
693	+	for (int i = 0; i < n; i++)
694	+	snap_->atomData.electricField[i] += field_tmp[i];
695	+	}
696		#endif
697		}
698
#	Line 569 \| Line 705 \| namespace OpenMD {
705		storageLayout_ = sman_->getStorageLayout();
706		#ifdef IS_MPI
707		if (storageLayout_ & DataStorage::dslFunctional) {
708	<	AtomCommRealRow->gather(snap_->atomData.functional,
708	>	AtomPlanRealRow->gather(snap_->atomData.functional,
709		atomRowData.functional);
710	<	AtomCommRealColumn->gather(snap_->atomData.functional,
710	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
711		atomColData.functional);
712		}
713
714		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
715	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
715	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
716		atomRowData.functionalDerivative);
717	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
717	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
718		atomColData.functionalDerivative);
719		}
720		#endif
#	Line 592 \| Line 728 \| namespace OpenMD {
728		int n = snap_->atomData.force.size();
729		vector<Vector3d> frc_tmp(n, V3Zero);
730
731	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
731	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
732		for (int i = 0; i < n; i++) {
733		snap_->atomData.force[i] += frc_tmp[i];
734		frc_tmp[i] = 0.0;
735		}
736
737	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
738	<	for (int i = 0; i < n; i++)
737	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
738	>	for (int i = 0; i < n; i++) {
739		snap_->atomData.force[i] += frc_tmp[i];
740	+	}
741
742		if (storageLayout_ & DataStorage::dslTorque) {
743
744		int nt = snap_->atomData.torque.size();
745		vector<Vector3d> trq_tmp(nt, V3Zero);
746
747	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
747	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
748		for (int i = 0; i < nt; i++) {
749		snap_->atomData.torque[i] += trq_tmp[i];
750		trq_tmp[i] = 0.0;
751		}
752
753	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
753	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
754		for (int i = 0; i < nt; i++)
755		snap_->atomData.torque[i] += trq_tmp[i];
756		}
#	Line 623 \| Line 760 \| namespace OpenMD {
760		int ns = snap_->atomData.skippedCharge.size();
761		vector<RealType> skch_tmp(ns, 0.0);
762
763	<	AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
763	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
764		for (int i = 0; i < ns; i++) {
765		snap_->atomData.skippedCharge[i] += skch_tmp[i];
766		skch_tmp[i] = 0.0;
767		}
768
769	<	AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
770	<	for (int i = 0; i < ns; i++)
769	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
770	>	for (int i = 0; i < ns; i++)
771		snap_->atomData.skippedCharge[i] += skch_tmp[i];
772	+
773		}
774
775	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
776	+
777	+	int nq = snap_->atomData.flucQFrc.size();
778	+	vector<RealType> fqfrc_tmp(nq, 0.0);
779	+
780	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
781	+	for (int i = 0; i < nq; i++) {
782	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
783	+	fqfrc_tmp[i] = 0.0;
784	+	}
785	+
786	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
787	+	for (int i = 0; i < nq; i++)
788	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
789	+
790	+	}
791	+
792	+	if (storageLayout_ & DataStorage::dslElectricField) {
793	+
794	+	int nef = snap_->atomData.electricField.size();
795	+	vector<Vector3d> efield_tmp(nef, V3Zero);
796	+
797	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
798	+	for (int i = 0; i < nef; i++) {
799	+	snap_->atomData.electricField[i] += efield_tmp[i];
800	+	efield_tmp[i] = 0.0;
801	+	}
802	+
803	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
804	+	for (int i = 0; i < nef; i++)
805	+	snap_->atomData.electricField[i] += efield_tmp[i];
806	+	}
807	+
808	+
809		nLocal_ = snap_->getNumberOfAtoms();
810
811		vector<potVec> pot_temp(nLocal_,
812		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
813	+	vector<potVec> expot_temp(nLocal_,
814	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
815
816		// scatter/gather pot_row into the members of my column
817
818	<	AtomCommPotRow->scatter(pot_row, pot_temp);
818	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
819	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
820
821	<	for (int ii = 0; ii < pot_temp.size(); ii++ )
821	>	for (int ii = 0; ii < pot_temp.size(); ii++ )
822		pairwisePot += pot_temp[ii];
823	<
823	>
824	>	for (int ii = 0; ii < expot_temp.size(); ii++ )
825	>	excludedPot += expot_temp[ii];
826	>
827	>	if (storageLayout_ & DataStorage::dslParticlePot) {
828	>	// This is the pairwise contribution to the particle pot. The
829	>	// embedding contribution is added in each of the low level
830	>	// non-bonded routines. In single processor, this is done in
831	>	// unpackInteractionData, not in collectData.
832	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
833	>	for (int i = 0; i < nLocal_; i++) {
834	>	// factor of two is because the total potential terms are divided
835	>	// by 2 in parallel due to row/ column scatter
836	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
837	>	}
838	>	}
839	>	}
840	>
841		fill(pot_temp.begin(), pot_temp.end(),
842		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
843	+	fill(expot_temp.begin(), expot_temp.end(),
844	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
845
846	<	AtomCommPotColumn->scatter(pot_col, pot_temp);
846	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
847	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
848
849		for (int ii = 0; ii < pot_temp.size(); ii++ )
850		pairwisePot += pot_temp[ii];
851	+
852	+	for (int ii = 0; ii < expot_temp.size(); ii++ )
853	+	excludedPot += expot_temp[ii];
854	+
855	+	if (storageLayout_ & DataStorage::dslParticlePot) {
856	+	// This is the pairwise contribution to the particle pot. The
857	+	// embedding contribution is added in each of the low level
858	+	// non-bonded routines. In single processor, this is done in
859	+	// unpackInteractionData, not in collectData.
860	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
861	+	for (int i = 0; i < nLocal_; i++) {
862	+	// factor of two is because the total potential terms are divided
863	+	// by 2 in parallel due to row/ column scatter
864	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
865	+	}
866	+	}
867	+	}
868	+
869	+	if (storageLayout_ & DataStorage::dslParticlePot) {
870	+	int npp = snap_->atomData.particlePot.size();
871	+	vector<RealType> ppot_temp(npp, 0.0);
872	+
873	+	// This is the direct or embedding contribution to the particle
874	+	// pot.
875	+
876	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
877	+	for (int i = 0; i < npp; i++) {
878	+	snap_->atomData.particlePot[i] += ppot_temp[i];
879	+	}
880	+
881	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
882	+
883	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
884	+	for (int i = 0; i < npp; i++) {
885	+	snap_->atomData.particlePot[i] += ppot_temp[i];
886	+	}
887	+	}
888	+
889	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
890	+	RealType ploc1 = pairwisePot[ii];
891	+	RealType ploc2 = 0.0;
892	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
893	+	pairwisePot[ii] = ploc2;
894	+	}
895	+
896	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
897	+	RealType ploc1 = excludedPot[ii];
898	+	RealType ploc2 = 0.0;
899	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
900	+	excludedPot[ii] = ploc2;
901	+	}
902	+
903	+	// Here be dragons.
904	+	MPI::Intracomm col = colComm.getComm();
905	+
906	+	col.Allreduce(MPI::IN_PLACE,
907	+	&snap_->frameData.conductiveHeatFlux[0], 3,
908	+	MPI::REALTYPE, MPI::SUM);
909	+
910	+
911		#endif
912
913		}
914
915	<	int ForceMatrixDecomposition::getNAtomsInRow() {
915	>	/**
916	>	* Collects information obtained during the post-pair (and embedding
917	>	* functional) loops onto local data structures.
918	>	*/
919	>	void ForceMatrixDecomposition::collectSelfData() {
920	>	snap_ = sman_->getCurrentSnapshot();
921	>	storageLayout_ = sman_->getStorageLayout();
922	>
923		#ifdef IS_MPI
924	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
925	+	RealType ploc1 = embeddingPot[ii];
926	+	RealType ploc2 = 0.0;
927	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
928	+	embeddingPot[ii] = ploc2;
929	+	}
930	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
931	+	RealType ploc1 = excludedSelfPot[ii];
932	+	RealType ploc2 = 0.0;
933	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
934	+	excludedSelfPot[ii] = ploc2;
935	+	}
936	+	#endif
937	+
938	+	}
939	+
940	+
941	+
942	+	int& ForceMatrixDecomposition::getNAtomsInRow() {
943	+	#ifdef IS_MPI
944		return nAtomsInRow_;
945		#else
946		return nLocal_;
#	Line 668 \| Line 950 \| namespace OpenMD {
950		/**
951		* returns the list of atoms belonging to this group.
952		*/
953	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
953	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
954		#ifdef IS_MPI
955		return groupListRow_[cg1];
956		#else
#	Line 676 \| Line 958 \| namespace OpenMD {
958		#endif
959		}
960
961	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
961	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
962		#ifdef IS_MPI
963		return groupListCol_[cg2];
964		#else
#	Line 693 \| Line 975 \| namespace OpenMD {
975		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
976		#endif
977
978	<	snap_->wrapVector(d);
978	>	if (usePeriodicBoundaryConditions_) {
979	>	snap_->wrapVector(d);
980	>	}
981		return d;
982		}
983
984	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
985	+	#ifdef IS_MPI
986	+	return cgColData.velocity[cg2];
987	+	#else
988	+	return snap_->cgData.velocity[cg2];
989	+	#endif
990	+	}
991
992	+	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
993	+	#ifdef IS_MPI
994	+	return atomColData.velocity[atom2];
995	+	#else
996	+	return snap_->atomData.velocity[atom2];
997	+	#endif
998	+	}
999	+
1000	+
1001		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
1002
1003		Vector3d d;
#	Line 707 \| Line 1007 \| namespace OpenMD {
1007		#else
1008		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1009		#endif
1010	<
1011	<	snap_->wrapVector(d);
1010	>	if (usePeriodicBoundaryConditions_) {
1011	>	snap_->wrapVector(d);
1012	>	}
1013		return d;
1014		}
1015
#	Line 720 \| Line 1021 \| namespace OpenMD {
1021		#else
1022		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1023		#endif
1024	<
1025	<	snap_->wrapVector(d);
1024	>	if (usePeriodicBoundaryConditions_) {
1025	>	snap_->wrapVector(d);
1026	>	}
1027		return d;
1028		}
1029
1030	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1030	>	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1031		#ifdef IS_MPI
1032		return massFactorsRow[atom1];
1033		#else
#	Line 733 \| Line 1035 \| namespace OpenMD {
1035		#endif
1036		}
1037
1038	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1038	>	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1039		#ifdef IS_MPI
1040		return massFactorsCol[atom2];
1041		#else
#	Line 750 \| Line 1052 \| namespace OpenMD {
1052		#else
1053		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1054		#endif
1055	<
1056	<	snap_->wrapVector(d);
1055	>	if (usePeriodicBoundaryConditions_) {
1056	>	snap_->wrapVector(d);
1057	>	}
1058		return d;
1059		}
1060
1061	<	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1061	>	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1062		return excludesForAtom[atom1];
1063		}
1064
#	Line 763 \| Line 1066 \| namespace OpenMD {
1066		* We need to exclude some overcounted interactions that result from
1067		* the parallel decomposition.
1068		*/
1069	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1069	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1070		int unique_id_1, unique_id_2;
1071	<
1071	>
1072		#ifdef IS_MPI
1073		// in MPI, we have to look up the unique IDs for each atom
1074		unique_id_1 = AtomRowToGlobal[atom1];
1075		unique_id_2 = AtomColToGlobal[atom2];
1076	+	// group1 = cgRowToGlobal[cg1];
1077	+	// group2 = cgColToGlobal[cg2];
1078	+	#else
1079	+	unique_id_1 = AtomLocalToGlobal[atom1];
1080	+	unique_id_2 = AtomLocalToGlobal[atom2];
1081	+	int group1 = cgLocalToGlobal[cg1];
1082	+	int group2 = cgLocalToGlobal[cg2];
1083	+	#endif
1084
774	–	// this situation should only arise in MPI simulations
1085		if (unique_id_1 == unique_id_2) return true;
1086	<
1086	>
1087	>	#ifdef IS_MPI
1088		// this prevents us from doing the pair on multiple processors
1089		if (unique_id_1 < unique_id_2) {
1090		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1091		} else {
1092	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1092	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1093		}
1094	+	#endif
1095	+
1096	+	#ifndef IS_MPI
1097	+	if (group1 == group2) {
1098	+	if (unique_id_1 < unique_id_2) return true;
1099	+	}
1100		#endif
1101	+
1102		return false;
1103		}
1104
#	Line 794 \| Line 1112 \| namespace OpenMD {
1112		* field) must still be handled for these pairs.
1113		*/
1114		bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1115	<	int unique_id_2;
1115	>
1116	>	// excludesForAtom was constructed to use row/column indices in the MPI
1117	>	// version, and to use local IDs in the non-MPI version:
1118
799	–	#ifdef IS_MPI
800	–	// in MPI, we have to look up the unique IDs for the row atom.
801	–	unique_id_2 = AtomColToGlobal[atom2];
802	–	#else
803	–	// in the normal loop, the atom numbers are unique
804	–	unique_id_2 = atom2;
805	–	#endif
806	–
1119		for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1120		i != excludesForAtom[atom1].end(); ++i) {
1121	<	if ( (*i) == unique_id_2 ) return true;
1121	>	if ( (*i) == atom2 ) return true;
1122		}
1123
1124		return false;
#	Line 836 \| Line 1148 \| namespace OpenMD {
1148		idat.excluded = excludeAtomPair(atom1, atom2);
1149
1150		#ifdef IS_MPI
1151	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1152	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1153	+	// ff_->getAtomType(identsCol[atom2]) );
1154
840	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
841	–	ff_->getAtomType(identsCol[atom2]) );
842	–
1155		if (storageLayout_ & DataStorage::dslAmat) {
1156		idat.A1 = &(atomRowData.aMat[atom1]);
1157		idat.A2 = &(atomColData.aMat[atom2]);
1158		}
1159
848	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
849	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
850	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
851	–	}
852	–
1160		if (storageLayout_ & DataStorage::dslTorque) {
1161		idat.t1 = &(atomRowData.torque[atom1]);
1162		idat.t2 = &(atomColData.torque[atom2]);
1163		}
1164
1165	+	if (storageLayout_ & DataStorage::dslDipole) {
1166	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1167	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1168	+	}
1169	+
1170	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1171	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1172	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1173	+	}
1174	+
1175		if (storageLayout_ & DataStorage::dslDensity) {
1176		idat.rho1 = &(atomRowData.density[atom1]);
1177		idat.rho2 = &(atomColData.density[atom2]);
#	Line 880 \| Line 1197 \| namespace OpenMD {
1197		idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1198		}
1199
1200	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1201	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1202	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1203	+	}
1204	+
1205		#else
1206	+
1207	+	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1208
885	–	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
886	–	ff_->getAtomType(idents[atom2]) );
887	–
1209		if (storageLayout_ & DataStorage::dslAmat) {
1210		idat.A1 = &(snap_->atomData.aMat[atom1]);
1211		idat.A2 = &(snap_->atomData.aMat[atom2]);
1212		}
1213
893	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
894	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
895	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
896	–	}
897	–
1214		if (storageLayout_ & DataStorage::dslTorque) {
1215		idat.t1 = &(snap_->atomData.torque[atom1]);
1216		idat.t2 = &(snap_->atomData.torque[atom2]);
1217		}
1218
1219	+	if (storageLayout_ & DataStorage::dslDipole) {
1220	+	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1221	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1222	+	}
1223	+
1224	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1225	+	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1226	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1227	+	}
1228	+
1229		if (storageLayout_ & DataStorage::dslDensity) {
1230		idat.rho1 = &(snap_->atomData.density[atom1]);
1231		idat.rho2 = &(snap_->atomData.density[atom2]);
#	Line 924 \| Line 1250 \| namespace OpenMD {
1250		idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1251		idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1252		}
1253	+
1254	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1255	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1256	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1257	+	}
1258	+
1259		#endif
1260		}
1261
1262
1263		void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1264		#ifdef IS_MPI
1265	<	pot_row[atom1] += 0.5 * *(idat.pot);
1266	<	pot_col[atom2] += 0.5 * *(idat.pot);
1265	>	pot_row[atom1] += RealType(0.5) * *(idat.pot);
1266	>	pot_col[atom2] += RealType(0.5) * *(idat.pot);
1267	>	expot_row[atom1] += RealType(0.5) * *(idat.excludedPot);
1268	>	expot_col[atom2] += RealType(0.5) * *(idat.excludedPot);
1269
1270		atomRowData.force[atom1] += *(idat.f1);
1271		atomColData.force[atom2] -= *(idat.f1);
1272	+
1273	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1274	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1275	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1276	+	}
1277	+
1278	+	if (storageLayout_ & DataStorage::dslElectricField) {
1279	+	atomRowData.electricField[atom1] += *(idat.eField1);
1280	+	atomColData.electricField[atom2] += *(idat.eField2);
1281	+	}
1282	+
1283		#else
1284		pairwisePot += *(idat.pot);
1285	+	excludedPot += *(idat.excludedPot);
1286
1287		snap_->atomData.force[atom1] += *(idat.f1);
1288		snap_->atomData.force[atom2] -= *(idat.f1);
1289	+
1290	+	if (idat.doParticlePot) {
1291	+	// This is the pairwise contribution to the particle pot. The
1292	+	// embedding contribution is added in each of the low level
1293	+	// non-bonded routines. In parallel, this calculation is done
1294	+	// in collectData, not in unpackInteractionData.
1295	+	snap_->atomData.particlePot[atom1] += (idat.vpair) *(idat.sw);
1296	+	snap_->atomData.particlePot[atom2] += (idat.vpair) *(idat.sw);
1297	+	}
1298	+
1299	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1300	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1301	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1302	+	}
1303	+
1304	+	if (storageLayout_ & DataStorage::dslElectricField) {
1305	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1306	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1307	+	}
1308	+
1309		#endif
1310
1311		}
#	Line 956 \| Line 1322 \| namespace OpenMD {
1322		groupCutoffs cuts;
1323		bool doAllPairs = false;
1324
1325	+	RealType rList_ = (largestRcut_ + skinThickness_);
1326	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1327	+	Mat3x3d box;
1328	+	Mat3x3d invBox;
1329	+
1330	+	Vector3d rs, scaled, dr;
1331	+	Vector3i whichCell;
1332	+	int cellIndex;
1333	+
1334		#ifdef IS_MPI
1335		cellListRow_.clear();
1336		cellListCol_.clear();
1337		#else
1338		cellList_.clear();
1339		#endif
1340	<
1341	<	RealType rList_ = (largestRcut_ + skinThickness_);
1342	<	RealType rl2 = rList_ * rList_;
1343	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
1344	<	Mat3x3d Hmat = snap_->getHmat();
1345	<	Vector3d Hx = Hmat.getColumn(0);
1346	<	Vector3d Hy = Hmat.getColumn(1);
1347	<	Vector3d Hz = Hmat.getColumn(2);
1348	<
1349	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
1350	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
1351	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
1352	<
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 boxX = box.getColumn(0);
1350	>	Vector3d boxY = box.getColumn(1);
1351	>	Vector3d boxZ = box.getColumn(2);
1352	>
1353	>	nCells_.x() = (int) ( boxX.length() )/ rList_;
1354	>	nCells_.y() = (int) ( boxY.length() )/ rList_;
1355	>	nCells_.z() = (int) ( boxZ.length() )/ rList_;
1356	>
1357		// handle small boxes where the cell offsets can end up repeating cells
1358
1359		if (nCells_.x() < 3) doAllPairs = true;
1360		if (nCells_.y() < 3) doAllPairs = true;
1361		if (nCells_.z() < 3) doAllPairs = true;
1362	<
984	<	Mat3x3d invHmat = snap_->getInvHmat();
985	<	Vector3d rs, scaled, dr;
986	<	Vector3i whichCell;
987	<	int cellIndex;
1362	>
1363		int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1364	<
1364	>
1365		#ifdef IS_MPI
1366		cellListRow_.resize(nCtot);
1367		cellListCol_.resize(nCtot);
1368		#else
1369		cellList_.resize(nCtot);
1370		#endif
1371	<
1371	>
1372		if (!doAllPairs) {
1373		#ifdef IS_MPI
1374	<
1374	>
1375		for (int i = 0; i < nGroupsInRow_; i++) {
1376		rs = cgRowData.position[i];
1377
1378		// scaled positions relative to the box vectors
1379	<	scaled = invHmat * rs;
1379	>	scaled = invBox * rs;
1380
1381		// wrap the vector back into the unit box by subtracting integer box
1382		// numbers
1383		for (int j = 0; j < 3; j++) {
1384		scaled[j] -= roundMe(scaled[j]);
1385		scaled[j] += 0.5;
1386	+	// Handle the special case when an object is exactly on the
1387	+	// boundary (a scaled coordinate of 1.0 is the same as
1388	+	// scaled coordinate of 0.0)
1389	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1390		}
1391
1392		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1021 \| Line 1400 \| namespace OpenMD {
1400		// add this cutoff group to the list of groups in this cell;
1401		cellListRow_[cellIndex].push_back(i);
1402		}
1024	–
1403		for (int i = 0; i < nGroupsInCol_; i++) {
1404		rs = cgColData.position[i];
1405
1406		// scaled positions relative to the box vectors
1407	<	scaled = invHmat * rs;
1407	>	scaled = invBox * rs;
1408
1409		// wrap the vector back into the unit box by subtracting integer box
1410		// numbers
1411		for (int j = 0; j < 3; j++) {
1412		scaled[j] -= roundMe(scaled[j]);
1413		scaled[j] += 0.5;
1414	+	// Handle the special case when an object is exactly on the
1415	+	// boundary (a scaled coordinate of 1.0 is the same as
1416	+	// scaled coordinate of 0.0)
1417	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1418		}
1419
1420		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1046 \| Line 1428 \| namespace OpenMD {
1428		// add this cutoff group to the list of groups in this cell;
1429		cellListCol_[cellIndex].push_back(i);
1430		}
1431	+
1432		#else
1433		for (int i = 0; i < nGroups_; i++) {
1434		rs = snap_->cgData.position[i];
1435
1436		// scaled positions relative to the box vectors
1437	<	scaled = invHmat * rs;
1437	>	scaled = invBox * rs;
1438
1439		// wrap the vector back into the unit box by subtracting integer box
1440		// numbers
1441		for (int j = 0; j < 3; j++) {
1442		scaled[j] -= roundMe(scaled[j]);
1443		scaled[j] += 0.5;
1444	+	// Handle the special case when an object is exactly on the
1445	+	// boundary (a scaled coordinate of 1.0 is the same as
1446	+	// scaled coordinate of 0.0)
1447	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1448		}
1449
1450		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1066 \| Line 1453 \| namespace OpenMD {
1453		whichCell.z() = nCells_.z() * scaled.z();
1454
1455		// find single index of this cell:
1456	<	cellIndex = Vlinear(whichCell, nCells_);
1456	>	cellIndex = Vlinear(whichCell, nCells_);
1457
1458		// add this cutoff group to the list of groups in this cell;
1459		cellList_[cellIndex].push_back(i);
1460		}
1461	+
1462		#endif
1463
1464		for (int m1z = 0; m1z < nCells_.z(); m1z++) {
#	Line 1083 \| Line 1471 \| namespace OpenMD {
1471		os != cellOffsets_.end(); ++os) {
1472
1473		Vector3i m2v = m1v + (*os);
1474	<
1474	>
1475	>
1476		if (m2v.x() >= nCells_.x()) {
1477		m2v.x() = 0;
1478		} else if (m2v.x() < 0) {
#	Line 1101 \| Line 1490 \| namespace OpenMD {
1490		} else if (m2v.z() < 0) {
1491		m2v.z() = nCells_.z() - 1;
1492		}
1493	<
1493	>
1494		int m2 = Vlinear (m2v, nCells_);
1495
1496		#ifdef IS_MPI
#	Line 1110 \| Line 1499 \| namespace OpenMD {
1499		for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1500		j2 != cellListCol_[m2].end(); ++j2) {
1501
1502	<	// Always do this if we're in different cells or if
1503	<	// we're in the same cell and the global index of the
1504	<	// j2 cutoff group is less than the j1 cutoff group
1505	<
1506	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1118	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1502	>	// In parallel, we need to visit all pairs of row
1503	>	// & column indicies and will divide labor in the
1504	>	// force evaluation later.
1505	>	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1506	>	if (usePeriodicBoundaryConditions_) {
1507		snap_->wrapVector(dr);
1120	–	cuts = getGroupCutoffs( (j1), (j2) );
1121	–	if (dr.lengthSquare() < cuts.third) {
1122	–	neighborList.push_back(make_pair((j1), (j2)));
1123	–	}
1508		}
1509	+	cuts = getGroupCutoffs( (j1), (j2) );
1510	+	if (dr.lengthSquare() < cuts.third) {
1511	+	neighborList.push_back(make_pair((j1), (j2)));
1512	+	}
1513		}
1514		}
1515		#else
1128	–
1516		for (vector<int>::iterator j1 = cellList_[m1].begin();
1517		j1 != cellList_[m1].end(); ++j1) {
1518		for (vector<int>::iterator j2 = cellList_[m2].begin();
1519		j2 != cellList_[m2].end(); ++j2) {
1520	<
1520	>
1521		// Always do this if we're in different cells or if
1522	<	// we're in the same cell and the global index of the
1523	<	// j2 cutoff group is less than the j1 cutoff group
1524	<
1525	<	if (m2 != m1 \|\| (j2) < (j1)) {
1522	>	// we're in the same cell and the global index of
1523	>	// the j2 cutoff group is greater than or equal to
1524	>	// the j1 cutoff group. Note that Rappaport's code
1525	>	// has a "less than" conditional here, but that
1526	>	// deals with atom-by-atom computation. OpenMD
1527	>	// allows atoms within a single cutoff group to
1528	>	// interact with each other.
1529	>
1530	>	if (m2 != m1 \|\| (j2) >= (j1) ) {
1531	>
1532		dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1533	<	snap_->wrapVector(dr);
1533	>	if (usePeriodicBoundaryConditions_) {
1534	>	snap_->wrapVector(dr);
1535	>	}
1536		cuts = getGroupCutoffs( (j1), (j2) );
1537		if (dr.lengthSquare() < cuts.third) {
1538		neighborList.push_back(make_pair((j1), (j2)));
#	Line 1154 \| Line 1549 \| namespace OpenMD {
1549		// branch to do all cutoff group pairs
1550		#ifdef IS_MPI
1551		for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1552	<	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1552	>	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1553		dr = cgColData.position[j2] - cgRowData.position[j1];
1554	<	snap_->wrapVector(dr);
1554	>	if (usePeriodicBoundaryConditions_) {
1555	>	snap_->wrapVector(dr);
1556	>	}
1557		cuts = getGroupCutoffs( j1, j2 );
1558		if (dr.lengthSquare() < cuts.third) {
1559		neighborList.push_back(make_pair(j1, j2));
1560		}
1561		}
1562	<	}
1562	>	}
1563		#else
1564	<	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1565	<	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1564	>	// include all groups here.
1565	>	for (int j1 = 0; j1 < nGroups_; j1++) {
1566	>	// include self group interactions j2 == j1
1567	>	for (int j2 = j1; j2 < nGroups_; j2++) {
1568		dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1569	<	snap_->wrapVector(dr);
1569	>	if (usePeriodicBoundaryConditions_) {
1570	>	snap_->wrapVector(dr);
1571	>	}
1572		cuts = getGroupCutoffs( j1, j2 );
1573		if (dr.lengthSquare() < cuts.third) {
1574		neighborList.push_back(make_pair(j1, j2));
1575		}
1576	<	}
1577	<	}
1576	>	}
1577	>	}
1578		#endif
1579		}
1580

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Comparing: branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1590 by gezelter, Mon Jul 11 01:39:49 2011 UTC vs. trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1893 by gezelter, Wed Jun 19 17:19:07 2013 UTC

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Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1590 by gezelter, Mon Jul 11 01:39:49 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1893 by gezelter, Wed Jun 19 17:19:07 2013 UTC