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

Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1931 by gezelter, Mon Aug 19 19:20:32 2013 UTC vs.
Revision 2057 by gezelter, Tue Mar 3 15:22:26 2015 UTC

#	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 119 \| 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 306 \| Line 302 \| namespace OpenMD {
302		groupList_[i].push_back(j);
303		}
304		}
305	<	}
310	<
311	<
312	<	createGtypeCutoffMap();
313	<
305	>	}
306		}
315	–
316	–	void ForceMatrixDecomposition::createGtypeCutoffMap() {
317	–
318	–	GrCut.clear();
319	–	GrCutSq.clear();
320	–	GrlistSq.clear();
321	–
322	–	RealType tol = 1e-6;
323	–	largestRcut_ = 0.0;
324	–	int atid;
325	–	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
326	–
327	–	map<int, RealType> atypeCutoff;
328	–
329	–	for (set<AtomType*>::iterator at = atypes.begin();
330	–	at != atypes.end(); ++at){
331	–	atid = (*at)->getIdent();
332	–	if (userChoseCutoff_)
333	–	atypeCutoff[atid] = userCutoff_;
334	–	else
335	–	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
336	–	}
337	–
338	–	vector<RealType> gTypeCutoffs;
339	–	// first we do a single loop over the cutoff groups to find the
340	–	// largest cutoff for any atypes present in this group.
341	–	#ifdef IS_MPI
342	–	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
343	–	groupRowToGtype.resize(nGroupsInRow_);
344	–	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
345	–	vector<int> atomListRow = getAtomsInGroupRow(cg1);
346	–	for (vector<int>::iterator ia = atomListRow.begin();
347	–	ia != atomListRow.end(); ++ia) {
348	–	int atom1 = (*ia);
349	–	atid = identsRow[atom1];
350	–	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
351	–	groupCutoffRow[cg1] = atypeCutoff[atid];
352	–	}
353	–	}
354	–
355	–	bool gTypeFound = false;
356	–	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
357	–	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
358	–	groupRowToGtype[cg1] = gt;
359	–	gTypeFound = true;
360	–	}
361	–	}
362	–	if (!gTypeFound) {
363	–	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
364	–	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
365	–	}
366	–
367	–	}
368	–	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
369	–	groupColToGtype.resize(nGroupsInCol_);
370	–	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
371	–	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
372	–	for (vector<int>::iterator jb = atomListCol.begin();
373	–	jb != atomListCol.end(); ++jb) {
374	–	int atom2 = (*jb);
375	–	atid = identsCol[atom2];
376	–	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
377	–	groupCutoffCol[cg2] = atypeCutoff[atid];
378	–	}
379	–	}
380	–	bool gTypeFound = false;
381	–	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
382	–	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
383	–	groupColToGtype[cg2] = gt;
384	–	gTypeFound = true;
385	–	}
386	–	}
387	–	if (!gTypeFound) {
388	–	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
389	–	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
390	–	}
391	–	}
392	–	#else
393	–
394	–	vector<RealType> groupCutoff(nGroups_, 0.0);
395	–	groupToGtype.resize(nGroups_);
396	–	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
397	–	groupCutoff[cg1] = 0.0;
398	–	vector<int> atomList = getAtomsInGroupRow(cg1);
399	–	for (vector<int>::iterator ia = atomList.begin();
400	–	ia != atomList.end(); ++ia) {
401	–	int atom1 = (*ia);
402	–	atid = idents[atom1];
403	–	if (atypeCutoff[atid] > groupCutoff[cg1])
404	–	groupCutoff[cg1] = atypeCutoff[atid];
405	–	}
406	–
407	–	bool gTypeFound = false;
408	–	for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
409	–	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
410	–	groupToGtype[cg1] = gt;
411	–	gTypeFound = true;
412	–	}
413	–	}
414	–	if (!gTypeFound) {
415	–	gTypeCutoffs.push_back( groupCutoff[cg1] );
416	–	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
417	–	}
418	–	}
419	–	#endif
420	–
421	–	// Now we find the maximum group cutoff value present in the simulation
422	–
423	–	RealType groupMax = *max_element(gTypeCutoffs.begin(),
424	–	gTypeCutoffs.end());
425	–
426	–	#ifdef IS_MPI
427	–	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
428	–	MPI::MAX);
429	–	#endif
307
431	–	RealType tradRcut = groupMax;
432	–
433	–	GrCut.resize( gTypeCutoffs.size() );
434	–	GrCutSq.resize( gTypeCutoffs.size() );
435	–	GrlistSq.resize( gTypeCutoffs.size() );
436	–
437	–
438	–	for (unsigned int i = 0; i < gTypeCutoffs.size(); i++) {
439	–	GrCut[i].resize( gTypeCutoffs.size() , 0.0);
440	–	GrCutSq[i].resize( gTypeCutoffs.size(), 0.0 );
441	–	GrlistSq[i].resize( gTypeCutoffs.size(), 0.0 );
442	–
443	–	for (unsigned int j = 0; j < gTypeCutoffs.size(); j++) {
444	–	RealType thisRcut;
445	–	switch(cutoffPolicy_) {
446	–	case TRADITIONAL:
447	–	thisRcut = tradRcut;
448	–	break;
449	–	case MIX:
450	–	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
451	–	break;
452	–	case MAX:
453	–	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
454	–	break;
455	–	default:
456	–	sprintf(painCave.errMsg,
457	–	"ForceMatrixDecomposition::createGtypeCutoffMap "
458	–	"hit an unknown cutoff policy!\n");
459	–	painCave.severity = OPENMD_ERROR;
460	–	painCave.isFatal = 1;
461	–	simError();
462	–	break;
463	–	}
464	–
465	–	GrCut[i][j] = thisRcut;
466	–	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
467	–	GrCutSq[i][j] = thisRcut * thisRcut;
468	–	GrlistSq[i][j] = pow(thisRcut + skinThickness_, 2);
469	–
470	–	// pair<int,int> key = make_pair(i,j);
471	–	// gTypeCutoffMap[key].first = thisRcut;
472	–	// gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
473	–	// sanity check
474	–
475	–	if (userChoseCutoff_) {
476	–	if (abs(GrCut[i][j] - userCutoff_) > 0.0001) {
477	–	sprintf(painCave.errMsg,
478	–	"ForceMatrixDecomposition::createGtypeCutoffMap "
479	–	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
480	–	painCave.severity = OPENMD_ERROR;
481	–	painCave.isFatal = 1;
482	–	simError();
483	–	}
484	–	}
485	–	}
486	–	}
487	–	}
488	–
489	–	void ForceMatrixDecomposition::getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) {
490	–	int i, j;
491	–	#ifdef IS_MPI
492	–	i = groupRowToGtype[cg1];
493	–	j = groupColToGtype[cg2];
494	–	#else
495	–	i = groupToGtype[cg1];
496	–	j = groupToGtype[cg2];
497	–	#endif
498	–	rcut = GrCut[i][j];
499	–	rcutsq = GrCutSq[i][j];
500	–	rlistsq = GrlistSq[i][j];
501	–	return;
502	–	//return gTypeCutoffMap[make_pair(i,j)];
503	–	}
504	–
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)
#	Line 586 \| Line 389 \| namespace OpenMD {
389		atomColData.electricField.end(), V3Zero);
390		}
391
392	+	if (storageLayout_ & DataStorage::dslSitePotential) {
393	+	fill(atomRowData.sitePotential.begin(),
394	+	atomRowData.sitePotential.end(), 0.0);
395	+	fill(atomColData.sitePotential.begin(),
396	+	atomColData.sitePotential.end(), 0.0);
397	+	}
398	+
399		#endif
400		// even in parallel, we need to zero out the local arrays:
401
#	Line 618 \| 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		snap_ = sman_->getCurrentSnapshot();
440		storageLayout_ = sman_->getStorageLayout();
441	+
442	+	bool needsCG = true;
443	+	if(info_->getNCutoffGroups() != info_->getNAtoms())
444	+	needsCG = false;
445	+
446		#ifdef IS_MPI
447
448		// gather up the atomic positions
#	Line 634 \| Line 453 \| namespace OpenMD {
453
454		// gather up the cutoff group positions
455
456	<	cgPlanVectorRow->gather(snap_->cgData.position,
457	<	cgRowData.position);
458	<
459	<	cgPlanVectorColumn->gather(snap_->cgData.position,
460	<	cgColData.position);
461	<
456	>	if (needsCG) {
457	>	cgPlanVectorRow->gather(snap_->cgData.position,
458	>	cgRowData.position);
459	>
460	>	cgPlanVectorColumn->gather(snap_->cgData.position,
461	>	cgColData.position);
462	>	}
463
464
465		if (needVelocities_) {
466		// gather up the atomic velocities
467		AtomPlanVectorColumn->gather(snap_->atomData.velocity,
468		atomColData.velocity);
469	<
470	<	cgPlanVectorColumn->gather(snap_->cgData.velocity,
471	<	cgColData.velocity);
469	>
470	>	if (needsCG) {
471	>	cgPlanVectorColumn->gather(snap_->cgData.velocity,
472	>	cgColData.velocity);
473	>	}
474		}
475
476
#	Line 832 \| Line 654 \| namespace OpenMD {
654		snap_->atomData.electricField[i] += efield_tmp[i];
655		}
656
657	+	if (storageLayout_ & DataStorage::dslSitePotential) {
658
659	+	int nsp = snap_->atomData.sitePotential.size();
660	+	vector<RealType> sp_tmp(nsp, 0.0);
661	+
662	+	AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
663	+	for (int i = 0; i < nsp; i++) {
664	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
665	+	sp_tmp[i] = 0.0;
666	+	}
667	+
668	+	AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
669	+	for (int i = 0; i < nsp; i++)
670	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
671	+	}
672	+
673		nLocal_ = snap_->getNumberOfAtoms();
674
675		vector<potVec> pot_temp(nLocal_,
#	Line 916 \| Line 753 \| namespace OpenMD {
753		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
754		RealType ploc1 = pairwisePot[ii];
755		RealType ploc2 = 0.0;
756	<	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
756	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
757		pairwisePot[ii] = ploc2;
758		}
759
760		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
761		RealType ploc1 = excludedPot[ii];
762		RealType ploc2 = 0.0;
763	<	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
763	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
764		excludedPot[ii] = ploc2;
765		}
766
767		// Here be dragons.
768	<	MPI::Intracomm col = colComm.getComm();
768	>	MPI_Comm col = colComm.getComm();
769
770	<	col.Allreduce(MPI::IN_PLACE,
770	>	MPI_Allreduce(MPI_IN_PLACE,
771		&snap_->frameData.conductiveHeatFlux[0], 3,
772	<	MPI::REALTYPE, MPI::SUM);
772	>	MPI_REALTYPE, MPI_SUM, col);
773
774
775		#endif
#	Line 951 \| Line 788 \| namespace OpenMD {
788		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
789		RealType ploc1 = embeddingPot[ii];
790		RealType ploc2 = 0.0;
791	<	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
791	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
792		embeddingPot[ii] = ploc2;
793		}
794		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
795		RealType ploc1 = excludedSelfPot[ii];
796		RealType ploc2 = 0.0;
797	<	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
797	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
798		excludedSelfPot[ii] = ploc2;
799		}
800		#endif
#	Line 1170 \| Line 1007 \| namespace OpenMD {
1007
1008		// filling interaction blocks with pointers
1009		void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1010	<	int atom1, int atom2) {
1010	>	int atom1, int atom2,
1011	>	bool newAtom1) {
1012
1013		idat.excluded = excludeAtomPair(atom1, atom2);
1014	<
1014	>
1015	>	if (newAtom1) {
1016	>
1017		#ifdef IS_MPI
1018	<	//idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1019	<	idat.atid1 = identsRow[atom1];
1018	>	idat.atid1 = identsRow[atom1];
1019	>	idat.atid2 = identsCol[atom2];
1020	>
1021	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1022	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1023	>	} else {
1024	>	idat.sameRegion = false;
1025	>	}
1026	>
1027	>	if (storageLayout_ & DataStorage::dslAmat) {
1028	>	idat.A1 = &(atomRowData.aMat[atom1]);
1029	>	idat.A2 = &(atomColData.aMat[atom2]);
1030	>	}
1031	>
1032	>	if (storageLayout_ & DataStorage::dslTorque) {
1033	>	idat.t1 = &(atomRowData.torque[atom1]);
1034	>	idat.t2 = &(atomColData.torque[atom2]);
1035	>	}
1036	>
1037	>	if (storageLayout_ & DataStorage::dslDipole) {
1038	>	idat.dipole1 = &(atomRowData.dipole[atom1]);
1039	>	idat.dipole2 = &(atomColData.dipole[atom2]);
1040	>	}
1041	>
1042	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1043	>	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1044	>	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1045	>	}
1046	>
1047	>	if (storageLayout_ & DataStorage::dslDensity) {
1048	>	idat.rho1 = &(atomRowData.density[atom1]);
1049	>	idat.rho2 = &(atomColData.density[atom2]);
1050	>	}
1051	>
1052	>	if (storageLayout_ & DataStorage::dslFunctional) {
1053	>	idat.frho1 = &(atomRowData.functional[atom1]);
1054	>	idat.frho2 = &(atomColData.functional[atom2]);
1055	>	}
1056	>
1057	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1058	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1059	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1060	>	}
1061	>
1062	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1063	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1064	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1065	>	}
1066	>
1067	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1068	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1069	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1070	>	}
1071	>
1072	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1073	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1074	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1075	>	}
1076	>
1077	>	#else
1078	>
1079	>	idat.atid1 = idents[atom1];
1080	>	idat.atid2 = idents[atom2];
1081	>
1082	>	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1083	>	idat.sameRegion = (regions[atom1] == regions[atom2]);
1084	>	} else {
1085	>	idat.sameRegion = false;
1086	>	}
1087	>
1088	>	if (storageLayout_ & DataStorage::dslAmat) {
1089	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1090	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1091	>	}
1092	>
1093	>	if (storageLayout_ & DataStorage::dslTorque) {
1094	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1095	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1096	>	}
1097	>
1098	>	if (storageLayout_ & DataStorage::dslDipole) {
1099	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1100	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1101	>	}
1102	>
1103	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1104	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1105	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1106	>	}
1107	>
1108	>	if (storageLayout_ & DataStorage::dslDensity) {
1109	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1110	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1111	>	}
1112	>
1113	>	if (storageLayout_ & DataStorage::dslFunctional) {
1114	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1115	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1116	>	}
1117	>
1118	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1119	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1120	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1121	>	}
1122	>
1123	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1124	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1125	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1126	>	}
1127	>
1128	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1129	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1130	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1131	>	}
1132	>
1133	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1134	>	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1135	>	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1136	>	}
1137	>	#endif
1138	>
1139	>	} else {
1140	>	// atom1 is not new, so don't bother updating properties of that atom:
1141	>	#ifdef IS_MPI
1142		idat.atid2 = identsCol[atom2];
1143
1144		if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
#	Line 1186 \| Line 1148 \| namespace OpenMD {
1148		}
1149
1150		if (storageLayout_ & DataStorage::dslAmat) {
1189	–	idat.A1 = &(atomRowData.aMat[atom1]);
1151		idat.A2 = &(atomColData.aMat[atom2]);
1152		}
1153
1154		if (storageLayout_ & DataStorage::dslTorque) {
1194	–	idat.t1 = &(atomRowData.torque[atom1]);
1155		idat.t2 = &(atomColData.torque[atom2]);
1156		}
1157
1158		if (storageLayout_ & DataStorage::dslDipole) {
1199	–	idat.dipole1 = &(atomRowData.dipole[atom1]);
1159		idat.dipole2 = &(atomColData.dipole[atom2]);
1160		}
1161
1162		if (storageLayout_ & DataStorage::dslQuadrupole) {
1204	–	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1163		idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1164		}
1165
1166		if (storageLayout_ & DataStorage::dslDensity) {
1209	–	idat.rho1 = &(atomRowData.density[atom1]);
1167		idat.rho2 = &(atomColData.density[atom2]);
1168		}
1169
1170		if (storageLayout_ & DataStorage::dslFunctional) {
1214	–	idat.frho1 = &(atomRowData.functional[atom1]);
1171		idat.frho2 = &(atomColData.functional[atom2]);
1172		}
1173
1174		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1219	–	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1175		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1176		}
1177
1178		if (storageLayout_ & DataStorage::dslParticlePot) {
1224	–	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1179		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1180		}
1181
1182		if (storageLayout_ & DataStorage::dslSkippedCharge) {
1229	–	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1183		idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1184		}
1185
1186	<	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1234	<	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1186	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1187		idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1188		}
1189
1190	<	#else
1239	<
1240	<	//idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1241	<	idat.atid1 = idents[atom1];
1190	>	#else
1191		idat.atid2 = idents[atom2];
1192
1193		if (regions[atom1] >= 0 && regions[atom2] >= 0) {
#	Line 1248 \| Line 1197 \| namespace OpenMD {
1197		}
1198
1199		if (storageLayout_ & DataStorage::dslAmat) {
1251	–	idat.A1 = &(snap_->atomData.aMat[atom1]);
1200		idat.A2 = &(snap_->atomData.aMat[atom2]);
1201		}
1202
1203		if (storageLayout_ & DataStorage::dslTorque) {
1256	–	idat.t1 = &(snap_->atomData.torque[atom1]);
1204		idat.t2 = &(snap_->atomData.torque[atom2]);
1205		}
1206
1207		if (storageLayout_ & DataStorage::dslDipole) {
1261	–	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1208		idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1209		}
1210
1211		if (storageLayout_ & DataStorage::dslQuadrupole) {
1266	–	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1212		idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1213		}
1214
1215		if (storageLayout_ & DataStorage::dslDensity) {
1271	–	idat.rho1 = &(snap_->atomData.density[atom1]);
1216		idat.rho2 = &(snap_->atomData.density[atom2]);
1217		}
1218
1219		if (storageLayout_ & DataStorage::dslFunctional) {
1276	–	idat.frho1 = &(snap_->atomData.functional[atom1]);
1220		idat.frho2 = &(snap_->atomData.functional[atom2]);
1221		}
1222
1223		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1281	–	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1224		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1225		}
1226
1227		if (storageLayout_ & DataStorage::dslParticlePot) {
1286	–	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1228		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1229		}
1230
1231		if (storageLayout_ & DataStorage::dslSkippedCharge) {
1291	–	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1232		idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1233		}
1234
1235		if (storageLayout_ & DataStorage::dslFlucQPosition) {
1296	–	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1236		idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1237		}
1238
1239		#endif
1240	+	}
1241		}
1302	–
1242
1243	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1243	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat,
1244	>	int atom1, int atom2) {
1245		#ifdef IS_MPI
1246		pot_row[atom1] += RealType(0.5) * *(idat.pot);
1247		pot_col[atom2] += RealType(0.5) * *(idat.pot);
#	Line 1321 \| Line 1261 \| namespace OpenMD {
1261		atomColData.electricField[atom2] += *(idat.eField2);
1262		}
1263
1264	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1265	+	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1266	+	atomColData.sitePotential[atom2] += *(idat.sPot2);
1267	+	}
1268	+
1269		#else
1270		pairwisePot += *(idat.pot);
1271		excludedPot += *(idat.excludedPot);
#	Line 1347 \| Line 1292 \| namespace OpenMD {
1292		snap_->atomData.electricField[atom2] += *(idat.eField2);
1293		}
1294
1295	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1296	+	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1297	+	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1298	+	}
1299	+
1300		#endif
1301
1302		}
#	Line 1354 \| Line 1304 \| namespace OpenMD {
1304		/*
1305		* buildNeighborList
1306		*
1307	<	* first element of pair is row-indexed CutoffGroup
1308	<	* second element of pair is column-indexed CutoffGroup
1307	>	* Constructs the Verlet neighbor list for a force-matrix
1308	>	* decomposition. In this case, each processor is responsible for
1309	>	* row-site interactions with column-sites.
1310	>	*
1311	>	* neighborList is returned as a packed array of neighboring
1312	>	* column-ordered CutoffGroups. The starting position in
1313	>	* neighborList for each row-ordered CutoffGroup is given by the
1314	>	* returned vector point.
1315		*/
1316	<	void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1317	<
1316	>	void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
1317	>	vector<int>& point) {
1318		neighborList.clear();
1319	<	groupCutoffs cuts;
1319	>	point.clear();
1320	>	int len = 0;
1321	>
1322		bool doAllPairs = false;
1323
1366	–	RealType rList_ = (largestRcut_ + skinThickness_);
1367	–	RealType rcut, rcutsq, rlistsq;
1324		Snapshot* snap_ = sman_->getCurrentSnapshot();
1325		Mat3x3d box;
1326		Mat3x3d invBox;
#	Line 1376 \| Line 1332 \| namespace OpenMD {
1332		#ifdef IS_MPI
1333		cellListRow_.clear();
1334		cellListCol_.clear();
1335	+	point.resize(nGroupsInRow_+1);
1336		#else
1337		cellList_.clear();
1338	+	point.resize(nGroups_+1);
1339		#endif
1340
1341		if (!usePeriodicBoundaryConditions_) {
#	Line 1388 \| Line 1346 \| namespace OpenMD {
1346		invBox = snap_->getInvHmat();
1347		}
1348
1349	<	Vector3d boxX = box.getColumn(0);
1350	<	Vector3d boxY = box.getColumn(1);
1351	<	Vector3d boxZ = box.getColumn(2);
1349	>	Vector3d A = box.getColumn(0);
1350	>	Vector3d B = box.getColumn(1);
1351	>	Vector3d C = box.getColumn(2);
1352	>
1353	>	// Required for triclinic cells
1354	>	Vector3d AxB = cross(A, B);
1355	>	Vector3d BxC = cross(B, C);
1356	>	Vector3d CxA = cross(C, A);
1357	>
1358	>	// unit vectors perpendicular to the faces of the triclinic cell:
1359	>	AxB.normalize();
1360	>	BxC.normalize();
1361	>	CxA.normalize();
1362	>
1363	>	// A set of perpendicular lengths in triclinic cells:
1364	>	RealType Wa = abs(dot(A, BxC));
1365	>	RealType Wb = abs(dot(B, CxA));
1366	>	RealType Wc = abs(dot(C, AxB));
1367
1368	<	nCells_.x() = (int) ( boxX.length() )/ rList_;
1369	<	nCells_.y() = (int) ( boxY.length() )/ rList_;
1370	<	nCells_.z() = (int) ( boxZ.length() )/ rList_;
1368	>	nCells_.x() = int( Wa / rList_ );
1369	>	nCells_.y() = int( Wb / rList_ );
1370	>	nCells_.z() = int( Wc / rList_ );
1371
1372		// handle small boxes where the cell offsets can end up repeating cells
1400	–
1373		if (nCells_.x() < 3) doAllPairs = true;
1374		if (nCells_.y() < 3) doAllPairs = true;
1375		if (nCells_.z() < 3) doAllPairs = true;
#	Line 1412 \| Line 1384 \| namespace OpenMD {
1384		#endif
1385
1386		if (!doAllPairs) {
1387	+
1388		#ifdef IS_MPI
1389
1390		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 1470 \| Line 1443 \| namespace OpenMD {
1443		// add this cutoff group to the list of groups in this cell;
1444		cellListCol_[cellIndex].push_back(i);
1445		}
1446	<
1446	>
1447		#else
1448		for (int i = 0; i < nGroups_; i++) {
1449		rs = snap_->cgData.position[i];
#	Line 1490 \| Line 1463 \| namespace OpenMD {
1463		}
1464
1465		// find xyz-indices of cell that cutoffGroup is in.
1466	<	whichCell.x() = nCells_.x() * scaled.x();
1467	<	whichCell.y() = nCells_.y() * scaled.y();
1468	<	whichCell.z() = nCells_.z() * scaled.z();
1466	>	whichCell.x() = int(nCells_.x() * scaled.x());
1467	>	whichCell.y() = int(nCells_.y() * scaled.y());
1468	>	whichCell.z() = int(nCells_.z() * scaled.z());
1469
1470		// find single index of this cell:
1471		cellIndex = Vlinear(whichCell, nCells_);
#	Line 1503 \| Line 1476 \| namespace OpenMD {
1476
1477		#endif
1478
1479	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1480	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1481	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1482	<	Vector3i m1v(m1x, m1y, m1z);
1510	<	int m1 = Vlinear(m1v, nCells_);
1511	<
1512	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1513	<	os != cellOffsets_.end(); ++os) {
1514	<
1515	<	Vector3i m2v = m1v + (*os);
1516	<
1479	>	#ifdef IS_MPI
1480	>	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1481	>	rs = cgRowData.position[j1];
1482	>	#else
1483
1484	<	if (m2v.x() >= nCells_.x()) {
1485	<	m2v.x() = 0;
1486	<	} else if (m2v.x() < 0) {
1487	<	m2v.x() = nCells_.x() - 1;
1488	<	}
1489	<
1490	<	if (m2v.y() >= nCells_.y()) {
1491	<	m2v.y() = 0;
1492	<	} else if (m2v.y() < 0) {
1493	<	m2v.y() = nCells_.y() - 1;
1494	<	}
1495	<
1496	<	if (m2v.z() >= nCells_.z()) {
1497	<	m2v.z() = 0;
1498	<	} else if (m2v.z() < 0) {
1499	<	m2v.z() = nCells_.z() - 1;
1500	<	}
1484	>	for (int j1 = 0; j1 < nGroups_; j1++) {
1485	>	rs = snap_->cgData.position[j1];
1486	>	#endif
1487	>	point[j1] = len;
1488	>
1489	>	// scaled positions relative to the box vectors
1490	>	scaled = invBox * rs;
1491	>
1492	>	// wrap the vector back into the unit box by subtracting integer box
1493	>	// numbers
1494	>	for (int j = 0; j < 3; j++) {
1495	>	scaled[j] -= roundMe(scaled[j]);
1496	>	scaled[j] += 0.5;
1497	>	// Handle the special case when an object is exactly on the
1498	>	// boundary (a scaled coordinate of 1.0 is the same as
1499	>	// scaled coordinate of 0.0)
1500	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1501	>	}
1502	>
1503	>	// find xyz-indices of cell that cutoffGroup is in.
1504	>	whichCell.x() = nCells_.x() * scaled.x();
1505	>	whichCell.y() = nCells_.y() * scaled.y();
1506	>	whichCell.z() = nCells_.z() * scaled.z();
1507	>
1508	>	// find single index of this cell:
1509	>	int m1 = Vlinear(whichCell, nCells_);
1510
1511	<	int m2 = Vlinear (m2v, nCells_);
1511	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1512	>	os != cellOffsets_.end(); ++os) {
1513
1514	+	Vector3i m2v = whichCell + (*os);
1515	+
1516	+	if (m2v.x() >= nCells_.x()) {
1517	+	m2v.x() = 0;
1518	+	} else if (m2v.x() < 0) {
1519	+	m2v.x() = nCells_.x() - 1;
1520	+	}
1521	+
1522	+	if (m2v.y() >= nCells_.y()) {
1523	+	m2v.y() = 0;
1524	+	} else if (m2v.y() < 0) {
1525	+	m2v.y() = nCells_.y() - 1;
1526	+	}
1527	+
1528	+	if (m2v.z() >= nCells_.z()) {
1529	+	m2v.z() = 0;
1530	+	} else if (m2v.z() < 0) {
1531	+	m2v.z() = nCells_.z() - 1;
1532	+	}
1533	+	int m2 = Vlinear (m2v, nCells_);
1534		#ifdef IS_MPI
1535	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1536	<	j1 != cellListRow_[m1].end(); ++j1) {
1537	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1538	<	j2 != cellListCol_[m2].end(); ++j2) {
1539	<
1540	<	// In parallel, we need to visit all pairs of row
1541	<	// & column indicies and will divide labor in the
1542	<	// force evaluation later.
1543	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1544	<	if (usePeriodicBoundaryConditions_) {
1545	<	snap_->wrapVector(dr);
1546	<	}
1547	<	getGroupCutoffs( (j1), (j2), rcut, rcutsq, rlistsq );
1548	<	if (dr.lengthSquare() < rlistsq) {
1549	<	neighborList.push_back(make_pair((j1), (j2)));
1554	<	}
1555	<	}
1556	<	}
1535	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1536	>	j2 != cellListCol_[m2].end(); ++j2) {
1537	>
1538	>	// In parallel, we need to visit all pairs of row
1539	>	// & column indicies and will divide labor in the
1540	>	// force evaluation later.
1541	>	dr = cgColData.position[(*j2)] - rs;
1542	>	if (usePeriodicBoundaryConditions_) {
1543	>	snap_->wrapVector(dr);
1544	>	}
1545	>	if (dr.lengthSquare() < rListSq_) {
1546	>	neighborList.push_back( (*j2) );
1547	>	++len;
1548	>	}
1549	>	}
1550		#else
1551	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1552	<	j1 != cellList_[m1].end(); ++j1) {
1553	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1554	<	j2 != cellList_[m2].end(); ++j2) {
1555	<
1556	<	// Always do this if we're in different cells or if
1557	<	// we're in the same cell and the global index of
1558	<	// the j2 cutoff group is greater than or equal to
1559	<	// the j1 cutoff group. Note that Rappaport's code
1560	<	// has a "less than" conditional here, but that
1561	<	// deals with atom-by-atom computation. OpenMD
1562	<	// allows atoms within a single cutoff group to
1563	<	// interact with each other.
1564	<
1565	<	if (m2 != m1 \|\| (j2) >= (j1) ) {
1566	<
1567	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1575	<	if (usePeriodicBoundaryConditions_) {
1576	<	snap_->wrapVector(dr);
1577	<	}
1578	<	getGroupCutoffs( (j1), (j2), rcut, rcutsq, rlistsq );
1579	<	if (dr.lengthSquare() < rlistsq) {
1580	<	neighborList.push_back(make_pair((j1), (j2)));
1581	<	}
1582	<	}
1583	<	}
1551	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1552	>	j2 != cellList_[m2].end(); ++j2) {
1553	>
1554	>	// Always do this if we're in different cells or if
1555	>	// we're in the same cell and the global index of
1556	>	// the j2 cutoff group is greater than or equal to
1557	>	// the j1 cutoff group. Note that Rappaport's code
1558	>	// has a "less than" conditional here, but that
1559	>	// deals with atom-by-atom computation. OpenMD
1560	>	// allows atoms within a single cutoff group to
1561	>	// interact with each other.
1562	>
1563	>	if ( (*j2) >= j1 ) {
1564	>
1565	>	dr = snap_->cgData.position[(*j2)] - rs;
1566	>	if (usePeriodicBoundaryConditions_) {
1567	>	snap_->wrapVector(dr);
1568		}
1569	<	#endif
1569	>	if ( dr.lengthSquare() < rListSq_) {
1570	>	neighborList.push_back( (*j2) );
1571	>	++len;
1572	>	}
1573		}
1574	<	}
1574	>	}
1575	>	#endif
1576		}
1577	<	}
1577	>	}
1578		} else {
1579		// branch to do all cutoff group pairs
1580		#ifdef IS_MPI
1581		for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1582	+	point[j1] = len;
1583	+	rs = cgRowData.position[j1];
1584		for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1585	<	dr = cgColData.position[j2] - cgRowData.position[j1];
1585	>	dr = cgColData.position[j2] - rs;
1586		if (usePeriodicBoundaryConditions_) {
1587		snap_->wrapVector(dr);
1588		}
1589	<	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1590	<	if (dr.lengthSquare() < rlistsq) {
1591	<	neighborList.push_back(make_pair(j1, j2));
1589	>	if (dr.lengthSquare() < rListSq_) {
1590	>	neighborList.push_back( j2 );
1591	>	++len;
1592		}
1593		}
1594		}
1595		#else
1596		// include all groups here.
1597		for (int j1 = 0; j1 < nGroups_; j1++) {
1598	+	point[j1] = len;
1599	+	rs = snap_->cgData.position[j1];
1600		// include self group interactions j2 == j1
1601		for (int j2 = j1; j2 < nGroups_; j2++) {
1602	<	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1602	>	dr = snap_->cgData.position[j2] - rs;
1603		if (usePeriodicBoundaryConditions_) {
1604		snap_->wrapVector(dr);
1605		}
1606	<	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1607	<	if (dr.lengthSquare() < rlistsq) {
1608	<	neighborList.push_back(make_pair(j1, j2));
1606	>	if (dr.lengthSquare() < rListSq_) {
1607	>	neighborList.push_back( j2 );
1608	>	++len;
1609		}
1610		}
1611		}
1612		#endif
1613		}
1614	<
1614	>
1615	>	#ifdef IS_MPI
1616	>	point[nGroupsInRow_] = len;
1617	>	#else
1618	>	point[nGroups_] = len;
1619	>	#endif
1620	>
1621		// save the local cutoff group positions for the check that is
1622		// done on each loop:
1623		saved_CG_positions_.clear();
1624	+	saved_CG_positions_.reserve(nGroups_);
1625		for (int i = 0; i < nGroups_; i++)
1626		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1627		}

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Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1931 by gezelter, Mon Aug 19 19:20:32 2013 UTC vs. Revision 2057 by gezelter, Tue Mar 3 15:22:26 2015 UTC

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Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1931 by gezelter, Mon Aug 19 19:20:32 2013 UTC vs.
Revision 2057 by gezelter, Tue Mar 3 15:22:26 2015 UTC