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

Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1612 by gezelter, Fri Aug 12 19:59:56 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1896 by gezelter, Tue Jul 2 20:02:31 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 94 \| Line 95 \| namespace OpenMD {
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 108 \| 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		MPI::Intracomm row = rowComm.getComm();
#	Line 144 \| 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
#	Line 164 \| Line 176 \| namespace OpenMD {
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);
#	Line 233 \| Line 248 \| namespace OpenMD {
248		}
249		}
250
251	<	#endif
237	<
238	<	// allocate memory for the parallel objects
239	<	atypesLocal.resize(nLocal_);
240	<
241	<	for (int i = 0; i < nLocal_; i++)
242	<	atypesLocal[i] = ff_->getAtomType(idents[i]);
243	<
244	<	groupList_.clear();
245	<	groupList_.resize(nGroups_);
246	<	for (int i = 0; i < nGroups_; i++) {
247	<	int gid = cgLocalToGlobal[i];
248	<	for (int j = 0; j < nLocal_; j++) {
249	<	int aid = AtomLocalToGlobal[j];
250	<	if (globalGroupMembership[aid] == gid) {
251	<	groupList_[i].push_back(j);
252	<	}
253	<	}
254	<	}
255	<
251	>	#else
252		excludesForAtom.clear();
253		excludesForAtom.resize(nLocal_);
254		toposForAtom.clear();
#	Line 285 \| 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		}
308
309		void ForceMatrixDecomposition::createGtypeCutoffMap() {
310
311	+	GrCut.clear();
312	+	GrCutSq.clear();
313	+	GrlistSq.clear();
314	+
315		RealType tol = 1e-6;
316		largestRcut_ = 0.0;
297	–	RealType rc;
317		int atid;
318		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
319
#	Line 379 \| Line 398 \| namespace OpenMD {
398		}
399
400		bool gTypeFound = false;
401	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
401	>	for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
402		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
403		groupToGtype[cg1] = gt;
404		gTypeFound = true;
#	Line 404 \| Line 423 \| namespace OpenMD {
423
424		RealType tradRcut = groupMax;
425
426	<	for (int i = 0; i < gTypeCutoffs.size(); i++) {
427	<	for (int j = 0; j < gTypeCutoffs.size(); j++) {
426	>	GrCut.resize( gTypeCutoffs.size() );
427	>	GrCutSq.resize( gTypeCutoffs.size() );
428	>	GrlistSq.resize( gTypeCutoffs.size() );
429	>
430	>
431	>	for (unsigned int i = 0; i < gTypeCutoffs.size(); i++) {
432	>	GrCut[i].resize( gTypeCutoffs.size() , 0.0);
433	>	GrCutSq[i].resize( gTypeCutoffs.size(), 0.0 );
434	>	GrlistSq[i].resize( gTypeCutoffs.size(), 0.0 );
435	>
436	>	for (unsigned int j = 0; j < gTypeCutoffs.size(); j++) {
437		RealType thisRcut;
438		switch(cutoffPolicy_) {
439		case TRADITIONAL:
#	Line 427 \| Line 455 \| namespace OpenMD {
455		break;
456		}
457
458	<	pair<int,int> key = make_pair(i,j);
431	<	gTypeCutoffMap[key].first = thisRcut;
458	>	GrCut[i][j] = thisRcut;
459		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
460	<	gTypeCutoffMap[key].second = thisRcut*thisRcut;
461	<	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
460	>	GrCutSq[i][j] = thisRcut * thisRcut;
461	>	GrlistSq[i][j] = pow(thisRcut + skinThickness_, 2);
462	>
463	>	// pair<int,int> key = make_pair(i,j);
464	>	// gTypeCutoffMap[key].first = thisRcut;
465	>	// gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
466		// sanity check
467
468		if (userChoseCutoff_) {
469	<	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
469	>	if (abs(GrCut[i][j] - userCutoff_) > 0.0001) {
470		sprintf(painCave.errMsg,
471		"ForceMatrixDecomposition::createGtypeCutoffMap "
472		"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
#	Line 448 \| Line 479 \| namespace OpenMD {
479		}
480		}
481
482	<
452	<	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
482	>	void ForceMatrixDecomposition::getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) {
483		int i, j;
484		#ifdef IS_MPI
485		i = groupRowToGtype[cg1];
#	Line 458 \| Line 488 \| namespace OpenMD {
488		i = groupToGtype[cg1];
489		j = groupToGtype[cg2];
490		#endif
491	<	return gTypeCutoffMap[make_pair(i,j)];
491	>	rcut = GrCut[i][j];
492	>	rcutsq = GrCutSq[i][j];
493	>	rlistsq = GrlistSq[i][j];
494	>	return;
495	>	//return gTypeCutoffMap[make_pair(i,j)];
496		}
497
498		int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
499	<	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
499	>	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
500		if (toposForAtom[atom1][j] == atom2)
501		return topoDist[atom1][j];
502	<	}
502	>	}
503		return 0;
504		}
505
506		void ForceMatrixDecomposition::zeroWorkArrays() {
507		pairwisePot = 0.0;
508		embeddingPot = 0.0;
509	+	excludedPot = 0.0;
510	+	excludedSelfPot = 0.0;
511
512		#ifdef IS_MPI
513		if (storageLayout_ & DataStorage::dslForce) {
#	Line 490 \| Line 526 \| namespace OpenMD {
526		fill(pot_col.begin(), pot_col.end(),
527		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
528
529	+	fill(expot_row.begin(), expot_row.end(),
530	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
531	+
532	+	fill(expot_col.begin(), expot_col.end(),
533	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
534	+
535		if (storageLayout_ & DataStorage::dslParticlePot) {
536		fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
537		0.0);
#	Line 523 \| Line 565 \| namespace OpenMD {
565		atomColData.skippedCharge.end(), 0.0);
566		}
567
568	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
569	+	fill(atomRowData.flucQFrc.begin(),
570	+	atomRowData.flucQFrc.end(), 0.0);
571	+	fill(atomColData.flucQFrc.begin(),
572	+	atomColData.flucQFrc.end(), 0.0);
573	+	}
574	+
575	+	if (storageLayout_ & DataStorage::dslElectricField) {
576	+	fill(atomRowData.electricField.begin(),
577	+	atomRowData.electricField.end(), V3Zero);
578	+	fill(atomColData.electricField.begin(),
579	+	atomColData.electricField.end(), V3Zero);
580	+	}
581	+
582		#endif
583		// even in parallel, we need to zero out the local arrays:
584
#	Line 535 \| Line 591 \| namespace OpenMD {
591		fill(snap_->atomData.density.begin(),
592		snap_->atomData.density.end(), 0.0);
593		}
594	+
595		if (storageLayout_ & DataStorage::dslFunctional) {
596		fill(snap_->atomData.functional.begin(),
597		snap_->atomData.functional.end(), 0.0);
598		}
599	+
600		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
601		fill(snap_->atomData.functionalDerivative.begin(),
602		snap_->atomData.functionalDerivative.end(), 0.0);
603		}
604	+
605		if (storageLayout_ & DataStorage::dslSkippedCharge) {
606		fill(snap_->atomData.skippedCharge.begin(),
607		snap_->atomData.skippedCharge.end(), 0.0);
608		}
609	<
609	>
610	>	if (storageLayout_ & DataStorage::dslElectricField) {
611	>	fill(snap_->atomData.electricField.begin(),
612	>	snap_->atomData.electricField.end(), V3Zero);
613	>	}
614		}
615
616
#	Line 570 \| Line 633 \| namespace OpenMD {
633		cgPlanVectorColumn->gather(snap_->cgData.position,
634		cgColData.position);
635
636	+
637	+
638	+	if (needVelocities_) {
639	+	// gather up the atomic velocities
640	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
641	+	atomColData.velocity);
642	+
643	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
644	+	cgColData.velocity);
645	+	}
646	+
647
648		// if needed, gather the atomic rotation matrices
649		if (storageLayout_ & DataStorage::dslAmat) {
#	Line 578 \| Line 652 \| namespace OpenMD {
652		AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
653		atomColData.aMat);
654		}
655	<
656	<	// if needed, gather the atomic eletrostatic frames
657	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
658	<	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
659	<	atomRowData.electroFrame);
660	<	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
661	<	atomColData.electroFrame);
655	>
656	>	// if needed, gather the atomic eletrostatic information
657	>	if (storageLayout_ & DataStorage::dslDipole) {
658	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
659	>	atomRowData.dipole);
660	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
661	>	atomColData.dipole);
662	>	}
663	>
664	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
665	>	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
666	>	atomRowData.quadrupole);
667	>	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
668	>	atomColData.quadrupole);
669		}
670	+
671	+	// if needed, gather the atomic fluctuating charge values
672	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
673	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
674	+	atomRowData.flucQPos);
675	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
676	+	atomColData.flucQPos);
677	+	}
678
679		#endif
680		}
#	Line 609 \| Line 698 \| namespace OpenMD {
698		for (int i = 0; i < n; i++)
699		snap_->atomData.density[i] += rho_tmp[i];
700		}
701	+
702	+	// this isn't necessary if we don't have polarizable atoms, but
703	+	// we'll leave it here for now.
704	+	if (storageLayout_ & DataStorage::dslElectricField) {
705	+
706	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
707	+	snap_->atomData.electricField);
708	+
709	+	int n = snap_->atomData.electricField.size();
710	+	vector<Vector3d> field_tmp(n, V3Zero);
711	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
712	+	field_tmp);
713	+	for (int i = 0; i < n; i++)
714	+	snap_->atomData.electricField[i] += field_tmp[i];
715	+	}
716		#endif
717		}
718
#	Line 683 \| Line 787 \| namespace OpenMD {
787		}
788
789		AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
790	<	for (int i = 0; i < ns; i++)
790	>	for (int i = 0; i < ns; i++)
791		snap_->atomData.skippedCharge[i] += skch_tmp[i];
792	+
793		}
794
795	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
796	+
797	+	int nq = snap_->atomData.flucQFrc.size();
798	+	vector<RealType> fqfrc_tmp(nq, 0.0);
799	+
800	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
801	+	for (int i = 0; i < nq; i++) {
802	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
803	+	fqfrc_tmp[i] = 0.0;
804	+	}
805	+
806	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
807	+	for (int i = 0; i < nq; i++)
808	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
809	+
810	+	}
811	+
812	+	if (storageLayout_ & DataStorage::dslElectricField) {
813	+
814	+	int nef = snap_->atomData.electricField.size();
815	+	vector<Vector3d> efield_tmp(nef, V3Zero);
816	+
817	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
818	+	for (int i = 0; i < nef; i++) {
819	+	snap_->atomData.electricField[i] += efield_tmp[i];
820	+	efield_tmp[i] = 0.0;
821	+	}
822	+
823	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
824	+	for (int i = 0; i < nef; i++)
825	+	snap_->atomData.electricField[i] += efield_tmp[i];
826	+	}
827	+
828	+
829		nLocal_ = snap_->getNumberOfAtoms();
830
831		vector<potVec> pot_temp(nLocal_,
832		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
833	+	vector<potVec> expot_temp(nLocal_,
834	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
835
836		// scatter/gather pot_row into the members of my column
837
838		AtomPlanPotRow->scatter(pot_row, pot_temp);
839	+	AtomPlanPotRow->scatter(expot_row, expot_temp);
840
841	<	for (int ii = 0; ii < pot_temp.size(); ii++ )
841	>	for (int ii = 0; ii < pot_temp.size(); ii++ )
842		pairwisePot += pot_temp[ii];
843	<
843	>
844	>	for (int ii = 0; ii < expot_temp.size(); ii++ )
845	>	excludedPot += expot_temp[ii];
846	>
847	>	if (storageLayout_ & DataStorage::dslParticlePot) {
848	>	// This is the pairwise contribution to the particle pot. The
849	>	// embedding contribution is added in each of the low level
850	>	// non-bonded routines. In single processor, this is done in
851	>	// unpackInteractionData, not in collectData.
852	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
853	>	for (int i = 0; i < nLocal_; i++) {
854	>	// factor of two is because the total potential terms are divided
855	>	// by 2 in parallel due to row/ column scatter
856	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
857	>	}
858	>	}
859	>	}
860	>
861		fill(pot_temp.begin(), pot_temp.end(),
862		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
863	+	fill(expot_temp.begin(), expot_temp.end(),
864	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
865
866		AtomPlanPotColumn->scatter(pot_col, pot_temp);
867	+	AtomPlanPotColumn->scatter(expot_col, expot_temp);
868
869		for (int ii = 0; ii < pot_temp.size(); ii++ )
870		pairwisePot += pot_temp[ii];
871	+
872	+	for (int ii = 0; ii < expot_temp.size(); ii++ )
873	+	excludedPot += expot_temp[ii];
874	+
875	+	if (storageLayout_ & DataStorage::dslParticlePot) {
876	+	// This is the pairwise contribution to the particle pot. The
877	+	// embedding contribution is added in each of the low level
878	+	// non-bonded routines. In single processor, this is done in
879	+	// unpackInteractionData, not in collectData.
880	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
881	+	for (int i = 0; i < nLocal_; i++) {
882	+	// factor of two is because the total potential terms are divided
883	+	// by 2 in parallel due to row/ column scatter
884	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
885	+	}
886	+	}
887	+	}
888
889	+	if (storageLayout_ & DataStorage::dslParticlePot) {
890	+	int npp = snap_->atomData.particlePot.size();
891	+	vector<RealType> ppot_temp(npp, 0.0);
892	+
893	+	// This is the direct or embedding contribution to the particle
894	+	// pot.
895	+
896	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
897	+	for (int i = 0; i < npp; i++) {
898	+	snap_->atomData.particlePot[i] += ppot_temp[i];
899	+	}
900	+
901	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
902	+
903	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
904	+	for (int i = 0; i < npp; i++) {
905	+	snap_->atomData.particlePot[i] += ppot_temp[i];
906	+	}
907	+	}
908	+
909		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
910		RealType ploc1 = pairwisePot[ii];
911		RealType ploc2 = 0.0;
#	Line 714 \| Line 913 \| namespace OpenMD {
913		pairwisePot[ii] = ploc2;
914		}
915
916	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
917	+	RealType ploc1 = excludedPot[ii];
918	+	RealType ploc2 = 0.0;
919	+	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
920	+	excludedPot[ii] = ploc2;
921	+	}
922	+
923	+	// Here be dragons.
924	+	MPI::Intracomm col = colComm.getComm();
925	+
926	+	col.Allreduce(MPI::IN_PLACE,
927	+	&snap_->frameData.conductiveHeatFlux[0], 3,
928	+	MPI::REALTYPE, MPI::SUM);
929	+
930	+
931		#endif
932
933		}
934
935	<	int ForceMatrixDecomposition::getNAtomsInRow() {
935	>	/**
936	>	* Collects information obtained during the post-pair (and embedding
937	>	* functional) loops onto local data structures.
938	>	*/
939	>	void ForceMatrixDecomposition::collectSelfData() {
940	>	snap_ = sman_->getCurrentSnapshot();
941	>	storageLayout_ = sman_->getStorageLayout();
942	>
943	>	#ifdef IS_MPI
944	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
945	>	RealType ploc1 = embeddingPot[ii];
946	>	RealType ploc2 = 0.0;
947	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
948	>	embeddingPot[ii] = ploc2;
949	>	}
950	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
951	>	RealType ploc1 = excludedSelfPot[ii];
952	>	RealType ploc2 = 0.0;
953	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
954	>	excludedSelfPot[ii] = ploc2;
955	>	}
956	>	#endif
957	>
958	>	}
959	>
960	>
961	>
962	>	int& ForceMatrixDecomposition::getNAtomsInRow() {
963		#ifdef IS_MPI
964		return nAtomsInRow_;
965		#else
#	Line 729 \| Line 970 \| namespace OpenMD {
970		/**
971		* returns the list of atoms belonging to this group.
972		*/
973	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
973	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
974		#ifdef IS_MPI
975		return groupListRow_[cg1];
976		#else
#	Line 737 \| Line 978 \| namespace OpenMD {
978		#endif
979		}
980
981	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
981	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
982		#ifdef IS_MPI
983		return groupListCol_[cg2];
984		#else
#	Line 754 \| Line 995 \| namespace OpenMD {
995		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
996		#endif
997
998	<	snap_->wrapVector(d);
998	>	if (usePeriodicBoundaryConditions_) {
999	>	snap_->wrapVector(d);
1000	>	}
1001		return d;
1002		}
1003
1004	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
1005	+	#ifdef IS_MPI
1006	+	return cgColData.velocity[cg2];
1007	+	#else
1008	+	return snap_->cgData.velocity[cg2];
1009	+	#endif
1010	+	}
1011
1012	+	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
1013	+	#ifdef IS_MPI
1014	+	return atomColData.velocity[atom2];
1015	+	#else
1016	+	return snap_->atomData.velocity[atom2];
1017	+	#endif
1018	+	}
1019	+
1020	+
1021		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
1022
1023		Vector3d d;
#	Line 768 \| Line 1027 \| namespace OpenMD {
1027		#else
1028		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1029		#endif
1030	<
1031	<	snap_->wrapVector(d);
1030	>	if (usePeriodicBoundaryConditions_) {
1031	>	snap_->wrapVector(d);
1032	>	}
1033		return d;
1034		}
1035
#	Line 781 \| Line 1041 \| namespace OpenMD {
1041		#else
1042		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1043		#endif
1044	<
1045	<	snap_->wrapVector(d);
1044	>	if (usePeriodicBoundaryConditions_) {
1045	>	snap_->wrapVector(d);
1046	>	}
1047		return d;
1048		}
1049
1050	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1050	>	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1051		#ifdef IS_MPI
1052		return massFactorsRow[atom1];
1053		#else
#	Line 794 \| Line 1055 \| namespace OpenMD {
1055		#endif
1056		}
1057
1058	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1058	>	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1059		#ifdef IS_MPI
1060		return massFactorsCol[atom2];
1061		#else
#	Line 811 \| Line 1072 \| namespace OpenMD {
1072		#else
1073		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1074		#endif
1075	<
1076	<	snap_->wrapVector(d);
1075	>	if (usePeriodicBoundaryConditions_) {
1076	>	snap_->wrapVector(d);
1077	>	}
1078		return d;
1079		}
1080
1081	<	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1081	>	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1082		return excludesForAtom[atom1];
1083		}
1084
#	Line 824 \| Line 1086 \| namespace OpenMD {
1086		* We need to exclude some overcounted interactions that result from
1087		* the parallel decomposition.
1088		*/
1089	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1089	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1090		int unique_id_1, unique_id_2;
1091	<
1091	>
1092		#ifdef IS_MPI
1093		// in MPI, we have to look up the unique IDs for each atom
1094		unique_id_1 = AtomRowToGlobal[atom1];
1095		unique_id_2 = AtomColToGlobal[atom2];
1096	+	// group1 = cgRowToGlobal[cg1];
1097	+	// group2 = cgColToGlobal[cg2];
1098	+	#else
1099	+	unique_id_1 = AtomLocalToGlobal[atom1];
1100	+	unique_id_2 = AtomLocalToGlobal[atom2];
1101	+	int group1 = cgLocalToGlobal[cg1];
1102	+	int group2 = cgLocalToGlobal[cg2];
1103	+	#endif
1104
835	–	// this situation should only arise in MPI simulations
1105		if (unique_id_1 == unique_id_2) return true;
1106	<
1106	>
1107	>	#ifdef IS_MPI
1108		// this prevents us from doing the pair on multiple processors
1109		if (unique_id_1 < unique_id_2) {
1110		if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1111		} else {
1112	<	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1112	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1113		}
1114	+	#endif
1115	+
1116	+	#ifndef IS_MPI
1117	+	if (group1 == group2) {
1118	+	if (unique_id_1 < unique_id_2) return true;
1119	+	}
1120		#endif
1121	+
1122		return false;
1123		}
1124
#	Line 855 \| Line 1132 \| namespace OpenMD {
1132		* field) must still be handled for these pairs.
1133		*/
1134		bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1135	<	int unique_id_2;
1136	<	#ifdef IS_MPI
1137	<	// in MPI, we have to look up the unique IDs for the row atom.
861	<	unique_id_2 = AtomColToGlobal[atom2];
862	<	#else
863	<	// in the normal loop, the atom numbers are unique
864	<	unique_id_2 = atom2;
865	<	#endif
1135	>
1136	>	// excludesForAtom was constructed to use row/column indices in the MPI
1137	>	// version, and to use local IDs in the non-MPI version:
1138
1139		for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1140		i != excludesForAtom[atom1].end(); ++i) {
1141	<	if ( (*i) == unique_id_2 ) return true;
1141	>	if ( (*i) == atom2 ) return true;
1142		}
1143
1144		return false;
#	Line 897 \| Line 1169 \| namespace OpenMD {
1169
1170		#ifdef IS_MPI
1171		idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1172	+	idat.atid1 = identsRow[atom1];
1173	+	idat.atid2 = identsCol[atom2];
1174		//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1175		// ff_->getAtomType(identsCol[atom2]) );
1176
#	Line 905 \| Line 1179 \| namespace OpenMD {
1179		idat.A2 = &(atomColData.aMat[atom2]);
1180		}
1181
908	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
909	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
910	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
911	–	}
912	–
1182		if (storageLayout_ & DataStorage::dslTorque) {
1183		idat.t1 = &(atomRowData.torque[atom1]);
1184		idat.t2 = &(atomColData.torque[atom2]);
1185		}
1186
1187	+	if (storageLayout_ & DataStorage::dslDipole) {
1188	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1189	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1190	+	}
1191	+
1192	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1193	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1194	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1195	+	}
1196	+
1197		if (storageLayout_ & DataStorage::dslDensity) {
1198		idat.rho1 = &(atomRowData.density[atom1]);
1199		idat.rho2 = &(atomColData.density[atom2]);
#	Line 940 \| Line 1219 \| namespace OpenMD {
1219		idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1220		}
1221
1222	<	#else
1222	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1223	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1224	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1225	>	}
1226
1227	+	#else
1228	+
1229		idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1230	<	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1231	<	// ff_->getAtomType(idents[atom2]) );
1230	>	idat.atid1 = idents[atom1];
1231	>	idat.atid2 = idents[atom2];
1232
1233		if (storageLayout_ & DataStorage::dslAmat) {
1234		idat.A1 = &(snap_->atomData.aMat[atom1]);
1235		idat.A2 = &(snap_->atomData.aMat[atom2]);
1236		}
1237
954	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
955	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
956	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
957	–	}
958	–
1238		if (storageLayout_ & DataStorage::dslTorque) {
1239		idat.t1 = &(snap_->atomData.torque[atom1]);
1240		idat.t2 = &(snap_->atomData.torque[atom2]);
1241		}
1242
1243	+	if (storageLayout_ & DataStorage::dslDipole) {
1244	+	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1245	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1246	+	}
1247	+
1248	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1249	+	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1250	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1251	+	}
1252	+
1253		if (storageLayout_ & DataStorage::dslDensity) {
1254		idat.rho1 = &(snap_->atomData.density[atom1]);
1255		idat.rho2 = &(snap_->atomData.density[atom2]);
#	Line 985 \| Line 1274 \| namespace OpenMD {
1274		idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1275		idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1276		}
1277	+
1278	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1279	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1280	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1281	+	}
1282	+
1283		#endif
1284		}
1285
1286
1287		void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1288		#ifdef IS_MPI
1289	<	pot_row[atom1] += 0.5 * *(idat.pot);
1290	<	pot_col[atom2] += 0.5 * *(idat.pot);
1289	>	pot_row[atom1] += RealType(0.5) * *(idat.pot);
1290	>	pot_col[atom2] += RealType(0.5) * *(idat.pot);
1291	>	expot_row[atom1] += RealType(0.5) * *(idat.excludedPot);
1292	>	expot_col[atom2] += RealType(0.5) * *(idat.excludedPot);
1293
1294		atomRowData.force[atom1] += *(idat.f1);
1295		atomColData.force[atom2] -= *(idat.f1);
1296	+
1297	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1298	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1299	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1300	+	}
1301	+
1302	+	if (storageLayout_ & DataStorage::dslElectricField) {
1303	+	atomRowData.electricField[atom1] += *(idat.eField1);
1304	+	atomColData.electricField[atom2] += *(idat.eField2);
1305	+	}
1306	+
1307		#else
1308		pairwisePot += *(idat.pot);
1309	+	excludedPot += *(idat.excludedPot);
1310
1311		snap_->atomData.force[atom1] += *(idat.f1);
1312		snap_->atomData.force[atom2] -= *(idat.f1);
1313	+
1314	+	if (idat.doParticlePot) {
1315	+	// This is the pairwise contribution to the particle pot. The
1316	+	// embedding contribution is added in each of the low level
1317	+	// non-bonded routines. In parallel, this calculation is done
1318	+	// in collectData, not in unpackInteractionData.
1319	+	snap_->atomData.particlePot[atom1] += (idat.vpair) *(idat.sw);
1320	+	snap_->atomData.particlePot[atom2] += (idat.vpair) *(idat.sw);
1321	+	}
1322	+
1323	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1324	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1325	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1326	+	}
1327	+
1328	+	if (storageLayout_ & DataStorage::dslElectricField) {
1329	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1330	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1331	+	}
1332	+
1333		#endif
1334
1335		}
#	Line 1011 \| Line 1340 \| namespace OpenMD {
1340		* first element of pair is row-indexed CutoffGroup
1341		* second element of pair is column-indexed CutoffGroup
1342		*/
1343	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1344	<
1345	<	vector<pair<int, int> > neighborList;
1343	>	void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1344	>
1345	>	neighborList.clear();
1346		groupCutoffs cuts;
1347		bool doAllPairs = false;
1348
1349	+	RealType rList_ = (largestRcut_ + skinThickness_);
1350	+	RealType rcut, rcutsq, rlistsq;
1351	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1352	+	Mat3x3d box;
1353	+	Mat3x3d invBox;
1354	+
1355	+	Vector3d rs, scaled, dr;
1356	+	Vector3i whichCell;
1357	+	int cellIndex;
1358	+
1359		#ifdef IS_MPI
1360		cellListRow_.clear();
1361		cellListCol_.clear();
1362		#else
1363		cellList_.clear();
1364		#endif
1365	<
1366	<	RealType rList_ = (largestRcut_ + skinThickness_);
1367	<	RealType rl2 = rList_ * rList_;
1368	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
1369	<	Mat3x3d Hmat = snap_->getHmat();
1370	<	Vector3d Hx = Hmat.getColumn(0);
1371	<	Vector3d Hy = Hmat.getColumn(1);
1372	<	Vector3d Hz = Hmat.getColumn(2);
1373	<
1374	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
1375	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
1376	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
1377	<
1365	>
1366	>	if (!usePeriodicBoundaryConditions_) {
1367	>	box = snap_->getBoundingBox();
1368	>	invBox = snap_->getInvBoundingBox();
1369	>	} else {
1370	>	box = snap_->getHmat();
1371	>	invBox = snap_->getInvHmat();
1372	>	}
1373	>
1374	>	Vector3d boxX = box.getColumn(0);
1375	>	Vector3d boxY = box.getColumn(1);
1376	>	Vector3d boxZ = box.getColumn(2);
1377	>
1378	>	nCells_.x() = (int) ( boxX.length() )/ rList_;
1379	>	nCells_.y() = (int) ( boxY.length() )/ rList_;
1380	>	nCells_.z() = (int) ( boxZ.length() )/ rList_;
1381	>
1382		// handle small boxes where the cell offsets can end up repeating cells
1383
1384		if (nCells_.x() < 3) doAllPairs = true;
1385		if (nCells_.y() < 3) doAllPairs = true;
1386		if (nCells_.z() < 3) doAllPairs = true;
1387	<
1045	<	Mat3x3d invHmat = snap_->getInvHmat();
1046	<	Vector3d rs, scaled, dr;
1047	<	Vector3i whichCell;
1048	<	int cellIndex;
1387	>
1388		int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1389	<
1389	>
1390		#ifdef IS_MPI
1391		cellListRow_.resize(nCtot);
1392		cellListCol_.resize(nCtot);
1393		#else
1394		cellList_.resize(nCtot);
1395		#endif
1396	<
1396	>
1397		if (!doAllPairs) {
1398		#ifdef IS_MPI
1399	<
1399	>
1400		for (int i = 0; i < nGroupsInRow_; i++) {
1401		rs = cgRowData.position[i];
1402
1403		// scaled positions relative to the box vectors
1404	<	scaled = invHmat * rs;
1404	>	scaled = invBox * rs;
1405
1406		// wrap the vector back into the unit box by subtracting integer box
1407		// numbers
1408		for (int j = 0; j < 3; j++) {
1409		scaled[j] -= roundMe(scaled[j]);
1410		scaled[j] += 0.5;
1411	+	// Handle the special case when an object is exactly on the
1412	+	// boundary (a scaled coordinate of 1.0 is the same as
1413	+	// scaled coordinate of 0.0)
1414	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1415		}
1416
1417		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1086 \| Line 1429 \| namespace OpenMD {
1429		rs = cgColData.position[i];
1430
1431		// scaled positions relative to the box vectors
1432	<	scaled = invHmat * rs;
1432	>	scaled = invBox * rs;
1433
1434		// wrap the vector back into the unit box by subtracting integer box
1435		// numbers
1436		for (int j = 0; j < 3; j++) {
1437		scaled[j] -= roundMe(scaled[j]);
1438		scaled[j] += 0.5;
1439	+	// Handle the special case when an object is exactly on the
1440	+	// boundary (a scaled coordinate of 1.0 is the same as
1441	+	// scaled coordinate of 0.0)
1442	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1443		}
1444
1445		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1106 \| Line 1453 \| namespace OpenMD {
1453		// add this cutoff group to the list of groups in this cell;
1454		cellListCol_[cellIndex].push_back(i);
1455		}
1456	<
1456	>
1457		#else
1458		for (int i = 0; i < nGroups_; i++) {
1459		rs = snap_->cgData.position[i];
1460
1461		// scaled positions relative to the box vectors
1462	<	scaled = invHmat * rs;
1462	>	scaled = invBox * rs;
1463
1464		// wrap the vector back into the unit box by subtracting integer box
1465		// numbers
1466		for (int j = 0; j < 3; j++) {
1467		scaled[j] -= roundMe(scaled[j]);
1468		scaled[j] += 0.5;
1469	+	// Handle the special case when an object is exactly on the
1470	+	// boundary (a scaled coordinate of 1.0 is the same as
1471	+	// scaled coordinate of 0.0)
1472	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1473		}
1474
1475		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1177 \| Line 1528 \| namespace OpenMD {
1528		// & column indicies and will divide labor in the
1529		// force evaluation later.
1530		dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1531	<	snap_->wrapVector(dr);
1532	<	cuts = getGroupCutoffs( (j1), (j2) );
1533	<	if (dr.lengthSquare() < cuts.third) {
1531	>	if (usePeriodicBoundaryConditions_) {
1532	>	snap_->wrapVector(dr);
1533	>	}
1534	>	getGroupCutoffs( (j1), (j2), rcut, rcutsq, rlistsq );
1535	>	if (dr.lengthSquare() < rlistsq) {
1536		neighborList.push_back(make_pair((j1), (j2)));
1537		}
1538		}
1539		}
1540		#else
1188	–
1541		for (vector<int>::iterator j1 = cellList_[m1].begin();
1542		j1 != cellList_[m1].end(); ++j1) {
1543		for (vector<int>::iterator j2 = cellList_[m2].begin();
1544		j2 != cellList_[m2].end(); ++j2) {
1545	<
1545	>
1546		// Always do this if we're in different cells or if
1547	<	// we're in the same cell and the global index of the
1548	<	// j2 cutoff group is less than the j1 cutoff group
1549	<
1550	<	if (m2 != m1 \|\| (j2) < (j1)) {
1547	>	// we're in the same cell and the global index of
1548	>	// the j2 cutoff group is greater than or equal to
1549	>	// the j1 cutoff group. Note that Rappaport's code
1550	>	// has a "less than" conditional here, but that
1551	>	// deals with atom-by-atom computation. OpenMD
1552	>	// allows atoms within a single cutoff group to
1553	>	// interact with each other.
1554	>
1555	>	if (m2 != m1 \|\| (j2) >= (j1) ) {
1556	>
1557		dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1558	<	snap_->wrapVector(dr);
1559	<	cuts = getGroupCutoffs( (j1), (j2) );
1560	<	if (dr.lengthSquare() < cuts.third) {
1558	>	if (usePeriodicBoundaryConditions_) {
1559	>	snap_->wrapVector(dr);
1560	>	}
1561	>	getGroupCutoffs( (j1), (j2), rcut, rcutsq, rlistsq );
1562	>	if (dr.lengthSquare() < rlistsq) {
1563		neighborList.push_back(make_pair((j1), (j2)));
1564		}
1565		}
#	Line 1214 \| Line 1574 \| namespace OpenMD {
1574		// branch to do all cutoff group pairs
1575		#ifdef IS_MPI
1576		for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1577	<	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1577	>	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1578		dr = cgColData.position[j2] - cgRowData.position[j1];
1579	<	snap_->wrapVector(dr);
1580	<	cuts = getGroupCutoffs( j1, j2 );
1581	<	if (dr.lengthSquare() < cuts.third) {
1579	>	if (usePeriodicBoundaryConditions_) {
1580	>	snap_->wrapVector(dr);
1581	>	}
1582	>	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1583	>	if (dr.lengthSquare() < rlistsq) {
1584		neighborList.push_back(make_pair(j1, j2));
1585		}
1586		}
1587	<	}
1587	>	}
1588		#else
1589	<	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1590	<	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1589	>	// include all groups here.
1590	>	for (int j1 = 0; j1 < nGroups_; j1++) {
1591	>	// include self group interactions j2 == j1
1592	>	for (int j2 = j1; j2 < nGroups_; j2++) {
1593		dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1594	<	snap_->wrapVector(dr);
1595	<	cuts = getGroupCutoffs( j1, j2 );
1596	<	if (dr.lengthSquare() < cuts.third) {
1594	>	if (usePeriodicBoundaryConditions_) {
1595	>	snap_->wrapVector(dr);
1596	>	}
1597	>	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1598	>	if (dr.lengthSquare() < rlistsq) {
1599		neighborList.push_back(make_pair(j1, j2));
1600		}
1601	<	}
1602	<	}
1601	>	}
1602	>	}
1603		#endif
1604		}
1605
#	Line 1242 \| Line 1608 \| namespace OpenMD {
1608		saved_CG_positions_.clear();
1609		for (int i = 0; i < nGroups_; i++)
1610		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1245	–
1246	–	return neighborList;
1611		}
1612		} //end namespace OpenMD

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Comparing: branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1612 by gezelter, Fri Aug 12 19:59:56 2011 UTC vs. trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1896 by gezelter, Tue Jul 2 20:02:31 2013 UTC

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Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1612 by gezelter, Fri Aug 12 19:59:56 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1896 by gezelter, Tue Jul 2 20:02:31 2013 UTC