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

Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1771 by gezelter, Fri Jul 27 17:34:10 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 2062 by gezelter, Tue Mar 3 16:40:39 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).
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		*/
#	Line 50 \| Line 50 \| 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
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) );
#	Line 82 \| Line 79 \| namespace OpenMD {
79		cellOffsets_.push_back( Vector3i(-1, 1, 1) );
80		cellOffsets_.push_back( Vector3i( 0, 1, 1) );
81		cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	–	#endif
82		}
83
84
#	Line 99 \| Line 95 \| namespace OpenMD {
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 118 \| Line 115 \| namespace OpenMD {
115
116		#ifdef IS_MPI
117
118	<	MPI::Intracomm row = rowComm.getComm();
119	<	MPI::Intracomm col = colComm.getComm();
118	>	MPI_Comm row = rowComm.getComm();
119	>	MPI_Comm col = colComm.getComm();
120
121		AtomPlanIntRow = new Plan<int>(row, nLocal_);
122		AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
#	Line 163 \| Line 160 \| namespace OpenMD {
160
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 299 \| Line 302 \| namespace OpenMD {
302		groupList_[i].push_back(j);
303		}
304		}
305	<	}
303	<
304	<
305	<	createGtypeCutoffMap();
306	<
305	>	}
306		}
308	–
309	–	void ForceMatrixDecomposition::createGtypeCutoffMap() {
307
311	–	RealType tol = 1e-6;
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();
319	–	at != atypes.end(); ++at){
320	–	atid = (*at)->getIdent();
321	–	if (userChoseCutoff_)
322	–	atypeCutoff[atid] = userCutoff_;
323	–	else
324	–	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
325	–	}
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.
330	–	#ifdef IS_MPI
331	–	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
332	–	groupRowToGtype.resize(nGroupsInRow_);
333	–	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
334	–	vector<int> atomListRow = getAtomsInGroupRow(cg1);
335	–	for (vector<int>::iterator ia = atomListRow.begin();
336	–	ia != atomListRow.end(); ++ia) {
337	–	int atom1 = (*ia);
338	–	atid = identsRow[atom1];
339	–	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
340	–	groupCutoffRow[cg1] = atypeCutoff[atid];
341	–	}
342	–	}
343	–
344	–	bool gTypeFound = false;
345	–	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
346	–	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
347	–	groupRowToGtype[cg1] = gt;
348	–	gTypeFound = true;
349	–	}
350	–	}
351	–	if (!gTypeFound) {
352	–	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
353	–	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
354	–	}
355	–
356	–	}
357	–	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
358	–	groupColToGtype.resize(nGroupsInCol_);
359	–	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
360	–	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
361	–	for (vector<int>::iterator jb = atomListCol.begin();
362	–	jb != atomListCol.end(); ++jb) {
363	–	int atom2 = (*jb);
364	–	atid = identsCol[atom2];
365	–	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
366	–	groupCutoffCol[cg2] = atypeCutoff[atid];
367	–	}
368	–	}
369	–	bool gTypeFound = false;
370	–	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
371	–	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
372	–	groupColToGtype[cg2] = gt;
373	–	gTypeFound = true;
374	–	}
375	–	}
376	–	if (!gTypeFound) {
377	–	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
378	–	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
379	–	}
380	–	}
381	–	#else
382	–
383	–	vector<RealType> groupCutoff(nGroups_, 0.0);
384	–	groupToGtype.resize(nGroups_);
385	–	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
386	–	groupCutoff[cg1] = 0.0;
387	–	vector<int> atomList = getAtomsInGroupRow(cg1);
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])
393	–	groupCutoff[cg1] = atypeCutoff[atid];
394	–	}
395	–
396	–	bool gTypeFound = false;
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) {
404	–	gTypeCutoffs.push_back( groupCutoff[cg1] );
405	–	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
406	–	}
407	–	}
408	–	#endif
409	–
410	–	// Now we find the maximum group cutoff value present in the simulation
411	–
412	–	RealType groupMax = *max_element(gTypeCutoffs.begin(),
413	–	gTypeCutoffs.end());
414	–
415	–	#ifdef IS_MPI
416	–	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
417	–	MPI::MAX);
418	–	#endif
419	–
420	–	RealType tradRcut = groupMax;
421	–
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:
427	–	thisRcut = tradRcut;
428	–	break;
429	–	case MIX:
430	–	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
431	–	break;
432	–	case MAX:
433	–	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
434	–	break;
435	–	default:
436	–	sprintf(painCave.errMsg,
437	–	"ForceMatrixDecomposition::createGtypeCutoffMap "
438	–	"hit an unknown cutoff policy!\n");
439	–	painCave.severity = OPENMD_ERROR;
440	–	painCave.isFatal = 1;
441	–	simError();
442	–	break;
443	–	}
444	–
445	–	pair<int,int> key = make_pair(i,j);
446	–	gTypeCutoffMap[key].first = thisRcut;
447	–	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
448	–	gTypeCutoffMap[key].second = thisRcut*thisRcut;
449	–	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
450	–	// sanity check
451	–
452	–	if (userChoseCutoff_) {
453	–	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
454	–	sprintf(painCave.errMsg,
455	–	"ForceMatrixDecomposition::createGtypeCutoffMap "
456	–	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
457	–	painCave.severity = OPENMD_ERROR;
458	–	painCave.isFatal = 1;
459	–	simError();
460	–	}
461	–	}
462	–	}
463	–	}
464	–	}
465	–
466	–	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467	–	int i, j;
468	–	#ifdef IS_MPI
469	–	i = groupRowToGtype[cg1];
470	–	j = groupColToGtype[cg2];
471	–	#else
472	–	i = groupToGtype[cg1];
473	–	j = groupToGtype[cg2];
474	–	#endif
475	–	return gTypeCutoffMap[make_pair(i,j)];
476	–	}
477	–
308		int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
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
#	Line 559 \| Line 389 \| namespace OpenMD {
389		atomColData.electricField.end(), V3Zero);
390		}
391
392	<	if (storageLayout_ & DataStorage::dslFlucQForce) {
393	<	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
394	<	0.0);
395	<	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
396	<	0.0);
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
#	Line 598 \| Line 428 \| namespace OpenMD {
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	+
440	+	#ifdef IS_MPI
441	+
442		snap_ = sman_->getCurrentSnapshot();
443		storageLayout_ = sman_->getStorageLayout();
607	–	#ifdef IS_MPI
444
445	+	bool needsCG = true;
446	+	if(info_->getNCutoffGroups() != info_->getNAtoms())
447	+	needsCG = false;
448	+
449		// gather up the atomic positions
450		AtomPlanVectorRow->gather(snap_->atomData.position,
451		atomRowData.position);
#	Line 614 \| Line 454 \| namespace OpenMD {
454
455		// gather up the cutoff group positions
456
457	<	cgPlanVectorRow->gather(snap_->cgData.position,
458	<	cgRowData.position);
457	>	if (needsCG) {
458	>	cgPlanVectorRow->gather(snap_->cgData.position,
459	>	cgRowData.position);
460	>
461	>	cgPlanVectorColumn->gather(snap_->cgData.position,
462	>	cgColData.position);
463	>	}
464
620	–	cgPlanVectorColumn->gather(snap_->cgData.position,
621	–	cgColData.position);
465
623	–
624	–
466		if (needVelocities_) {
467		// gather up the atomic velocities
468		AtomPlanVectorColumn->gather(snap_->atomData.velocity,
469		atomColData.velocity);
470	<
471	<	cgPlanVectorColumn->gather(snap_->cgData.velocity,
472	<	cgColData.velocity);
470	>
471	>	if (needsCG) {
472	>	cgPlanVectorColumn->gather(snap_->cgData.velocity,
473	>	cgColData.velocity);
474	>	}
475		}
476
477
#	Line 639 \| Line 482 \| namespace OpenMD {
482		AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
483		atomColData.aMat);
484		}
485	<
486	<	// if needed, gather the atomic eletrostatic frames
487	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
488	<	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
489	<	atomRowData.electroFrame);
490	<	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
491	<	atomColData.electroFrame);
485	>
486	>	// if needed, gather the atomic eletrostatic information
487	>	if (storageLayout_ & DataStorage::dslDipole) {
488	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
489	>	atomRowData.dipole);
490	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
491	>	atomColData.dipole);
492		}
493
494	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
495	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
496	+	atomRowData.quadrupole);
497	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
498	+	atomColData.quadrupole);
499	+	}
500	+
501		// if needed, gather the atomic fluctuating charge values
502		if (storageLayout_ & DataStorage::dslFlucQPosition) {
503		AtomPlanRealRow->gather(snap_->atomData.flucQPos,
#	Line 663 \| Line 513 \| namespace OpenMD {
513		* data structures.
514		*/
515		void ForceMatrixDecomposition::collectIntermediateData() {
516	+	#ifdef IS_MPI
517	+
518		snap_ = sman_->getCurrentSnapshot();
519		storageLayout_ = sman_->getStorageLayout();
520	<	#ifdef IS_MPI
669	<
520	>
521		if (storageLayout_ & DataStorage::dslDensity) {
522
523		AtomPlanRealRow->scatter(atomRowData.density,
#	Line 679 \| Line 530 \| namespace OpenMD {
530		snap_->atomData.density[i] += rho_tmp[i];
531		}
532
533	+	// this isn't necessary if we don't have polarizable atoms, but
534	+	// we'll leave it here for now.
535		if (storageLayout_ & DataStorage::dslElectricField) {
536
537		AtomPlanVectorRow->scatter(atomRowData.electricField,
#	Line 686 \| Line 539 \| namespace OpenMD {
539
540		int n = snap_->atomData.electricField.size();
541		vector<Vector3d> field_tmp(n, V3Zero);
542	<	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
542	>	AtomPlanVectorColumn->scatter(atomColData.electricField,
543	>	field_tmp);
544		for (int i = 0; i < n; i++)
545		snap_->atomData.electricField[i] += field_tmp[i];
546		}
#	Line 698 \| Line 552 \| namespace OpenMD {
552		* row and column-indexed data structures
553		*/
554		void ForceMatrixDecomposition::distributeIntermediateData() {
555	+	#ifdef IS_MPI
556		snap_ = sman_->getCurrentSnapshot();
557		storageLayout_ = sman_->getStorageLayout();
558	<	#ifdef IS_MPI
558	>
559		if (storageLayout_ & DataStorage::dslFunctional) {
560		AtomPlanRealRow->gather(snap_->atomData.functional,
561		atomRowData.functional);
#	Line 719 \| Line 574 \| namespace OpenMD {
574
575
576		void ForceMatrixDecomposition::collectData() {
577	+	#ifdef IS_MPI
578		snap_ = sman_->getCurrentSnapshot();
579		storageLayout_ = sman_->getStorageLayout();
580	<	#ifdef IS_MPI
580	>
581		int n = snap_->atomData.force.size();
582		vector<Vector3d> frc_tmp(n, V3Zero);
583
#	Line 786 \| Line 642 \| namespace OpenMD {
642
643		}
644
645	+	if (storageLayout_ & DataStorage::dslElectricField) {
646	+
647	+	int nef = snap_->atomData.electricField.size();
648	+	vector<Vector3d> efield_tmp(nef, V3Zero);
649	+
650	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
651	+	for (int i = 0; i < nef; i++) {
652	+	snap_->atomData.electricField[i] += efield_tmp[i];
653	+	efield_tmp[i] = 0.0;
654	+	}
655	+
656	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
657	+	for (int i = 0; i < nef; i++)
658	+	snap_->atomData.electricField[i] += efield_tmp[i];
659	+	}
660	+
661	+	if (storageLayout_ & DataStorage::dslSitePotential) {
662	+
663	+	int nsp = snap_->atomData.sitePotential.size();
664	+	vector<RealType> sp_tmp(nsp, 0.0);
665	+
666	+	AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
667	+	for (int i = 0; i < nsp; i++) {
668	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
669	+	sp_tmp[i] = 0.0;
670	+	}
671	+
672	+	AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
673	+	for (int i = 0; i < nsp; i++)
674	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
675	+	}
676	+
677		nLocal_ = snap_->getNumberOfAtoms();
678
679		vector<potVec> pot_temp(nLocal_,
#	Line 869 \| Line 757 \| namespace OpenMD {
757		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
758		RealType ploc1 = pairwisePot[ii];
759		RealType ploc2 = 0.0;
760	<	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
760	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
761		pairwisePot[ii] = ploc2;
762		}
763
764		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
765		RealType ploc1 = excludedPot[ii];
766		RealType ploc2 = 0.0;
767	<	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
767	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
768		excludedPot[ii] = ploc2;
769		}
770
771		// Here be dragons.
772	<	MPI::Intracomm col = colComm.getComm();
772	>	MPI_Comm col = colComm.getComm();
773
774	<	col.Allreduce(MPI::IN_PLACE,
774	>	MPI_Allreduce(MPI_IN_PLACE,
775		&snap_->frameData.conductiveHeatFlux[0], 3,
776	<	MPI::REALTYPE, MPI::SUM);
776	>	MPI_REALTYPE, MPI_SUM, col);
777
778
779		#endif
#	Line 897 \| Line 785 \| namespace OpenMD {
785		* functional) loops onto local data structures.
786		*/
787		void ForceMatrixDecomposition::collectSelfData() {
788	+
789	+	#ifdef IS_MPI
790		snap_ = sman_->getCurrentSnapshot();
791		storageLayout_ = sman_->getStorageLayout();
792
903	–	#ifdef IS_MPI
793		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
794		RealType ploc1 = embeddingPot[ii];
795		RealType ploc2 = 0.0;
796	<	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
796	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
797		embeddingPot[ii] = ploc2;
798		}
799		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
800		RealType ploc1 = excludedSelfPot[ii];
801		RealType ploc2 = 0.0;
802	<	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
802	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
803		excludedSelfPot[ii] = ploc2;
804		}
805		#endif
806
807		}
808
809	<
921	<
922	<	int ForceMatrixDecomposition::getNAtomsInRow() {
809	>	int& ForceMatrixDecomposition::getNAtomsInRow() {
810		#ifdef IS_MPI
811		return nAtomsInRow_;
812		#else
#	Line 930 \| Line 817 \| namespace OpenMD {
817		/**
818		* returns the list of atoms belonging to this group.
819		*/
820	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
820	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
821		#ifdef IS_MPI
822		return groupListRow_[cg1];
823		#else
#	Line 938 \| Line 825 \| namespace OpenMD {
825		#endif
826		}
827
828	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
828	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
829		#ifdef IS_MPI
830		return groupListCol_[cg2];
831		#else
#	Line 946 \| Line 833 \| namespace OpenMD {
833		#endif
834		}
835
836	<	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
836	>	inline Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1,
837	>	int cg2){
838	>
839		Vector3d d;
951	–
840		#ifdef IS_MPI
841		d = cgColData.position[cg2] - cgRowData.position[cg1];
842		#else
843		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
844		#endif
845
846	<	snap_->wrapVector(d);
846	>	if (usePeriodicBoundaryConditions_) {
847	>	snap_->wrapVector(d);
848	>	}
849		return d;
850		}
851
852	<	Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
852	>	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
853		#ifdef IS_MPI
854		return cgColData.velocity[cg2];
855		#else
#	Line 967 \| Line 857 \| namespace OpenMD {
857		#endif
858		}
859
860	<	Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
860	>	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
861		#ifdef IS_MPI
862		return atomColData.velocity[atom2];
863		#else
#	Line 976 \| Line 866 \| namespace OpenMD {
866		}
867
868
869	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
870	<
869	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1,
870	>	int cg1) {
871		Vector3d d;
872
873		#ifdef IS_MPI
#	Line 985 \| Line 875 \| namespace OpenMD {
875		#else
876		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
877		#endif
878	<
879	<	snap_->wrapVector(d);
878	>	if (usePeriodicBoundaryConditions_) {
879	>	snap_->wrapVector(d);
880	>	}
881		return d;
882		}
883
884	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
884	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2,
885	>	int cg2) {
886		Vector3d d;
887
888		#ifdef IS_MPI
#	Line 998 \| Line 890 \| namespace OpenMD {
890		#else
891		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
892		#endif
893	<
894	<	snap_->wrapVector(d);
893	>	if (usePeriodicBoundaryConditions_) {
894	>	snap_->wrapVector(d);
895	>	}
896		return d;
897		}
898
899	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
899	>	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
900		#ifdef IS_MPI
901		return massFactorsRow[atom1];
902		#else
#	Line 1011 \| Line 904 \| namespace OpenMD {
904		#endif
905		}
906
907	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
907	>	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
908		#ifdef IS_MPI
909		return massFactorsCol[atom2];
910		#else
#	Line 1020 \| Line 913 \| namespace OpenMD {
913
914		}
915
916	<	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
916	>	inline Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1,
917	>	int atom2){
918		Vector3d d;
919
920		#ifdef IS_MPI
#	Line 1028 \| Line 922 \| namespace OpenMD {
922		#else
923		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
924		#endif
925	<
926	<	snap_->wrapVector(d);
925	>	if (usePeriodicBoundaryConditions_) {
926	>	snap_->wrapVector(d);
927	>	}
928		return d;
929		}
930
931	<	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
931	>	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
932		return excludesForAtom[atom1];
933		}
934
#	Line 1041 \| Line 936 \| namespace OpenMD {
936		* We need to exclude some overcounted interactions that result from
937		* the parallel decomposition.
938		*/
939	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
940	<	int unique_id_1, unique_id_2, group1, group2;
939	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2,
940	>	int cg1, int cg2) {
941	>	int unique_id_1, unique_id_2;
942
943		#ifdef IS_MPI
944		// in MPI, we have to look up the unique IDs for each atom
945		unique_id_1 = AtomRowToGlobal[atom1];
946		unique_id_2 = AtomColToGlobal[atom2];
947	<	group1 = cgRowToGlobal[cg1];
948	<	group2 = cgColToGlobal[cg2];
947	>	// group1 = cgRowToGlobal[cg1];
948	>	// group2 = cgColToGlobal[cg2];
949		#else
950		unique_id_1 = AtomLocalToGlobal[atom1];
951		unique_id_2 = AtomLocalToGlobal[atom2];
952	<	group1 = cgLocalToGlobal[cg1];
953	<	group2 = cgLocalToGlobal[cg2];
952	>	int group1 = cgLocalToGlobal[cg1];
953	>	int group2 = cgLocalToGlobal[cg2];
954		#endif
955
956		if (unique_id_1 == unique_id_2) return true;
#	Line 1118 \| Line 1014 \| namespace OpenMD {
1014
1015		// filling interaction blocks with pointers
1016		void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1017	<	int atom1, int atom2) {
1017	>	int atom1, int atom2,
1018	>	bool newAtom1) {
1019
1020		idat.excluded = excludeAtomPair(atom1, atom2);
1021	<
1021	>
1022	>	if (newAtom1) {
1023	>
1024		#ifdef IS_MPI
1025	<	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1026	<	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1027	<	// ff_->getAtomType(identsCol[atom2]) );
1028	<
1025	>	idat.atid1 = identsRow[atom1];
1026	>	idat.atid2 = identsCol[atom2];
1027	>
1028	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1029	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1030	>	} else {
1031	>	idat.sameRegion = false;
1032	>	}
1033	>
1034	>	if (storageLayout_ & DataStorage::dslAmat) {
1035	>	idat.A1 = &(atomRowData.aMat[atom1]);
1036	>	idat.A2 = &(atomColData.aMat[atom2]);
1037	>	}
1038	>
1039	>	if (storageLayout_ & DataStorage::dslTorque) {
1040	>	idat.t1 = &(atomRowData.torque[atom1]);
1041	>	idat.t2 = &(atomColData.torque[atom2]);
1042	>	}
1043	>
1044	>	if (storageLayout_ & DataStorage::dslDipole) {
1045	>	idat.dipole1 = &(atomRowData.dipole[atom1]);
1046	>	idat.dipole2 = &(atomColData.dipole[atom2]);
1047	>	}
1048	>
1049	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1050	>	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1051	>	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1052	>	}
1053	>
1054	>	if (storageLayout_ & DataStorage::dslDensity) {
1055	>	idat.rho1 = &(atomRowData.density[atom1]);
1056	>	idat.rho2 = &(atomColData.density[atom2]);
1057	>	}
1058	>
1059	>	if (storageLayout_ & DataStorage::dslFunctional) {
1060	>	idat.frho1 = &(atomRowData.functional[atom1]);
1061	>	idat.frho2 = &(atomColData.functional[atom2]);
1062	>	}
1063	>
1064	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1065	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1066	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1067	>	}
1068	>
1069	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1070	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1071	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1072	>	}
1073	>
1074	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1075	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1076	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1077	>	}
1078	>
1079	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1080	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1081	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1082	>	}
1083	>
1084	>	#else
1085	>
1086	>	idat.atid1 = idents[atom1];
1087	>	idat.atid2 = idents[atom2];
1088	>
1089	>	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1090	>	idat.sameRegion = (regions[atom1] == regions[atom2]);
1091	>	} else {
1092	>	idat.sameRegion = false;
1093	>	}
1094	>
1095	>	if (storageLayout_ & DataStorage::dslAmat) {
1096	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1097	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1098	>	}
1099	>
1100	>	if (storageLayout_ & DataStorage::dslTorque) {
1101	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1102	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1103	>	}
1104	>
1105	>	if (storageLayout_ & DataStorage::dslDipole) {
1106	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1107	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1108	>	}
1109	>
1110	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1111	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1112	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1113	>	}
1114	>
1115	>	if (storageLayout_ & DataStorage::dslDensity) {
1116	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1117	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1118	>	}
1119	>
1120	>	if (storageLayout_ & DataStorage::dslFunctional) {
1121	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1122	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1123	>	}
1124	>
1125	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1126	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1127	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1128	>	}
1129	>
1130	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1131	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1132	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1133	>	}
1134	>
1135	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1136	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1137	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1138	>	}
1139	>
1140	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1141	>	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1142	>	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1143	>	}
1144	>	#endif
1145	>
1146	>	} else {
1147	>	// atom1 is not new, so don't bother updating properties of that atom:
1148	>	#ifdef IS_MPI
1149	>	idat.atid2 = identsCol[atom2];
1150	>
1151	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1152	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1153	>	} else {
1154	>	idat.sameRegion = false;
1155	>	}
1156	>
1157		if (storageLayout_ & DataStorage::dslAmat) {
1131	–	idat.A1 = &(atomRowData.aMat[atom1]);
1158		idat.A2 = &(atomColData.aMat[atom2]);
1159		}
1160
1135	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
1136	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1137	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1138	–	}
1139	–
1161		if (storageLayout_ & DataStorage::dslTorque) {
1141	–	idat.t1 = &(atomRowData.torque[atom1]);
1162		idat.t2 = &(atomColData.torque[atom2]);
1163		}
1164
1165	+	if (storageLayout_ & DataStorage::dslDipole) {
1166	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1167	+	}
1168	+
1169	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1170	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1171	+	}
1172	+
1173		if (storageLayout_ & DataStorage::dslDensity) {
1146	–	idat.rho1 = &(atomRowData.density[atom1]);
1174		idat.rho2 = &(atomColData.density[atom2]);
1175		}
1176
1177		if (storageLayout_ & DataStorage::dslFunctional) {
1151	–	idat.frho1 = &(atomRowData.functional[atom1]);
1178		idat.frho2 = &(atomColData.functional[atom2]);
1179		}
1180
1181		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1156	–	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1182		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1183		}
1184
1185		if (storageLayout_ & DataStorage::dslParticlePot) {
1161	–	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1186		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1187		}
1188
1189		if (storageLayout_ & DataStorage::dslSkippedCharge) {
1166	–	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1190		idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1191		}
1192
1193	<	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1171	<	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1193	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1194		idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1195		}
1196
1197	<	#else
1198	<
1177	<	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1197	>	#else
1198	>	idat.atid2 = idents[atom2];
1199
1200	+	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1201	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1202	+	} else {
1203	+	idat.sameRegion = false;
1204	+	}
1205	+
1206		if (storageLayout_ & DataStorage::dslAmat) {
1180	–	idat.A1 = &(snap_->atomData.aMat[atom1]);
1207		idat.A2 = &(snap_->atomData.aMat[atom2]);
1208		}
1209
1184	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
1185	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1186	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1187	–	}
1188	–
1210		if (storageLayout_ & DataStorage::dslTorque) {
1190	–	idat.t1 = &(snap_->atomData.torque[atom1]);
1211		idat.t2 = &(snap_->atomData.torque[atom2]);
1212		}
1213
1214	+	if (storageLayout_ & DataStorage::dslDipole) {
1215	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1216	+	}
1217	+
1218	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1219	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1220	+	}
1221	+
1222		if (storageLayout_ & DataStorage::dslDensity) {
1195	–	idat.rho1 = &(snap_->atomData.density[atom1]);
1223		idat.rho2 = &(snap_->atomData.density[atom2]);
1224		}
1225
1226		if (storageLayout_ & DataStorage::dslFunctional) {
1200	–	idat.frho1 = &(snap_->atomData.functional[atom1]);
1227		idat.frho2 = &(snap_->atomData.functional[atom2]);
1228		}
1229
1230		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1205	–	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1231		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1232		}
1233
1234		if (storageLayout_ & DataStorage::dslParticlePot) {
1210	–	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1235		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1236		}
1237
1238		if (storageLayout_ & DataStorage::dslSkippedCharge) {
1215	–	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1239		idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1240		}
1241
1242		if (storageLayout_ & DataStorage::dslFlucQPosition) {
1220	–	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1243		idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1244		}
1245
1246		#endif
1247	+	}
1248		}
1226	–
1249
1250	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1250	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat,
1251	>	int atom1, int atom2) {
1252		#ifdef IS_MPI
1253		pot_row[atom1] += RealType(0.5) * *(idat.pot);
1254		pot_col[atom2] += RealType(0.5) * *(idat.pot);
#	Line 1245 \| Line 1268 \| namespace OpenMD {
1268		atomColData.electricField[atom2] += *(idat.eField2);
1269		}
1270
1271	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1272	+	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1273	+	atomColData.sitePotential[atom2] += *(idat.sPot2);
1274	+	}
1275	+
1276		#else
1277		pairwisePot += *(idat.pot);
1278		excludedPot += *(idat.excludedPot);
#	Line 1271 \| Line 1299 \| namespace OpenMD {
1299		snap_->atomData.electricField[atom2] += *(idat.eField2);
1300		}
1301
1302	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1303	+	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1304	+	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1305	+	}
1306	+
1307		#endif
1308
1309		}
#	Line 1278 \| Line 1311 \| namespace OpenMD {
1311		/*
1312		* buildNeighborList
1313		*
1314	<	* first element of pair is row-indexed CutoffGroup
1315	<	* second element of pair is column-indexed CutoffGroup
1314	>	* Constructs the Verlet neighbor list for a force-matrix
1315	>	* decomposition. In this case, each processor is responsible for
1316	>	* row-site interactions with column-sites.
1317	>	*
1318	>	* neighborList is returned as a packed array of neighboring
1319	>	* column-ordered CutoffGroups. The starting position in
1320	>	* neighborList for each row-ordered CutoffGroup is given by the
1321	>	* returned vector point.
1322		*/
1323	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1324	<
1325	<	vector<pair<int, int> > neighborList;
1326	<	groupCutoffs cuts;
1323	>	void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
1324	>	vector<int>& point) {
1325	>	neighborList.clear();
1326	>	point.clear();
1327	>	int len = 0;
1328	>
1329		bool doAllPairs = false;
1330
1331	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1332	+	Mat3x3d box;
1333	+	Mat3x3d invBox;
1334	+
1335	+	Vector3d rs, scaled, dr;
1336	+	Vector3i whichCell;
1337	+	int cellIndex;
1338	+
1339		#ifdef IS_MPI
1340		cellListRow_.clear();
1341		cellListCol_.clear();
1342	+	point.resize(nGroupsInRow_+1);
1343		#else
1344		cellList_.clear();
1345	+	point.resize(nGroups_+1);
1346		#endif
1347	+
1348	+	if (!usePeriodicBoundaryConditions_) {
1349	+	box = snap_->getBoundingBox();
1350	+	invBox = snap_->getInvBoundingBox();
1351	+	} else {
1352	+	box = snap_->getHmat();
1353	+	invBox = snap_->getInvHmat();
1354	+	}
1355	+
1356	+	Vector3d A = box.getColumn(0);
1357	+	Vector3d B = box.getColumn(1);
1358	+	Vector3d C = box.getColumn(2);
1359
1360	<	RealType rList_ = (largestRcut_ + skinThickness_);
1361	<	RealType rl2 = rList_ * rList_;
1362	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
1363	<	Mat3x3d Hmat = snap_->getHmat();
1301	<	Vector3d Hx = Hmat.getColumn(0);
1302	<	Vector3d Hy = Hmat.getColumn(1);
1303	<	Vector3d Hz = Hmat.getColumn(2);
1360	>	// Required for triclinic cells
1361	>	Vector3d AxB = cross(A, B);
1362	>	Vector3d BxC = cross(B, C);
1363	>	Vector3d CxA = cross(C, A);
1364
1365	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
1366	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
1367	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
1365	>	// unit vectors perpendicular to the faces of the triclinic cell:
1366	>	AxB.normalize();
1367	>	BxC.normalize();
1368	>	CxA.normalize();
1369
1370	<	// handle small boxes where the cell offsets can end up repeating cells
1370	>	// A set of perpendicular lengths in triclinic cells:
1371	>	RealType Wa = abs(dot(A, BxC));
1372	>	RealType Wb = abs(dot(B, CxA));
1373	>	RealType Wc = abs(dot(C, AxB));
1374
1375	+	nCells_.x() = int( Wa / rList_ );
1376	+	nCells_.y() = int( Wb / rList_ );
1377	+	nCells_.z() = int( Wc / rList_ );
1378	+
1379	+	// handle small boxes where the cell offsets can end up repeating cells
1380		if (nCells_.x() < 3) doAllPairs = true;
1381		if (nCells_.y() < 3) doAllPairs = true;
1382		if (nCells_.z() < 3) doAllPairs = true;
1383	<
1315	<	Mat3x3d invHmat = snap_->getInvHmat();
1316	<	Vector3d rs, scaled, dr;
1317	<	Vector3i whichCell;
1318	<	int cellIndex;
1383	>
1384		int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1385	<
1385	>
1386		#ifdef IS_MPI
1387		cellListRow_.resize(nCtot);
1388		cellListCol_.resize(nCtot);
1389		#else
1390		cellList_.resize(nCtot);
1391		#endif
1392	<
1392	>
1393		if (!doAllPairs) {
1394	+
1395		#ifdef IS_MPI
1396	<
1396	>
1397		for (int i = 0; i < nGroupsInRow_; i++) {
1398		rs = cgRowData.position[i];
1399
1400		// scaled positions relative to the box vectors
1401	<	scaled = invHmat * rs;
1401	>	scaled = invBox * rs;
1402
1403		// wrap the vector back into the unit box by subtracting integer box
1404		// numbers
1405		for (int j = 0; j < 3; j++) {
1406		scaled[j] -= roundMe(scaled[j]);
1407		scaled[j] += 0.5;
1408	+	// Handle the special case when an object is exactly on the
1409	+	// boundary (a scaled coordinate of 1.0 is the same as
1410	+	// scaled coordinate of 0.0)
1411	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1412		}
1413
1414		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1356 \| Line 1426 \| namespace OpenMD {
1426		rs = cgColData.position[i];
1427
1428		// scaled positions relative to the box vectors
1429	<	scaled = invHmat * rs;
1429	>	scaled = invBox * rs;
1430
1431		// wrap the vector back into the unit box by subtracting integer box
1432		// numbers
1433		for (int j = 0; j < 3; j++) {
1434		scaled[j] -= roundMe(scaled[j]);
1435		scaled[j] += 0.5;
1436	+	// Handle the special case when an object is exactly on the
1437	+	// boundary (a scaled coordinate of 1.0 is the same as
1438	+	// scaled coordinate of 0.0)
1439	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1440		}
1441
1442		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1376 \| Line 1450 \| namespace OpenMD {
1450		// add this cutoff group to the list of groups in this cell;
1451		cellListCol_[cellIndex].push_back(i);
1452		}
1453	<
1453	>
1454		#else
1455		for (int i = 0; i < nGroups_; i++) {
1456		rs = snap_->cgData.position[i];
1457
1458		// scaled positions relative to the box vectors
1459	<	scaled = invHmat * rs;
1459	>	scaled = invBox * rs;
1460
1461		// wrap the vector back into the unit box by subtracting integer box
1462		// numbers
#	Line 1396 \| Line 1470 \| namespace OpenMD {
1470		}
1471
1472		// find xyz-indices of cell that cutoffGroup is in.
1473	<	whichCell.x() = nCells_.x() * scaled.x();
1474	<	whichCell.y() = nCells_.y() * scaled.y();
1475	<	whichCell.z() = nCells_.z() * scaled.z();
1473	>	whichCell.x() = int(nCells_.x() * scaled.x());
1474	>	whichCell.y() = int(nCells_.y() * scaled.y());
1475	>	whichCell.z() = int(nCells_.z() * scaled.z());
1476
1477		// find single index of this cell:
1478		cellIndex = Vlinear(whichCell, nCells_);
#	Line 1409 \| Line 1483 \| namespace OpenMD {
1483
1484		#endif
1485
1412	–	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1413	–	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1414	–	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1415	–	Vector3i m1v(m1x, m1y, m1z);
1416	–	int m1 = Vlinear(m1v, nCells_);
1417	–
1418	–	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1419	–	os != cellOffsets_.end(); ++os) {
1420	–
1421	–	Vector3i m2v = m1v + (*os);
1422	–
1423	–
1424	–	if (m2v.x() >= nCells_.x()) {
1425	–	m2v.x() = 0;
1426	–	} else if (m2v.x() < 0) {
1427	–	m2v.x() = nCells_.x() - 1;
1428	–	}
1429	–
1430	–	if (m2v.y() >= nCells_.y()) {
1431	–	m2v.y() = 0;
1432	–	} else if (m2v.y() < 0) {
1433	–	m2v.y() = nCells_.y() - 1;
1434	–	}
1435	–
1436	–	if (m2v.z() >= nCells_.z()) {
1437	–	m2v.z() = 0;
1438	–	} else if (m2v.z() < 0) {
1439	–	m2v.z() = nCells_.z() - 1;
1440	–	}
1441	–
1442	–	int m2 = Vlinear (m2v, nCells_);
1443	–
1486		#ifdef IS_MPI
1487	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1488	<	j1 != cellListRow_[m1].end(); ++j1) {
1447	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1448	<	j2 != cellListCol_[m2].end(); ++j2) {
1449	<
1450	<	// In parallel, we need to visit all pairs of row
1451	<	// & column indicies and will divide labor in the
1452	<	// force evaluation later.
1453	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1454	<	snap_->wrapVector(dr);
1455	<	cuts = getGroupCutoffs( (j1), (j2) );
1456	<	if (dr.lengthSquare() < cuts.third) {
1457	<	neighborList.push_back(make_pair((j1), (j2)));
1458	<	}
1459	<	}
1460	<	}
1487	>	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1488	>	rs = cgRowData.position[j1];
1489		#else
1462	–	for (vector<int>::iterator j1 = cellList_[m1].begin();
1463	–	j1 != cellList_[m1].end(); ++j1) {
1464	–	for (vector<int>::iterator j2 = cellList_[m2].begin();
1465	–	j2 != cellList_[m2].end(); ++j2) {
1466	–
1467	–	// Always do this if we're in different cells or if
1468	–	// we're in the same cell and the global index of
1469	–	// the j2 cutoff group is greater than or equal to
1470	–	// the j1 cutoff group. Note that Rappaport's code
1471	–	// has a "less than" conditional here, but that
1472	–	// deals with atom-by-atom computation. OpenMD
1473	–	// allows atoms within a single cutoff group to
1474	–	// interact with each other.
1490
1491	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1492	+	rs = snap_->cgData.position[j1];
1493	+	#endif
1494	+	point[j1] = len;
1495	+
1496	+	// scaled positions relative to the box vectors
1497	+	scaled = invBox * rs;
1498	+
1499	+	// wrap the vector back into the unit box by subtracting integer box
1500	+	// numbers
1501	+	for (int j = 0; j < 3; j++) {
1502	+	scaled[j] -= roundMe(scaled[j]);
1503	+	scaled[j] += 0.5;
1504	+	// Handle the special case when an object is exactly on the
1505	+	// boundary (a scaled coordinate of 1.0 is the same as
1506	+	// scaled coordinate of 0.0)
1507	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1508	+	}
1509	+
1510	+	// find xyz-indices of cell that cutoffGroup is in.
1511	+	whichCell.x() = nCells_.x() * scaled.x();
1512	+	whichCell.y() = nCells_.y() * scaled.y();
1513	+	whichCell.z() = nCells_.z() * scaled.z();
1514	+
1515	+	// find single index of this cell:
1516	+	int m1 = Vlinear(whichCell, nCells_);
1517
1518	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1519	+	os != cellOffsets_.end(); ++os) {
1520	+
1521	+	Vector3i m2v = whichCell + (*os);
1522
1523	<	if (m2 != m1 \|\| (j2) >= (j1) ) {
1524	<
1525	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1526	<	snap_->wrapVector(dr);
1527	<	cuts = getGroupCutoffs( (j1), (j2) );
1528	<	if (dr.lengthSquare() < cuts.third) {
1529	<	neighborList.push_back(make_pair((j1), (j2)));
1530	<	}
1531	<	}
1532	<	}
1523	>	if (m2v.x() >= nCells_.x()) {
1524	>	m2v.x() = 0;
1525	>	} else if (m2v.x() < 0) {
1526	>	m2v.x() = nCells_.x() - 1;
1527	>	}
1528	>
1529	>	if (m2v.y() >= nCells_.y()) {
1530	>	m2v.y() = 0;
1531	>	} else if (m2v.y() < 0) {
1532	>	m2v.y() = nCells_.y() - 1;
1533	>	}
1534	>
1535	>	if (m2v.z() >= nCells_.z()) {
1536	>	m2v.z() = 0;
1537	>	} else if (m2v.z() < 0) {
1538	>	m2v.z() = nCells_.z() - 1;
1539	>	}
1540	>	int m2 = Vlinear (m2v, nCells_);
1541	>	#ifdef IS_MPI
1542	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1543	>	j2 != cellListCol_[m2].end(); ++j2) {
1544	>
1545	>	// In parallel, we need to visit all pairs of row
1546	>	// & column indicies and will divide labor in the
1547	>	// force evaluation later.
1548	>	dr = cgColData.position[(*j2)] - rs;
1549	>	if (usePeriodicBoundaryConditions_) {
1550	>	snap_->wrapVector(dr);
1551	>	}
1552	>	if (dr.lengthSquare() < rListSq_) {
1553	>	neighborList.push_back( (*j2) );
1554	>	++len;
1555	>	}
1556	>	}
1557	>	#else
1558	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1559	>	j2 != cellList_[m2].end(); ++j2) {
1560	>
1561	>	// Always do this if we're in different cells or if
1562	>	// we're in the same cell and the global index of
1563	>	// the j2 cutoff group is greater than or equal to
1564	>	// the j1 cutoff group. Note that Rappaport's code
1565	>	// has a "less than" conditional here, but that
1566	>	// deals with atom-by-atom computation. OpenMD
1567	>	// allows atoms within a single cutoff group to
1568	>	// interact with each other.
1569	>
1570	>	if ( (*j2) >= j1 ) {
1571	>
1572	>	dr = snap_->cgData.position[(*j2)] - rs;
1573	>	if (usePeriodicBoundaryConditions_) {
1574	>	snap_->wrapVector(dr);
1575		}
1576	<	#endif
1576	>	if ( dr.lengthSquare() < rListSq_) {
1577	>	neighborList.push_back( (*j2) );
1578	>	++len;
1579	>	}
1580		}
1581	<	}
1581	>	}
1582	>	#endif
1583		}
1584	<	}
1584	>	}
1585		} else {
1586		// branch to do all cutoff group pairs
1587		#ifdef IS_MPI
1588		for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1589	+	point[j1] = len;
1590	+	rs = cgRowData.position[j1];
1591		for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1592	<	dr = cgColData.position[j2] - cgRowData.position[j1];
1593	<	snap_->wrapVector(dr);
1594	<	cuts = getGroupCutoffs( j1, j2 );
1502	<	if (dr.lengthSquare() < cuts.third) {
1503	<	neighborList.push_back(make_pair(j1, j2));
1592	>	dr = cgColData.position[j2] - rs;
1593	>	if (usePeriodicBoundaryConditions_) {
1594	>	snap_->wrapVector(dr);
1595		}
1596	+	if (dr.lengthSquare() < rListSq_) {
1597	+	neighborList.push_back( j2 );
1598	+	++len;
1599	+	}
1600		}
1601		}
1602		#else
1603		// include all groups here.
1604		for (int j1 = 0; j1 < nGroups_; j1++) {
1605	+	point[j1] = len;
1606	+	rs = snap_->cgData.position[j1];
1607		// include self group interactions j2 == j1
1608		for (int j2 = j1; j2 < nGroups_; j2++) {
1609	<	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1610	<	snap_->wrapVector(dr);
1611	<	cuts = getGroupCutoffs( j1, j2 );
1515	<	if (dr.lengthSquare() < cuts.third) {
1516	<	neighborList.push_back(make_pair(j1, j2));
1609	>	dr = snap_->cgData.position[j2] - rs;
1610	>	if (usePeriodicBoundaryConditions_) {
1611	>	snap_->wrapVector(dr);
1612		}
1613	+	if (dr.lengthSquare() < rListSq_) {
1614	+	neighborList.push_back( j2 );
1615	+	++len;
1616	+	}
1617		}
1618		}
1619		#endif
1620		}
1621	<
1621	>
1622	>	#ifdef IS_MPI
1623	>	point[nGroupsInRow_] = len;
1624	>	#else
1625	>	point[nGroups_] = len;
1626	>	#endif
1627	>
1628		// save the local cutoff group positions for the check that is
1629		// done on each loop:
1630		saved_CG_positions_.clear();
1631	+	saved_CG_positions_.reserve(nGroups_);
1632		for (int i = 0; i < nGroups_; i++)
1633		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1528	–
1529	–	return neighborList;
1634		}
1635		} //end namespace OpenMD

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Comparing: branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1771 by gezelter, Fri Jul 27 17:34:10 2012 UTC vs. trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 2062 by gezelter, Tue Mar 3 16:40:39 2015 UTC

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Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1771 by gezelter, Fri Jul 27 17:34:10 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 2062 by gezelter, Tue Mar 3 16:40:39 2015 UTC