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

Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1971 by gezelter, Fri Feb 28 13:25:13 2014 UTC vs.
Revision 2061 by gezelter, Tue Mar 3 16:24:44 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 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_Allreduce(MPI_IN_PLACE, &groupMax, 1, MPI_REALTYPE,
428	–	MPI_MAX, MPI_COMM_WORLD);
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	+
440	+	#ifdef IS_MPI
441	+
442		snap_ = sman_->getCurrentSnapshot();
443		storageLayout_ = sman_->getStorageLayout();
627	–	#ifdef IS_MPI
444
445	+	bool needsCG = true;
446	+	if(info_->getNCutoffGroups() != info_->getNAtoms())
447	+	needsCG = false;
448	+
449		// gather up the atomic positions
450		AtomPlanVectorRow->gather(snap_->atomData.position,
451		atomRowData.position);
#	Line 634 \| Line 454 \| namespace OpenMD {
454
455		// gather up the cutoff group positions
456
457	<	cgPlanVectorRow->gather(snap_->cgData.position,
458	<	cgRowData.position);
459	<
460	<	cgPlanVectorColumn->gather(snap_->cgData.position,
461	<	cgColData.position);
457	>	if (needsCG) {
458	>	cgPlanVectorRow->gather(snap_->cgData.position,
459	>	cgRowData.position);
460	>
461	>	cgPlanVectorColumn->gather(snap_->cgData.position,
462	>	cgColData.position);
463	>	}
464
465
644	–
466		if (needVelocities_) {
467		// gather up the atomic velocities
468		AtomPlanVectorColumn->gather(snap_->atomData.velocity,
469		atomColData.velocity);
470	<
471	<	cgPlanVectorColumn->gather(snap_->cgData.velocity,
472	<	cgColData.velocity);
470	>
471	>	if (needsCG) {
472	>	cgPlanVectorColumn->gather(snap_->cgData.velocity,
473	>	cgColData.velocity);
474	>	}
475		}
476
477
#	Line 831 \| Line 654 \| namespace OpenMD {
654		for (int i = 0; i < nef; i++)
655		snap_->atomData.electricField[i] += efield_tmp[i];
656		}
657	+
658	+	if (storageLayout_ & DataStorage::dslSitePotential) {
659	+
660	+	int nsp = snap_->atomData.sitePotential.size();
661	+	vector<RealType> sp_tmp(nsp, 0.0);
662
663	+	AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
664	+	for (int i = 0; i < nsp; i++) {
665	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
666	+	sp_tmp[i] = 0.0;
667	+	}
668	+
669	+	AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
670	+	for (int i = 0; i < nsp; i++)
671	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
672	+	}
673
674		nLocal_ = snap_->getNumberOfAtoms();
675
#	Line 1170 \| Line 1008 \| namespace OpenMD {
1008
1009		// filling interaction blocks with pointers
1010		void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1011	<	int atom1, int atom2) {
1011	>	int atom1, int atom2,
1012	>	bool newAtom1) {
1013
1014		idat.excluded = excludeAtomPair(atom1, atom2);
1015	<
1015	>
1016	>	if (newAtom1) {
1017	>
1018		#ifdef IS_MPI
1019	<	//idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1020	<	idat.atid1 = identsRow[atom1];
1019	>	idat.atid1 = identsRow[atom1];
1020	>	idat.atid2 = identsCol[atom2];
1021	>
1022	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1023	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1024	>	} else {
1025	>	idat.sameRegion = false;
1026	>	}
1027	>
1028	>	if (storageLayout_ & DataStorage::dslAmat) {
1029	>	idat.A1 = &(atomRowData.aMat[atom1]);
1030	>	idat.A2 = &(atomColData.aMat[atom2]);
1031	>	}
1032	>
1033	>	if (storageLayout_ & DataStorage::dslTorque) {
1034	>	idat.t1 = &(atomRowData.torque[atom1]);
1035	>	idat.t2 = &(atomColData.torque[atom2]);
1036	>	}
1037	>
1038	>	if (storageLayout_ & DataStorage::dslDipole) {
1039	>	idat.dipole1 = &(atomRowData.dipole[atom1]);
1040	>	idat.dipole2 = &(atomColData.dipole[atom2]);
1041	>	}
1042	>
1043	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1044	>	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1045	>	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1046	>	}
1047	>
1048	>	if (storageLayout_ & DataStorage::dslDensity) {
1049	>	idat.rho1 = &(atomRowData.density[atom1]);
1050	>	idat.rho2 = &(atomColData.density[atom2]);
1051	>	}
1052	>
1053	>	if (storageLayout_ & DataStorage::dslFunctional) {
1054	>	idat.frho1 = &(atomRowData.functional[atom1]);
1055	>	idat.frho2 = &(atomColData.functional[atom2]);
1056	>	}
1057	>
1058	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1059	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1060	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1061	>	}
1062	>
1063	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1064	>	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1065	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1066	>	}
1067	>
1068	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1069	>	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1070	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1071	>	}
1072	>
1073	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1074	>	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1075	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1076	>	}
1077	>
1078	>	#else
1079	>
1080	>	idat.atid1 = idents[atom1];
1081	>	idat.atid2 = idents[atom2];
1082	>
1083	>	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1084	>	idat.sameRegion = (regions[atom1] == regions[atom2]);
1085	>	} else {
1086	>	idat.sameRegion = false;
1087	>	}
1088	>
1089	>	if (storageLayout_ & DataStorage::dslAmat) {
1090	>	idat.A1 = &(snap_->atomData.aMat[atom1]);
1091	>	idat.A2 = &(snap_->atomData.aMat[atom2]);
1092	>	}
1093	>
1094	>	if (storageLayout_ & DataStorage::dslTorque) {
1095	>	idat.t1 = &(snap_->atomData.torque[atom1]);
1096	>	idat.t2 = &(snap_->atomData.torque[atom2]);
1097	>	}
1098	>
1099	>	if (storageLayout_ & DataStorage::dslDipole) {
1100	>	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1101	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1102	>	}
1103	>
1104	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1105	>	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1106	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1107	>	}
1108	>
1109	>	if (storageLayout_ & DataStorage::dslDensity) {
1110	>	idat.rho1 = &(snap_->atomData.density[atom1]);
1111	>	idat.rho2 = &(snap_->atomData.density[atom2]);
1112	>	}
1113	>
1114	>	if (storageLayout_ & DataStorage::dslFunctional) {
1115	>	idat.frho1 = &(snap_->atomData.functional[atom1]);
1116	>	idat.frho2 = &(snap_->atomData.functional[atom2]);
1117	>	}
1118	>
1119	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1120	>	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1121	>	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1122	>	}
1123	>
1124	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1125	>	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1126	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1127	>	}
1128	>
1129	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1130	>	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1131	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1132	>	}
1133	>
1134	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1135	>	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1136	>	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1137	>	}
1138	>	#endif
1139	>
1140	>	} else {
1141	>	// atom1 is not new, so don't bother updating properties of that atom:
1142	>	#ifdef IS_MPI
1143		idat.atid2 = identsCol[atom2];
1144
1145		if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
#	Line 1186 \| Line 1149 \| namespace OpenMD {
1149		}
1150
1151		if (storageLayout_ & DataStorage::dslAmat) {
1189	–	idat.A1 = &(atomRowData.aMat[atom1]);
1152		idat.A2 = &(atomColData.aMat[atom2]);
1153		}
1154
1155		if (storageLayout_ & DataStorage::dslTorque) {
1194	–	idat.t1 = &(atomRowData.torque[atom1]);
1156		idat.t2 = &(atomColData.torque[atom2]);
1157		}
1158
1159		if (storageLayout_ & DataStorage::dslDipole) {
1199	–	idat.dipole1 = &(atomRowData.dipole[atom1]);
1160		idat.dipole2 = &(atomColData.dipole[atom2]);
1161		}
1162
1163		if (storageLayout_ & DataStorage::dslQuadrupole) {
1204	–	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1164		idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1165		}
1166
1167		if (storageLayout_ & DataStorage::dslDensity) {
1209	–	idat.rho1 = &(atomRowData.density[atom1]);
1168		idat.rho2 = &(atomColData.density[atom2]);
1169		}
1170
1171		if (storageLayout_ & DataStorage::dslFunctional) {
1214	–	idat.frho1 = &(atomRowData.functional[atom1]);
1172		idat.frho2 = &(atomColData.functional[atom2]);
1173		}
1174
1175		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1219	–	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1176		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1177		}
1178
1179		if (storageLayout_ & DataStorage::dslParticlePot) {
1224	–	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1180		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1181		}
1182
1183		if (storageLayout_ & DataStorage::dslSkippedCharge) {
1229	–	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1184		idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1185		}
1186
1187	<	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1234	<	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1187	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1188		idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1189		}
1190
1191	<	#else
1239	<
1240	<	//idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1241	<	idat.atid1 = idents[atom1];
1191	>	#else
1192		idat.atid2 = idents[atom2];
1193
1194		if (regions[atom1] >= 0 && regions[atom2] >= 0) {
#	Line 1248 \| Line 1198 \| namespace OpenMD {
1198		}
1199
1200		if (storageLayout_ & DataStorage::dslAmat) {
1251	–	idat.A1 = &(snap_->atomData.aMat[atom1]);
1201		idat.A2 = &(snap_->atomData.aMat[atom2]);
1202		}
1203
1204		if (storageLayout_ & DataStorage::dslTorque) {
1256	–	idat.t1 = &(snap_->atomData.torque[atom1]);
1205		idat.t2 = &(snap_->atomData.torque[atom2]);
1206		}
1207
1208		if (storageLayout_ & DataStorage::dslDipole) {
1261	–	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1209		idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1210		}
1211
1212		if (storageLayout_ & DataStorage::dslQuadrupole) {
1266	–	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1213		idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1214		}
1215
1216		if (storageLayout_ & DataStorage::dslDensity) {
1271	–	idat.rho1 = &(snap_->atomData.density[atom1]);
1217		idat.rho2 = &(snap_->atomData.density[atom2]);
1218		}
1219
1220		if (storageLayout_ & DataStorage::dslFunctional) {
1276	–	idat.frho1 = &(snap_->atomData.functional[atom1]);
1221		idat.frho2 = &(snap_->atomData.functional[atom2]);
1222		}
1223
1224		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1281	–	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1225		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1226		}
1227
1228		if (storageLayout_ & DataStorage::dslParticlePot) {
1286	–	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1229		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1230		}
1231
1232		if (storageLayout_ & DataStorage::dslSkippedCharge) {
1291	–	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1233		idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1234		}
1235
1236		if (storageLayout_ & DataStorage::dslFlucQPosition) {
1296	–	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1237		idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1238		}
1239
1240		#endif
1241	+	}
1242		}
1302	–
1243
1244	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1244	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat,
1245	>	int atom1, int atom2) {
1246		#ifdef IS_MPI
1247		pot_row[atom1] += RealType(0.5) * *(idat.pot);
1248		pot_col[atom2] += RealType(0.5) * *(idat.pot);
#	Line 1321 \| Line 1262 \| namespace OpenMD {
1262		atomColData.electricField[atom2] += *(idat.eField2);
1263		}
1264
1265	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1266	+	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1267	+	atomColData.sitePotential[atom2] += *(idat.sPot2);
1268	+	}
1269	+
1270		#else
1271		pairwisePot += *(idat.pot);
1272		excludedPot += *(idat.excludedPot);
#	Line 1347 \| Line 1293 \| namespace OpenMD {
1293		snap_->atomData.electricField[atom2] += *(idat.eField2);
1294		}
1295
1296	+	if (storageLayout_ & DataStorage::dslSitePotential) {
1297	+	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1298	+	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1299	+	}
1300	+
1301		#endif
1302
1303		}
#	Line 1354 \| Line 1305 \| namespace OpenMD {
1305		/*
1306		* buildNeighborList
1307		*
1308	<	* first element of pair is row-indexed CutoffGroup
1309	<	* second element of pair is column-indexed CutoffGroup
1308	>	* Constructs the Verlet neighbor list for a force-matrix
1309	>	* decomposition. In this case, each processor is responsible for
1310	>	* row-site interactions with column-sites.
1311	>	*
1312	>	* neighborList is returned as a packed array of neighboring
1313	>	* column-ordered CutoffGroups. The starting position in
1314	>	* neighborList for each row-ordered CutoffGroup is given by the
1315	>	* returned vector point.
1316		*/
1317	<	void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1318	<
1317	>	void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
1318	>	vector<int>& point) {
1319		neighborList.clear();
1320	<	groupCutoffs cuts;
1320	>	point.clear();
1321	>	int len = 0;
1322	>
1323		bool doAllPairs = false;
1324
1366	–	RealType rList_ = (largestRcut_ + skinThickness_);
1367	–	RealType rcut, rcutsq, rlistsq;
1325		Snapshot* snap_ = sman_->getCurrentSnapshot();
1326		Mat3x3d box;
1327		Mat3x3d invBox;
#	Line 1376 \| Line 1333 \| namespace OpenMD {
1333		#ifdef IS_MPI
1334		cellListRow_.clear();
1335		cellListCol_.clear();
1336	+	point.resize(nGroupsInRow_+1);
1337		#else
1338		cellList_.clear();
1339	+	point.resize(nGroups_+1);
1340		#endif
1341
1342		if (!usePeriodicBoundaryConditions_) {
#	Line 1388 \| Line 1347 \| namespace OpenMD {
1347		invBox = snap_->getInvHmat();
1348		}
1349
1350	<	Vector3d boxX = box.getColumn(0);
1351	<	Vector3d boxY = box.getColumn(1);
1352	<	Vector3d boxZ = box.getColumn(2);
1350	>	Vector3d A = box.getColumn(0);
1351	>	Vector3d B = box.getColumn(1);
1352	>	Vector3d C = box.getColumn(2);
1353	>
1354	>	// Required for triclinic cells
1355	>	Vector3d AxB = cross(A, B);
1356	>	Vector3d BxC = cross(B, C);
1357	>	Vector3d CxA = cross(C, A);
1358	>
1359	>	// unit vectors perpendicular to the faces of the triclinic cell:
1360	>	AxB.normalize();
1361	>	BxC.normalize();
1362	>	CxA.normalize();
1363	>
1364	>	// A set of perpendicular lengths in triclinic cells:
1365	>	RealType Wa = abs(dot(A, BxC));
1366	>	RealType Wb = abs(dot(B, CxA));
1367	>	RealType Wc = abs(dot(C, AxB));
1368
1369	<	nCells_.x() = int( boxX.length() / rList_ );
1370	<	nCells_.y() = int( boxY.length() / rList_ );
1371	<	nCells_.z() = int( boxZ.length() / rList_ );
1369	>	nCells_.x() = int( Wa / rList_ );
1370	>	nCells_.y() = int( Wb / rList_ );
1371	>	nCells_.z() = int( Wc / rList_ );
1372
1373		// handle small boxes where the cell offsets can end up repeating cells
1400	–
1374		if (nCells_.x() < 3) doAllPairs = true;
1375		if (nCells_.y() < 3) doAllPairs = true;
1376		if (nCells_.z() < 3) doAllPairs = true;
#	Line 1412 \| Line 1385 \| namespace OpenMD {
1385		#endif
1386
1387		if (!doAllPairs) {
1388	+
1389		#ifdef IS_MPI
1390
1391		for (int i = 0; i < nGroupsInRow_; i++) {
#	Line 1470 \| Line 1444 \| namespace OpenMD {
1444		// add this cutoff group to the list of groups in this cell;
1445		cellListCol_[cellIndex].push_back(i);
1446		}
1447	<
1447	>
1448		#else
1449		for (int i = 0; i < nGroups_; i++) {
1450		rs = snap_->cgData.position[i];
#	Line 1503 \| Line 1477 \| namespace OpenMD {
1477
1478		#endif
1479
1480	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1481	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1482	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1483	<	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	<
1480	>	#ifdef IS_MPI
1481	>	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1482	>	rs = cgRowData.position[j1];
1483	>	#else
1484
1485	<	if (m2v.x() >= nCells_.x()) {
1486	<	m2v.x() = 0;
1487	<	} else if (m2v.x() < 0) {
1488	<	m2v.x() = nCells_.x() - 1;
1489	<	}
1490	<
1491	<	if (m2v.y() >= nCells_.y()) {
1492	<	m2v.y() = 0;
1493	<	} else if (m2v.y() < 0) {
1494	<	m2v.y() = nCells_.y() - 1;
1495	<	}
1496	<
1497	<	if (m2v.z() >= nCells_.z()) {
1498	<	m2v.z() = 0;
1499	<	} else if (m2v.z() < 0) {
1500	<	m2v.z() = nCells_.z() - 1;
1501	<	}
1502	<
1503	<	int m2 = Vlinear (m2v, nCells_);
1485	>	for (int j1 = 0; j1 < nGroups_; j1++) {
1486	>	rs = snap_->cgData.position[j1];
1487	>	#endif
1488	>	point[j1] = len;
1489	>
1490	>	// scaled positions relative to the box vectors
1491	>	scaled = invBox * rs;
1492	>
1493	>	// wrap the vector back into the unit box by subtracting integer box
1494	>	// numbers
1495	>	for (int j = 0; j < 3; j++) {
1496	>	scaled[j] -= roundMe(scaled[j]);
1497	>	scaled[j] += 0.5;
1498	>	// Handle the special case when an object is exactly on the
1499	>	// boundary (a scaled coordinate of 1.0 is the same as
1500	>	// scaled coordinate of 0.0)
1501	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1502	>	}
1503	>
1504	>	// find xyz-indices of cell that cutoffGroup is in.
1505	>	whichCell.x() = nCells_.x() * scaled.x();
1506	>	whichCell.y() = nCells_.y() * scaled.y();
1507	>	whichCell.z() = nCells_.z() * scaled.z();
1508	>
1509	>	// find single index of this cell:
1510	>	int m1 = Vlinear(whichCell, nCells_);
1511	>
1512	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1513	>	os != cellOffsets_.end(); ++os) {
1514
1515	+	Vector3i m2v = whichCell + (*os);
1516	+
1517	+	if (m2v.x() >= nCells_.x()) {
1518	+	m2v.x() = 0;
1519	+	} else if (m2v.x() < 0) {
1520	+	m2v.x() = nCells_.x() - 1;
1521	+	}
1522	+
1523	+	if (m2v.y() >= nCells_.y()) {
1524	+	m2v.y() = 0;
1525	+	} else if (m2v.y() < 0) {
1526	+	m2v.y() = nCells_.y() - 1;
1527	+	}
1528	+
1529	+	if (m2v.z() >= nCells_.z()) {
1530	+	m2v.z() = 0;
1531	+	} else if (m2v.z() < 0) {
1532	+	m2v.z() = nCells_.z() - 1;
1533	+	}
1534	+	int m2 = Vlinear (m2v, nCells_);
1535		#ifdef IS_MPI
1536	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1537	<	j1 != cellListRow_[m1].end(); ++j1) {
1538	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1539	<	j2 != cellListCol_[m2].end(); ++j2) {
1540	<
1541	<	// In parallel, we need to visit all pairs of row
1542	<	// & column indicies and will divide labor in the
1543	<	// force evaluation later.
1544	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1545	<	if (usePeriodicBoundaryConditions_) {
1546	<	snap_->wrapVector(dr);
1547	<	}
1548	<	getGroupCutoffs( (j1), (j2), rcut, rcutsq, rlistsq );
1549	<	if (dr.lengthSquare() < rlistsq) {
1550	<	neighborList.push_back(make_pair((j1), (j2)));
1554	<	}
1555	<	}
1556	<	}
1536	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1537	>	j2 != cellListCol_[m2].end(); ++j2) {
1538	>
1539	>	// In parallel, we need to visit all pairs of row
1540	>	// & column indicies and will divide labor in the
1541	>	// force evaluation later.
1542	>	dr = cgColData.position[(*j2)] - rs;
1543	>	if (usePeriodicBoundaryConditions_) {
1544	>	snap_->wrapVector(dr);
1545	>	}
1546	>	if (dr.lengthSquare() < rListSq_) {
1547	>	neighborList.push_back( (*j2) );
1548	>	++len;
1549	>	}
1550	>	}
1551		#else
1552	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1553	<	j1 != cellList_[m1].end(); ++j1) {
1554	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1555	<	j2 != cellList_[m2].end(); ++j2) {
1556	<
1557	<	// Always do this if we're in different cells or if
1558	<	// we're in the same cell and the global index of
1559	<	// the j2 cutoff group is greater than or equal to
1560	<	// the j1 cutoff group. Note that Rappaport's code
1561	<	// has a "less than" conditional here, but that
1562	<	// deals with atom-by-atom computation. OpenMD
1563	<	// allows atoms within a single cutoff group to
1564	<	// interact with each other.
1565	<
1566	<	if (m2 != m1 \|\| (j2) >= (j1) ) {
1567	<
1568	<	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	<	}
1552	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1553	>	j2 != cellList_[m2].end(); ++j2) {
1554	>
1555	>	// Always do this if we're in different cells or if
1556	>	// we're in the same cell and the global index of
1557	>	// the j2 cutoff group is greater than or equal to
1558	>	// the j1 cutoff group. Note that Rappaport's code
1559	>	// has a "less than" conditional here, but that
1560	>	// deals with atom-by-atom computation. OpenMD
1561	>	// allows atoms within a single cutoff group to
1562	>	// interact with each other.
1563	>
1564	>	if ( (*j2) >= j1 ) {
1565	>
1566	>	dr = snap_->cgData.position[(*j2)] - rs;
1567	>	if (usePeriodicBoundaryConditions_) {
1568	>	snap_->wrapVector(dr);
1569		}
1570	<	#endif
1570	>	if ( dr.lengthSquare() < rListSq_) {
1571	>	neighborList.push_back( (*j2) );
1572	>	++len;
1573	>	}
1574		}
1575	<	}
1575	>	}
1576	>	#endif
1577		}
1578	<	}
1578	>	}
1579		} else {
1580		// branch to do all cutoff group pairs
1581		#ifdef IS_MPI
1582		for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1583	+	point[j1] = len;
1584	+	rs = cgRowData.position[j1];
1585		for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1586	<	dr = cgColData.position[j2] - cgRowData.position[j1];
1586	>	dr = cgColData.position[j2] - rs;
1587		if (usePeriodicBoundaryConditions_) {
1588		snap_->wrapVector(dr);
1589		}
1590	<	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1591	<	if (dr.lengthSquare() < rlistsq) {
1592	<	neighborList.push_back(make_pair(j1, j2));
1590	>	if (dr.lengthSquare() < rListSq_) {
1591	>	neighborList.push_back( j2 );
1592	>	++len;
1593		}
1594		}
1595		}
1596		#else
1597		// include all groups here.
1598		for (int j1 = 0; j1 < nGroups_; j1++) {
1599	+	point[j1] = len;
1600	+	rs = snap_->cgData.position[j1];
1601		// include self group interactions j2 == j1
1602		for (int j2 = j1; j2 < nGroups_; j2++) {
1603	<	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1603	>	dr = snap_->cgData.position[j2] - rs;
1604		if (usePeriodicBoundaryConditions_) {
1605		snap_->wrapVector(dr);
1606		}
1607	<	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1608	<	if (dr.lengthSquare() < rlistsq) {
1609	<	neighborList.push_back(make_pair(j1, j2));
1607	>	if (dr.lengthSquare() < rListSq_) {
1608	>	neighborList.push_back( j2 );
1609	>	++len;
1610		}
1611		}
1612		}
1613		#endif
1614		}
1615	<
1615	>
1616	>	#ifdef IS_MPI
1617	>	point[nGroupsInRow_] = len;
1618	>	#else
1619	>	point[nGroups_] = len;
1620	>	#endif
1621	>
1622		// save the local cutoff group positions for the check that is
1623		// done on each loop:
1624		saved_CG_positions_.clear();
1625	+	saved_CG_positions_.reserve(nGroups_);
1626		for (int i = 0; i < nGroups_; i++)
1627		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1628		}

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Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1971 by gezelter, Fri Feb 28 13:25:13 2014 UTC vs. Revision 2061 by gezelter, Tue Mar 3 16:24:44 2015 UTC

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Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1971 by gezelter, Fri Feb 28 13:25:13 2014 UTC vs.
Revision 2061 by gezelter, Tue Mar 3 16:24:44 2015 UTC