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

Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1721 by gezelter, Thu May 24 14:17:42 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1895 by gezelter, Mon Jul 1 21:09:37 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).
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 95 \| 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 109 \| 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 145 \| 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 165 \| 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 296 \| Line 310 \| namespace OpenMD {
310
311		RealType tol = 1e-6;
312		largestRcut_ = 0.0;
299	–	RealType rc;
313		int atid;
314		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315
#	Line 381 \| Line 394 \| namespace OpenMD {
394		}
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;
#	Line 406 \| 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 450 \| Line 463 \| namespace OpenMD {
463		}
464		}
465
453	–
466		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467		int i, j;
468		#ifdef IS_MPI
#	Line 464 \| 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 492 \| 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 539 \| Line 559 \| namespace OpenMD {
559		atomColData.electricField.end(), V3Zero);
560		}
561
542	–	if (storageLayout_ & DataStorage::dslFlucQForce) {
543	–	fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
544	–	0.0);
545	–	fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
546	–	0.0);
547	–	}
548	–
562		#endif
563		// even in parallel, we need to zero out the local arrays:
564
#	Line 600 \| Line 613 \| namespace OpenMD {
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) {
#	Line 608 \| Line 632 \| namespace OpenMD {
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	<	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
639	<	atomRowData.electroFrame);
640	<	AtomPlanMatrixColumn->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,
#	Line 648 \| Line 679 \| namespace OpenMD {
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,
#	Line 655 \| Line 688 \| namespace OpenMD {
688
689		int n = snap_->atomData.electricField.size();
690		vector<Vector3d> field_tmp(n, V3Zero);
691	<	AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
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		}
#	Line 755 \| Line 789 \| namespace OpenMD {
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		AtomPlanPotRow->scatter(pot_row, pot_temp);
819	<
820	<	for (int ii = 0; ii < pot_temp.size(); ii++ )
819	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
820	>
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		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;
#	Line 783 \| Line 894 \| namespace OpenMD {
894		}
895
896		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
897	<	RealType ploc1 = embeddingPot[ii];
897	>	RealType ploc1 = excludedPot[ii];
898		RealType ploc2 = 0.0;
899		MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
900	<	embeddingPot[ii] = ploc2;
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 804 \| 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 812 \| 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 829 \| 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 843 \| 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 856 \| 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 869 \| 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 886 \| 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 899 \| 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
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
1085		if (unique_id_1 == unique_id_2) return true;
#	Line 920 \| Line 1091 \| namespace OpenMD {
1091		} else {
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;
#	Line 972 \| Line 1149 \| namespace OpenMD {
1149
1150		#ifdef IS_MPI
1151		idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1152	+	idat.atid1 = identsRow[atom1];
1153	+	idat.atid2 = identsCol[atom2];
1154		//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1155		// ff_->getAtomType(identsCol[atom2]) );
1156
#	Line 980 \| Line 1159 \| namespace OpenMD {
1159		idat.A2 = &(atomColData.aMat[atom2]);
1160		}
1161
983	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
984	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
985	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
986	–	}
987	–
1162		if (storageLayout_ & DataStorage::dslTorque) {
1163		idat.t1 = &(atomRowData.torque[atom1]);
1164		idat.t2 = &(atomColData.torque[atom2]);
1165		}
1166
1167	+	if (storageLayout_ & DataStorage::dslDipole) {
1168	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1169	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1170	+	}
1171	+
1172	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1173	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1174	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1175	+	}
1176	+
1177		if (storageLayout_ & DataStorage::dslDensity) {
1178		idat.rho1 = &(atomRowData.density[atom1]);
1179		idat.rho2 = &(atomColData.density[atom2]);
#	Line 1022 \| Line 1206 \| namespace OpenMD {
1206
1207		#else
1208
1025	–
1026	–	// cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1027	–	// cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1028	–	// cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1029	–
1209		idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1210	<	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1211	<	// ff_->getAtomType(idents[atom2]) );
1210	>	idat.atid1 = idents[atom1];
1211	>	idat.atid2 = idents[atom2];
1212
1213		if (storageLayout_ & DataStorage::dslAmat) {
1214		idat.A1 = &(snap_->atomData.aMat[atom1]);
1215		idat.A2 = &(snap_->atomData.aMat[atom2]);
1216		}
1217
1039	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
1040	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1041	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1042	–	}
1043	–
1218		if (storageLayout_ & DataStorage::dslTorque) {
1219		idat.t1 = &(snap_->atomData.torque[atom1]);
1220		idat.t2 = &(snap_->atomData.torque[atom2]);
1221		}
1222
1223	+	if (storageLayout_ & DataStorage::dslDipole) {
1224	+	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1225	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1226	+	}
1227	+
1228	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1229	+	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1230	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1231	+	}
1232	+
1233		if (storageLayout_ & DataStorage::dslDensity) {
1234		idat.rho1 = &(snap_->atomData.density[atom1]);
1235		idat.rho2 = &(snap_->atomData.density[atom2]);
#	Line 1084 \| Line 1268 \| namespace OpenMD {
1268		#ifdef IS_MPI
1269		pot_row[atom1] += RealType(0.5) * *(idat.pot);
1270		pot_col[atom2] += RealType(0.5) * *(idat.pot);
1271	+	expot_row[atom1] += RealType(0.5) * *(idat.excludedPot);
1272	+	expot_col[atom2] += RealType(0.5) * *(idat.excludedPot);
1273
1274		atomRowData.force[atom1] += *(idat.f1);
1275		atomColData.force[atom2] -= *(idat.f1);
1276
1277		if (storageLayout_ & DataStorage::dslFlucQForce) {
1278	<	atomRowData.flucQFrc[atom1] += *(idat.dVdFQ1);
1279	<	atomColData.flucQFrc[atom2] += *(idat.dVdFQ2);
1278	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1279	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1280		}
1281
1282		if (storageLayout_ & DataStorage::dslElectricField) {
#	Line 1098 \| Line 1284 \| namespace OpenMD {
1284		atomColData.electricField[atom2] += *(idat.eField2);
1285		}
1286
1101	–	// should particle pot be done here also?
1287		#else
1288		pairwisePot += *(idat.pot);
1289	+	excludedPot += *(idat.excludedPot);
1290
1291		snap_->atomData.force[atom1] += *(idat.f1);
1292		snap_->atomData.force[atom2] -= *(idat.f1);
1293
1294		if (idat.doParticlePot) {
1295	+	// This is the pairwise contribution to the particle pot. The
1296	+	// embedding contribution is added in each of the low level
1297	+	// non-bonded routines. In parallel, this calculation is done
1298	+	// in collectData, not in unpackInteractionData.
1299		snap_->atomData.particlePot[atom1] += (idat.vpair) *(idat.sw);
1300	<	snap_->atomData.particlePot[atom2] -= (idat.vpair) *(idat.sw);
1300	>	snap_->atomData.particlePot[atom2] += (idat.vpair) *(idat.sw);
1301		}
1302
1303		if (storageLayout_ & DataStorage::dslFlucQForce) {
1304	<	snap_->atomData.flucQFrc[atom1] += *(idat.dVdFQ1);
1304	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1305		snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1306		}
1307
#	Line 1130 \| Line 1320 \| namespace OpenMD {
1320		* first element of pair is row-indexed CutoffGroup
1321		* second element of pair is column-indexed CutoffGroup
1322		*/
1323	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1324	<
1325	<	vector<pair<int, int> > neighborList;
1323	>	void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1324	>
1325	>	neighborList.clear();
1326		groupCutoffs cuts;
1327		bool doAllPairs = false;
1328
1329	+	RealType rList_ = (largestRcut_ + skinThickness_);
1330	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1331	+	Mat3x3d box;
1332	+	Mat3x3d invBox;
1333	+
1334	+	Vector3d rs, scaled, dr;
1335	+	Vector3i whichCell;
1336	+	int cellIndex;
1337	+
1338		#ifdef IS_MPI
1339		cellListRow_.clear();
1340		cellListCol_.clear();
1341		#else
1342		cellList_.clear();
1343		#endif
1344	<
1345	<	RealType rList_ = (largestRcut_ + skinThickness_);
1346	<	RealType rl2 = rList_ * rList_;
1347	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
1348	<	Mat3x3d Hmat = snap_->getHmat();
1349	<	Vector3d Hx = Hmat.getColumn(0);
1350	<	Vector3d Hy = Hmat.getColumn(1);
1351	<	Vector3d Hz = Hmat.getColumn(2);
1352	<
1353	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
1354	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
1355	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
1356	<
1344	>
1345	>	if (!usePeriodicBoundaryConditions_) {
1346	>	box = snap_->getBoundingBox();
1347	>	invBox = snap_->getInvBoundingBox();
1348	>	} else {
1349	>	box = snap_->getHmat();
1350	>	invBox = snap_->getInvHmat();
1351	>	}
1352	>
1353	>	Vector3d boxX = box.getColumn(0);
1354	>	Vector3d boxY = box.getColumn(1);
1355	>	Vector3d boxZ = box.getColumn(2);
1356	>
1357	>	nCells_.x() = (int) ( boxX.length() )/ rList_;
1358	>	nCells_.y() = (int) ( boxY.length() )/ rList_;
1359	>	nCells_.z() = (int) ( boxZ.length() )/ rList_;
1360	>
1361		// handle small boxes where the cell offsets can end up repeating cells
1362
1363		if (nCells_.x() < 3) doAllPairs = true;
1364		if (nCells_.y() < 3) doAllPairs = true;
1365		if (nCells_.z() < 3) doAllPairs = true;
1366	<
1164	<	Mat3x3d invHmat = snap_->getInvHmat();
1165	<	Vector3d rs, scaled, dr;
1166	<	Vector3i whichCell;
1167	<	int cellIndex;
1366	>
1367		int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1368	<
1368	>
1369		#ifdef IS_MPI
1370		cellListRow_.resize(nCtot);
1371		cellListCol_.resize(nCtot);
1372		#else
1373		cellList_.resize(nCtot);
1374		#endif
1375	<
1375	>
1376		if (!doAllPairs) {
1377		#ifdef IS_MPI
1378	<
1378	>
1379		for (int i = 0; i < nGroupsInRow_; i++) {
1380		rs = cgRowData.position[i];
1381
1382		// scaled positions relative to the box vectors
1383	<	scaled = invHmat * rs;
1383	>	scaled = invBox * rs;
1384
1385		// wrap the vector back into the unit box by subtracting integer box
1386		// numbers
1387		for (int j = 0; j < 3; j++) {
1388		scaled[j] -= roundMe(scaled[j]);
1389		scaled[j] += 0.5;
1390	+	// Handle the special case when an object is exactly on the
1391	+	// boundary (a scaled coordinate of 1.0 is the same as
1392	+	// scaled coordinate of 0.0)
1393	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1394		}
1395
1396		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1205 \| Line 1408 \| namespace OpenMD {
1408		rs = cgColData.position[i];
1409
1410		// scaled positions relative to the box vectors
1411	<	scaled = invHmat * rs;
1411	>	scaled = invBox * rs;
1412
1413		// wrap the vector back into the unit box by subtracting integer box
1414		// numbers
1415		for (int j = 0; j < 3; j++) {
1416		scaled[j] -= roundMe(scaled[j]);
1417		scaled[j] += 0.5;
1418	+	// Handle the special case when an object is exactly on the
1419	+	// boundary (a scaled coordinate of 1.0 is the same as
1420	+	// scaled coordinate of 0.0)
1421	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1422		}
1423
1424		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1225 \| Line 1432 \| namespace OpenMD {
1432		// add this cutoff group to the list of groups in this cell;
1433		cellListCol_[cellIndex].push_back(i);
1434		}
1435	<
1435	>
1436		#else
1437		for (int i = 0; i < nGroups_; i++) {
1438		rs = snap_->cgData.position[i];
1439
1440		// scaled positions relative to the box vectors
1441	<	scaled = invHmat * rs;
1441	>	scaled = invBox * rs;
1442
1443		// wrap the vector back into the unit box by subtracting integer box
1444		// numbers
1445		for (int j = 0; j < 3; j++) {
1446		scaled[j] -= roundMe(scaled[j]);
1447		scaled[j] += 0.5;
1448	+	// Handle the special case when an object is exactly on the
1449	+	// boundary (a scaled coordinate of 1.0 is the same as
1450	+	// scaled coordinate of 0.0)
1451	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1452		}
1453
1454		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1296 \| Line 1507 \| namespace OpenMD {
1507		// & column indicies and will divide labor in the
1508		// force evaluation later.
1509		dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1510	<	snap_->wrapVector(dr);
1510	>	if (usePeriodicBoundaryConditions_) {
1511	>	snap_->wrapVector(dr);
1512	>	}
1513		cuts = getGroupCutoffs( (j1), (j2) );
1514		if (dr.lengthSquare() < cuts.third) {
1515		neighborList.push_back(make_pair((j1), (j2)));
#	Line 1318 \| Line 1531 \| namespace OpenMD {
1531		// allows atoms within a single cutoff group to
1532		// interact with each other.
1533
1321	–
1322	–
1534		if (m2 != m1 \|\| (j2) >= (j1) ) {
1535
1536		dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1537	<	snap_->wrapVector(dr);
1537	>	if (usePeriodicBoundaryConditions_) {
1538	>	snap_->wrapVector(dr);
1539	>	}
1540		cuts = getGroupCutoffs( (j1), (j2) );
1541		if (dr.lengthSquare() < cuts.third) {
1542		neighborList.push_back(make_pair((j1), (j2)));
#	Line 1342 \| Line 1555 \| namespace OpenMD {
1555		for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1556		for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1557		dr = cgColData.position[j2] - cgRowData.position[j1];
1558	<	snap_->wrapVector(dr);
1558	>	if (usePeriodicBoundaryConditions_) {
1559	>	snap_->wrapVector(dr);
1560	>	}
1561		cuts = getGroupCutoffs( j1, j2 );
1562		if (dr.lengthSquare() < cuts.third) {
1563		neighborList.push_back(make_pair(j1, j2));
#	Line 1355 \| Line 1570 \| namespace OpenMD {
1570		// include self group interactions j2 == j1
1571		for (int j2 = j1; j2 < nGroups_; j2++) {
1572		dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1573	<	snap_->wrapVector(dr);
1573	>	if (usePeriodicBoundaryConditions_) {
1574	>	snap_->wrapVector(dr);
1575	>	}
1576		cuts = getGroupCutoffs( j1, j2 );
1577		if (dr.lengthSquare() < cuts.third) {
1578		neighborList.push_back(make_pair(j1, j2));
#	Line 1370 \| Line 1587 \| namespace OpenMD {
1587		saved_CG_positions_.clear();
1588		for (int i = 0; i < nGroups_; i++)
1589		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1373	–
1374	–	return neighborList;
1590		}
1591		} //end namespace OpenMD

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Comparing: branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1721 by gezelter, Thu May 24 14:17:42 2012 UTC vs. trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1895 by gezelter, Mon Jul 1 21:09:37 2013 UTC

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Comparing:
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1721 by gezelter, Thu May 24 14:17:42 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1895 by gezelter, Mon Jul 1 21:09:37 2013 UTC