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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1688 by gezelter, Wed Mar 14 17:56:01 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 2061 by gezelter, Tue Mar 3 16:24:44 2015 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39		* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40		* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
#	Line 50 | Line 50 | namespace OpenMD {
50
51		ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52
53	<	// In a parallel computation, row and colum scans must visit all
54	<	// surrounding cells (not just the 14 upper triangular blocks that
55	<	// are used when the processor can see all pairs)
56	<	#ifdef IS_MPI
53	>	// Row and colum scans must visit all surrounding cells
54		cellOffsets_.clear();
55		cellOffsets_.push_back( Vector3i(-1,-1,-1) );
56		cellOffsets_.push_back( Vector3i( 0,-1,-1) );
#	Line 82 | Line 79 | namespace OpenMD {
79		cellOffsets_.push_back( Vector3i(-1, 1, 1) );
80		cellOffsets_.push_back( Vector3i( 0, 1, 1) );
81		cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	–	#endif
82		}
83
84
#	Line 95 | Line 91 | namespace OpenMD {
91		storageLayout_ = sman_->getStorageLayout();
92		ff_ = info_->getForceField();
93		nLocal_ = snap_->getNumberOfAtoms();
94	<
94	>
95		nGroups_ = info_->getNLocalCutoffGroups();
96		// gather the information for atomtype IDs (atids):
97		idents = info_->getIdentArray();
98	+	regions = info_->getRegions();
99		AtomLocalToGlobal = info_->getGlobalAtomIndices();
100		cgLocalToGlobal = info_->getGlobalGroupIndices();
101		vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
#	Line 109 | Line 106 | namespace OpenMD {
106		PairList* oneTwo = info_->getOneTwoInteractions();
107		PairList* oneThree = info_->getOneThreeInteractions();
108		PairList* oneFour = info_->getOneFourInteractions();
109	<
109	>
110	>	if (needVelocities_)
111	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
112	>	DataStorage::dslVelocity);
113	>	else
114	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
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 145 | Line 148 | namespace OpenMD {
148		cgRowData.resize(nGroupsInRow_);
149		cgRowData.setStorageLayout(DataStorage::dslPosition);
150		cgColData.resize(nGroupsInCol_);
151	<	cgColData.setStorageLayout(DataStorage::dslPosition);
152	<
151	>	if (needVelocities_)
152	>	// we only need column velocities if we need them.
153	>	cgColData.setStorageLayout(DataStorage::dslPosition |
154	>	DataStorage::dslVelocity);
155	>	else
156	>	cgColData.setStorageLayout(DataStorage::dslPosition);
157	>
158		identsRow.resize(nAtomsInRow_);
159		identsCol.resize(nAtomsInCol_);
160
161		AtomPlanIntRow->gather(idents, identsRow);
162		AtomPlanIntColumn->gather(idents, identsCol);
163	+
164	+	regionsRow.resize(nAtomsInRow_);
165	+	regionsCol.resize(nAtomsInCol_);
166
167	+	AtomPlanIntRow->gather(regions, regionsRow);
168	+	AtomPlanIntColumn->gather(regions, regionsCol);
169	+
170		// allocate memory for the parallel objects
171		atypesRow.resize(nAtomsInRow_);
172		atypesCol.resize(nAtomsInCol_);
#	Line 165 | Line 179 | namespace OpenMD {
179		pot_row.resize(nAtomsInRow_);
180		pot_col.resize(nAtomsInCol_);
181
182	+	expot_row.resize(nAtomsInRow_);
183	+	expot_col.resize(nAtomsInCol_);
184	+
185		AtomRowToGlobal.resize(nAtomsInRow_);
186		AtomColToGlobal.resize(nAtomsInCol_);
187		AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
#	Line 285 | Line 302 | namespace OpenMD {
302		groupList_[i].push_back(j);
303		}
304		}
305	<	}
289	<
290	<
291	<	createGtypeCutoffMap();
292	<
305	>	}
306		}
294	–
295	–	void ForceMatrixDecomposition::createGtypeCutoffMap() {
307
308	<	RealType tol = 1e-6;
309	<	largestRcut_ = 0.0;
299	<	RealType rc;
300	<	int atid;
301	<	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302	<
303	<	map<int, RealType> atypeCutoff;
304	<
305	<	for (set<AtomType*>::iterator at = atypes.begin();
306	<	at != atypes.end(); ++at){
307	<	atid = (*at)->getIdent();
308	<	if (userChoseCutoff_)
309	<	atypeCutoff[atid] = userCutoff_;
310	<	else
311	<	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312	<	}
313	<
314	<	vector<RealType> gTypeCutoffs;
315	<	// first we do a single loop over the cutoff groups to find the
316	<	// largest cutoff for any atypes present in this group.
317	<	#ifdef IS_MPI
318	<	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
319	<	groupRowToGtype.resize(nGroupsInRow_);
320	<	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
321	<	vector<int> atomListRow = getAtomsInGroupRow(cg1);
322	<	for (vector<int>::iterator ia = atomListRow.begin();
323	<	ia != atomListRow.end(); ++ia) {
324	<	int atom1 = (*ia);
325	<	atid = identsRow[atom1];
326	<	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
327	<	groupCutoffRow[cg1] = atypeCutoff[atid];
328	<	}
329	<	}
330	<
331	<	bool gTypeFound = false;
332	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
333	<	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
334	<	groupRowToGtype[cg1] = gt;
335	<	gTypeFound = true;
336	<	}
337	<	}
338	<	if (!gTypeFound) {
339	<	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
340	<	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
341	<	}
342	<
343	<	}
344	<	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
345	<	groupColToGtype.resize(nGroupsInCol_);
346	<	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
347	<	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
348	<	for (vector<int>::iterator jb = atomListCol.begin();
349	<	jb != atomListCol.end(); ++jb) {
350	<	int atom2 = (*jb);
351	<	atid = identsCol[atom2];
352	<	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
353	<	groupCutoffCol[cg2] = atypeCutoff[atid];
354	<	}
355	<	}
356	<	bool gTypeFound = false;
357	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
358	<	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
359	<	groupColToGtype[cg2] = gt;
360	<	gTypeFound = true;
361	<	}
362	<	}
363	<	if (!gTypeFound) {
364	<	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
365	<	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
366	<	}
367	<	}
368	<	#else
369	<
370	<	vector<RealType> groupCutoff(nGroups_, 0.0);
371	<	groupToGtype.resize(nGroups_);
372	<	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
373	<	groupCutoff[cg1] = 0.0;
374	<	vector<int> atomList = getAtomsInGroupRow(cg1);
375	<	for (vector<int>::iterator ia = atomList.begin();
376	<	ia != atomList.end(); ++ia) {
377	<	int atom1 = (*ia);
378	<	atid = idents[atom1];
379	<	if (atypeCutoff[atid] > groupCutoff[cg1])
380	<	groupCutoff[cg1] = atypeCutoff[atid];
381	<	}
382	<
383	<	bool gTypeFound = false;
384	<	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385	<	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
386	<	groupToGtype[cg1] = gt;
387	<	gTypeFound = true;
388	<	}
389	<	}
390	<	if (!gTypeFound) {
391	<	gTypeCutoffs.push_back( groupCutoff[cg1] );
392	<	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393	<	}
394	<	}
395	<	#endif
396	<
397	<	// Now we find the maximum group cutoff value present in the simulation
398	<
399	<	RealType groupMax = *max_element(gTypeCutoffs.begin(),
400	<	gTypeCutoffs.end());
401	<
402	<	#ifdef IS_MPI
403	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
404	<	MPI::MAX);
405	<	#endif
406	<
407	<	RealType tradRcut = groupMax;
408	<
409	<	for (int i = 0; i < gTypeCutoffs.size();  i++) {
410	<	for (int j = 0; j < gTypeCutoffs.size();  j++) {
411	<	RealType thisRcut;
412	<	switch(cutoffPolicy_) {
413	<	case TRADITIONAL:
414	<	thisRcut = tradRcut;
415	<	break;
416	<	case MIX:
417	<	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
418	<	break;
419	<	case MAX:
420	<	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
421	<	break;
422	<	default:
423	<	sprintf(painCave.errMsg,
424	<	"ForceMatrixDecomposition::createGtypeCutoffMap "
425	<	"hit an unknown cutoff policy!\n");
426	<	painCave.severity = OPENMD_ERROR;
427	<	painCave.isFatal = 1;
428	<	simError();
429	<	break;
430	<	}
431	<
432	<	pair<int,int> key = make_pair(i,j);
433	<	gTypeCutoffMap[key].first = thisRcut;
434	<	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
435	<	gTypeCutoffMap[key].second = thisRcut*thisRcut;
436	<	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
437	<	// sanity check
438	<
439	<	if (userChoseCutoff_) {
440	<	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
441	<	sprintf(painCave.errMsg,
442	<	"ForceMatrixDecomposition::createGtypeCutoffMap "
443	<	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
444	<	painCave.severity = OPENMD_ERROR;
445	<	painCave.isFatal = 1;
446	<	simError();
447	<	}
448	<	}
449	<	}
450	<	}
451	<	}
452	<
453	<
454	<	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
455	<	int i, j;
456	<	#ifdef IS_MPI
457	<	i = groupRowToGtype[cg1];
458	<	j = groupColToGtype[cg2];
459	<	#else
460	<	i = groupToGtype[cg1];
461	<	j = groupToGtype[cg2];
462	<	#endif
463	<	return gTypeCutoffMap[make_pair(i,j)];
464	<	}
465	<
466	<	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
467	<	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
308	>	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
309	>	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
310		if (toposForAtom[atom1][j] == atom2)
311		return topoDist[atom1][j];
312	<	}
312	>	}
313		return 0;
314		}
315
316		void ForceMatrixDecomposition::zeroWorkArrays() {
317		pairwisePot = 0.0;
318		embeddingPot = 0.0;
319	+	excludedPot = 0.0;
320	+	excludedSelfPot = 0.0;
321
322		#ifdef IS_MPI
323		if (storageLayout_ & DataStorage::dslForce) {
#	Line 492 | Line 336 | namespace OpenMD {
336		fill(pot_col.begin(), pot_col.end(),
337		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
338
339	+	fill(expot_row.begin(), expot_row.end(),
340	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
341	+
342	+	fill(expot_col.begin(), expot_col.end(),
343	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
344	+
345		if (storageLayout_ & DataStorage::dslParticlePot) {
346		fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
347		0.0);
#	Line 525 | Line 375 | namespace OpenMD {
375		atomColData.skippedCharge.end(), 0.0);
376		}
377
378	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
379	+	fill(atomRowData.flucQFrc.begin(),
380	+	atomRowData.flucQFrc.end(), 0.0);
381	+	fill(atomColData.flucQFrc.begin(),
382	+	atomColData.flucQFrc.end(), 0.0);
383	+	}
384	+
385	+	if (storageLayout_ & DataStorage::dslElectricField) {
386	+	fill(atomRowData.electricField.begin(),
387	+	atomRowData.electricField.end(), V3Zero);
388	+	fill(atomColData.electricField.begin(),
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 537 | Line 408 | namespace OpenMD {
408		fill(snap_->atomData.density.begin(),
409		snap_->atomData.density.end(), 0.0);
410		}
411	+
412		if (storageLayout_ & DataStorage::dslFunctional) {
413		fill(snap_->atomData.functional.begin(),
414		snap_->atomData.functional.end(), 0.0);
415		}
416	+
417		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
418		fill(snap_->atomData.functionalDerivative.begin(),
419		snap_->atomData.functionalDerivative.end(), 0.0);
420		}
421	+
422		if (storageLayout_ & DataStorage::dslSkippedCharge) {
423		fill(snap_->atomData.skippedCharge.begin(),
424		snap_->atomData.skippedCharge.end(), 0.0);
425		}
426	<
426	>
427	>	if (storageLayout_ & DataStorage::dslElectricField) {
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();
559	–	#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 566 | Line 454 | namespace OpenMD {
454
455		// gather up the cutoff group positions
456
457	<	cgPlanVectorRow->gather(snap_->cgData.position,
458	<	cgRowData.position);
457	>	if (needsCG) {
458	>	cgPlanVectorRow->gather(snap_->cgData.position,
459	>	cgRowData.position);
460	>
461	>	cgPlanVectorColumn->gather(snap_->cgData.position,
462	>	cgColData.position);
463	>	}
464
572	–	cgPlanVectorColumn->gather(snap_->cgData.position,
573	–	cgColData.position);
465
466	+	if (needVelocities_) {
467	+	// gather up the atomic velocities
468	+	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
469	+	atomColData.velocity);
470	+
471	+	if (needsCG) {
472	+	cgPlanVectorColumn->gather(snap_->cgData.velocity,
473	+	cgColData.velocity);
474	+	}
475	+	}
476	+
477
478		// if needed, gather the atomic rotation matrices
479		if (storageLayout_ & DataStorage::dslAmat) {
#	Line 580 | Line 482 | namespace OpenMD {
482		AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
483		atomColData.aMat);
484		}
485	<
486	<	// if needed, gather the atomic eletrostatic frames
487	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
488	<	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
489	<	atomRowData.electroFrame);
490	<	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
491	<	atomColData.electroFrame);
485	>
486	>	// if needed, gather the atomic eletrostatic information
487	>	if (storageLayout_ & DataStorage::dslDipole) {
488	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
489	>	atomRowData.dipole);
490	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
491	>	atomColData.dipole);
492		}
493
494	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
495	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
496	+	atomRowData.quadrupole);
497	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
498	+	atomColData.quadrupole);
499	+	}
500	+
501	+	// if needed, gather the atomic fluctuating charge values
502	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
503	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
504	+	atomRowData.flucQPos);
505	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
506	+	atomColData.flucQPos);
507	+	}
508	+
509		#endif
510		}
511
#	Line 611 | Line 528 | namespace OpenMD {
528		for (int i = 0; i < n; i++)
529		snap_->atomData.density[i] += rho_tmp[i];
530		}
531	+
532	+	// this isn't necessary if we don't have polarizable atoms, but
533	+	// we'll leave it here for now.
534	+	if (storageLayout_ & DataStorage::dslElectricField) {
535	+
536	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
537	+	snap_->atomData.electricField);
538	+
539	+	int n = snap_->atomData.electricField.size();
540	+	vector<Vector3d> field_tmp(n, V3Zero);
541	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
542	+	field_tmp);
543	+	for (int i = 0; i < n; i++)
544	+	snap_->atomData.electricField[i] += field_tmp[i];
545	+	}
546		#endif
547		}
548
#	Line 690 | Line 622 | namespace OpenMD {
622
623		}
624
625	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
626	+
627	+	int nq = snap_->atomData.flucQFrc.size();
628	+	vector<RealType> fqfrc_tmp(nq, 0.0);
629	+
630	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
631	+	for (int i = 0; i < nq; i++) {
632	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
633	+	fqfrc_tmp[i] = 0.0;
634	+	}
635	+
636	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
637	+	for (int i = 0; i < nq; i++)
638	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
639	+
640	+	}
641	+
642	+	if (storageLayout_ & DataStorage::dslElectricField) {
643	+
644	+	int nef = snap_->atomData.electricField.size();
645	+	vector<Vector3d> efield_tmp(nef, V3Zero);
646	+
647	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
648	+	for (int i = 0; i < nef; i++) {
649	+	snap_->atomData.electricField[i] += efield_tmp[i];
650	+	efield_tmp[i] = 0.0;
651	+	}
652	+
653	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
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
676		vector<potVec> pot_temp(nLocal_,
677		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
678	+	vector<potVec> expot_temp(nLocal_,
679	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
680
681		// scatter/gather pot_row into the members of my column
682
683		AtomPlanPotRow->scatter(pot_row, pot_temp);
684	+	AtomPlanPotRow->scatter(expot_row, expot_temp);
685
686	<	for (int ii = 0;  ii < pot_temp.size(); ii++ )
686	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
687		pairwisePot += pot_temp[ii];
688	<
688	>
689	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
690	>	excludedPot += expot_temp[ii];
691	>
692	>	if (storageLayout_ & DataStorage::dslParticlePot) {
693	>	// This is the pairwise contribution to the particle pot.  The
694	>	// embedding contribution is added in each of the low level
695	>	// non-bonded routines.  In single processor, this is done in
696	>	// unpackInteractionData, not in collectData.
697	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
698	>	for (int i = 0; i < nLocal_; i++) {
699	>	// factor of two is because the total potential terms are divided
700	>	// by 2 in parallel due to row/ column scatter
701	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
702	>	}
703	>	}
704	>	}
705	>
706		fill(pot_temp.begin(), pot_temp.end(),
707		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
708	+	fill(expot_temp.begin(), expot_temp.end(),
709	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
710
711		AtomPlanPotColumn->scatter(pot_col, pot_temp);
712	+	AtomPlanPotColumn->scatter(expot_col, expot_temp);
713
714		for (int ii = 0;  ii < pot_temp.size(); ii++ )
715		pairwisePot += pot_temp[ii];
716	+
717	+	for (int ii = 0;  ii < expot_temp.size(); ii++ )
718	+	excludedPot += expot_temp[ii];
719	+
720	+	if (storageLayout_ & DataStorage::dslParticlePot) {
721	+	// This is the pairwise contribution to the particle pot.  The
722	+	// embedding contribution is added in each of the low level
723	+	// non-bonded routines.  In single processor, this is done in
724	+	// unpackInteractionData, not in collectData.
725	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
726	+	for (int i = 0; i < nLocal_; i++) {
727	+	// factor of two is because the total potential terms are divided
728	+	// by 2 in parallel due to row/ column scatter
729	+	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
730	+	}
731	+	}
732	+	}
733
734	+	if (storageLayout_ & DataStorage::dslParticlePot) {
735	+	int npp = snap_->atomData.particlePot.size();
736	+	vector<RealType> ppot_temp(npp, 0.0);
737	+
738	+	// This is the direct or embedding contribution to the particle
739	+	// pot.
740	+
741	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
742	+	for (int i = 0; i < npp; i++) {
743	+	snap_->atomData.particlePot[i] += ppot_temp[i];
744	+	}
745	+
746	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
747	+
748	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
749	+	for (int i = 0; i < npp; i++) {
750	+	snap_->atomData.particlePot[i] += ppot_temp[i];
751	+	}
752	+	}
753	+
754		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
755		RealType ploc1 = pairwisePot[ii];
756		RealType ploc2 = 0.0;
757	<	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
757	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
758		pairwisePot[ii] = ploc2;
759		}
760
761		for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
762	<	RealType ploc1 = embeddingPot[ii];
762	>	RealType ploc1 = excludedPot[ii];
763		RealType ploc2 = 0.0;
764	<	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
765	<	embeddingPot[ii] = ploc2;
764	>	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
765	>	excludedPot[ii] = ploc2;
766		}
767
768	+	// Here be dragons.
769	+	MPI_Comm col = colComm.getComm();
770	+
771	+	MPI_Allreduce(MPI_IN_PLACE,
772	+	&snap_->frameData.conductiveHeatFlux[0], 3,
773	+	MPI_REALTYPE, MPI_SUM, col);
774	+
775	+
776		#endif
777
778		}
779
780	<	int ForceMatrixDecomposition::getNAtomsInRow() {
780	>	/**
781	>	* Collects information obtained during the post-pair (and embedding
782	>	* functional) loops onto local data structures.
783	>	*/
784	>	void ForceMatrixDecomposition::collectSelfData() {
785	>	snap_ = sman_->getCurrentSnapshot();
786	>	storageLayout_ = sman_->getStorageLayout();
787	>
788		#ifdef IS_MPI
789	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
790	+	RealType ploc1 = embeddingPot[ii];
791	+	RealType ploc2 = 0.0;
792	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
793	+	embeddingPot[ii] = ploc2;
794	+	}
795	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
796	+	RealType ploc1 = excludedSelfPot[ii];
797	+	RealType ploc2 = 0.0;
798	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
799	+	excludedSelfPot[ii] = ploc2;
800	+	}
801	+	#endif
802	+
803	+	}
804	+
805	+
806	+
807	+	int& ForceMatrixDecomposition::getNAtomsInRow() {
808	+	#ifdef IS_MPI
809		return nAtomsInRow_;
810		#else
811		return nLocal_;
#	Line 739 | Line 815 | namespace OpenMD {
815		/**
816		* returns the list of atoms belonging to this group.
817		*/
818	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
818	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
819		#ifdef IS_MPI
820		return groupListRow_[cg1];
821		#else
#	Line 747 | Line 823 | namespace OpenMD {
823		#endif
824		}
825
826	<	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
826	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
827		#ifdef IS_MPI
828		return groupListCol_[cg2];
829		#else
#	Line 764 | Line 840 | namespace OpenMD {
840		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
841		#endif
842
843	<	snap_->wrapVector(d);
843	>	if (usePeriodicBoundaryConditions_) {
844	>	snap_->wrapVector(d);
845	>	}
846		return d;
847		}
848
849	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
850	+	#ifdef IS_MPI
851	+	return cgColData.velocity[cg2];
852	+	#else
853	+	return snap_->cgData.velocity[cg2];
854	+	#endif
855	+	}
856
857	+	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
858	+	#ifdef IS_MPI
859	+	return atomColData.velocity[atom2];
860	+	#else
861	+	return snap_->atomData.velocity[atom2];
862	+	#endif
863	+	}
864	+
865	+
866		Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
867
868		Vector3d d;
#	Line 778 | Line 872 | namespace OpenMD {
872		#else
873		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
874		#endif
875	<
876	<	snap_->wrapVector(d);
875	>	if (usePeriodicBoundaryConditions_) {
876	>	snap_->wrapVector(d);
877	>	}
878		return d;
879		}
880
#	Line 791 | Line 886 | namespace OpenMD {
886		#else
887		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
888		#endif
889	<
890	<	snap_->wrapVector(d);
889	>	if (usePeriodicBoundaryConditions_) {
890	>	snap_->wrapVector(d);
891	>	}
892		return d;
893		}
894
895	<	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
895	>	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
896		#ifdef IS_MPI
897		return massFactorsRow[atom1];
898		#else
#	Line 804 | Line 900 | namespace OpenMD {
900		#endif
901		}
902
903	<	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
903	>	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
904		#ifdef IS_MPI
905		return massFactorsCol[atom2];
906		#else
#	Line 821 | Line 917 | namespace OpenMD {
917		#else
918		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
919		#endif
920	<
921	<	snap_->wrapVector(d);
920	>	if (usePeriodicBoundaryConditions_) {
921	>	snap_->wrapVector(d);
922	>	}
923		return d;
924		}
925
926	<	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
926	>	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
927		return excludesForAtom[atom1];
928		}
929
#	Line 834 | Line 931 | namespace OpenMD {
931		* We need to exclude some overcounted interactions that result from
932		* the parallel decomposition.
933		*/
934	<	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
934	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
935		int unique_id_1, unique_id_2;
936
937		#ifdef IS_MPI
938		// in MPI, we have to look up the unique IDs for each atom
939		unique_id_1 = AtomRowToGlobal[atom1];
940		unique_id_2 = AtomColToGlobal[atom2];
941	+	// group1 = cgRowToGlobal[cg1];
942	+	// group2 = cgColToGlobal[cg2];
943		#else
944		unique_id_1 = AtomLocalToGlobal[atom1];
945		unique_id_2 = AtomLocalToGlobal[atom2];
946	+	int group1 = cgLocalToGlobal[cg1];
947	+	int group2 = cgLocalToGlobal[cg2];
948		#endif
949
950		if (unique_id_1 == unique_id_2) return true;
#	Line 855 | Line 956 | namespace OpenMD {
956		} else {
957		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
958		}
959	+	#endif
960	+
961	+	#ifndef IS_MPI
962	+	if (group1 == group2) {
963	+	if (unique_id_1 < unique_id_2) return true;
964	+	}
965		#endif
966
967		return false;
#	Line 901 | 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.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1021	<	//                         ff_->getAtomType(identsCol[atom2]) );
1022	<
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) {
1146	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1147	>	} else {
1148	>	idat.sameRegion = false;
1149	>	}
1150	>
1151		if (storageLayout_ & DataStorage::dslAmat) {
914	–	idat.A1 = &(atomRowData.aMat[atom1]);
1152		idat.A2 = &(atomColData.aMat[atom2]);
1153		}
1154
918	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
919	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
920	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
921	–	}
922	–
1155		if (storageLayout_ & DataStorage::dslTorque) {
924	–	idat.t1 = &(atomRowData.torque[atom1]);
1156		idat.t2 = &(atomColData.torque[atom2]);
1157		}
1158
1159	+	if (storageLayout_ & DataStorage::dslDipole) {
1160	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1161	+	}
1162	+
1163	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1164	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1165	+	}
1166	+
1167		if (storageLayout_ & DataStorage::dslDensity) {
929	–	idat.rho1 = &(atomRowData.density[atom1]);
1168		idat.rho2 = &(atomColData.density[atom2]);
1169		}
1170
1171		if (storageLayout_ & DataStorage::dslFunctional) {
934	–	idat.frho1 = &(atomRowData.functional[atom1]);
1172		idat.frho2 = &(atomColData.functional[atom2]);
1173		}
1174
1175		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
939	–	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1176		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1177		}
1178
1179		if (storageLayout_ & DataStorage::dslParticlePot) {
944	–	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1180		idat.particlePot2 = &(atomColData.particlePot[atom2]);
1181		}
1182
1183		if (storageLayout_ & DataStorage::dslSkippedCharge) {
949	–	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1184		idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1185		}
1186
1187	<	#else
1188	<
1187	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1188	>	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1189	>	}
1190
1191	<	// cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1192	<	// cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
958	<	// cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1191	>	#else
1192	>	idat.atid2 = idents[atom2];
1193
1194	<	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1195	<	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1196	<	//                         ff_->getAtomType(idents[atom2]) );
1194	>	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1195	>	idat.sameRegion = (regions[atom1] == regions[atom2]);
1196	>	} else {
1197	>	idat.sameRegion = false;
1198	>	}
1199
1200		if (storageLayout_ & DataStorage::dslAmat) {
965	–	idat.A1 = &(snap_->atomData.aMat[atom1]);
1201		idat.A2 = &(snap_->atomData.aMat[atom2]);
1202		}
1203
969	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
970	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
971	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
972	–	}
973	–
1204		if (storageLayout_ & DataStorage::dslTorque) {
975	–	idat.t1 = &(snap_->atomData.torque[atom1]);
1205		idat.t2 = &(snap_->atomData.torque[atom2]);
1206		}
1207
1208	+	if (storageLayout_ & DataStorage::dslDipole) {
1209	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1210	+	}
1211	+
1212	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1213	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1214	+	}
1215	+
1216		if (storageLayout_ & DataStorage::dslDensity) {
980	–	idat.rho1 = &(snap_->atomData.density[atom1]);
1217		idat.rho2 = &(snap_->atomData.density[atom2]);
1218		}
1219
1220		if (storageLayout_ & DataStorage::dslFunctional) {
985	–	idat.frho1 = &(snap_->atomData.functional[atom1]);
1221		idat.frho2 = &(snap_->atomData.functional[atom2]);
1222		}
1223
1224		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
990	–	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1225		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1226		}
1227
1228		if (storageLayout_ & DataStorage::dslParticlePot) {
995	–	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1229		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1230		}
1231
1232		if (storageLayout_ & DataStorage::dslSkippedCharge) {
1000	–	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1233		idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1234		}
1235	+
1236	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1237	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1238	+	}
1239	+
1240		#endif
1241	+	}
1242		}
1005	–
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);
1249	+	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1250	+	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1251
1252		atomRowData.force[atom1] += *(idat.f1);
1253		atomColData.force[atom2] -= *(idat.f1);
1254	+
1255	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1256	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1257	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1258	+	}
1259	+
1260	+	if (storageLayout_ & DataStorage::dslElectricField) {
1261	+	atomRowData.electricField[atom1] += *(idat.eField1);
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);
1273
1274		snap_->atomData.force[atom1] += *(idat.f1);
1275		snap_->atomData.force[atom2] -= *(idat.f1);
1276	+
1277	+	if (idat.doParticlePot) {
1278	+	// This is the pairwise contribution to the particle pot.  The
1279	+	// embedding contribution is added in each of the low level
1280	+	// non-bonded routines.  In parallel, this calculation is done
1281	+	// in collectData, not in unpackInteractionData.
1282	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1283	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1284	+	}
1285	+
1286	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1287	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1288	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1289	+	}
1290	+
1291	+	if (storageLayout_ & DataStorage::dslElectricField) {
1292	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
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 1023 | 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	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1318	<
1319	<	vector<pair<int, int> > neighborList;
1320	<	groupCutoffs cuts;
1317	>	void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
1318	>	vector<int>& point) {
1319	>	neighborList.clear();
1320	>	point.clear();
1321	>	int len = 0;
1322	>
1323		bool doAllPairs = false;
1324
1325	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1326	+	Mat3x3d box;
1327	+	Mat3x3d invBox;
1328	+
1329	+	Vector3d rs, scaled, dr;
1330	+	Vector3i whichCell;
1331	+	int cellIndex;
1332	+
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_) {
1343	+	box = snap_->getBoundingBox();
1344	+	invBox = snap_->getInvBoundingBox();
1345	+	} else {
1346	+	box = snap_->getHmat();
1347	+	invBox = snap_->getInvHmat();
1348	+	}
1349	+
1350	+	Vector3d A = box.getColumn(0);
1351	+	Vector3d B = box.getColumn(1);
1352	+	Vector3d C = box.getColumn(2);
1353
1354	<	RealType rList_ = (largestRcut_ + skinThickness_);
1355	<	RealType rl2 = rList_ * rList_;
1356	<	Snapshot* snap_ = sman_->getCurrentSnapshot();
1357	<	Mat3x3d Hmat = snap_->getHmat();
1046	<	Vector3d Hx = Hmat.getColumn(0);
1047	<	Vector3d Hy = Hmat.getColumn(1);
1048	<	Vector3d Hz = Hmat.getColumn(2);
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	<	nCells_.x() = (int) ( Hx.length() )/ rList_;
1360	<	nCells_.y() = (int) ( Hy.length() )/ rList_;
1361	<	nCells_.z() = (int) ( Hz.length() )/ rList_;
1359	>	// unit vectors perpendicular to the faces of the triclinic cell:
1360	>	AxB.normalize();
1361	>	BxC.normalize();
1362	>	CxA.normalize();
1363
1364	<	// handle small boxes where the cell offsets can end up repeating cells
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( 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
1374		if (nCells_.x() < 3) doAllPairs = true;
1375		if (nCells_.y() < 3) doAllPairs = true;
1376		if (nCells_.z() < 3) doAllPairs = true;
1377	<
1060	<	Mat3x3d invHmat = snap_->getInvHmat();
1061	<	Vector3d rs, scaled, dr;
1062	<	Vector3i whichCell;
1063	<	int cellIndex;
1377	>
1378		int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1379	<
1379	>
1380		#ifdef IS_MPI
1381		cellListRow_.resize(nCtot);
1382		cellListCol_.resize(nCtot);
1383		#else
1384		cellList_.resize(nCtot);
1385		#endif
1386	<
1386	>
1387		if (!doAllPairs) {
1388	+
1389		#ifdef IS_MPI
1390	<
1390	>
1391		for (int i = 0; i < nGroupsInRow_; i++) {
1392		rs = cgRowData.position[i];
1393
1394		// scaled positions relative to the box vectors
1395	<	scaled = invHmat * rs;
1395	>	scaled = invBox * rs;
1396
1397		// wrap the vector back into the unit box by subtracting integer box
1398		// numbers
1399		for (int j = 0; j < 3; j++) {
1400		scaled[j] -= roundMe(scaled[j]);
1401		scaled[j] += 0.5;
1402	+	// Handle the special case when an object is exactly on the
1403	+	// boundary (a scaled coordinate of 1.0 is the same as
1404	+	// scaled coordinate of 0.0)
1405	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1406		}
1407
1408		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1101 | Line 1420 | namespace OpenMD {
1420		rs = cgColData.position[i];
1421
1422		// scaled positions relative to the box vectors
1423	<	scaled = invHmat * rs;
1423	>	scaled = invBox * rs;
1424
1425		// wrap the vector back into the unit box by subtracting integer box
1426		// numbers
1427		for (int j = 0; j < 3; j++) {
1428		scaled[j] -= roundMe(scaled[j]);
1429		scaled[j] += 0.5;
1430	+	// Handle the special case when an object is exactly on the
1431	+	// boundary (a scaled coordinate of 1.0 is the same as
1432	+	// scaled coordinate of 0.0)
1433	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1434		}
1435
1436		// find xyz-indices of cell that cutoffGroup is in.
#	Line 1121 | 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];
1451
1452		// scaled positions relative to the box vectors
1453	<	scaled = invHmat * rs;
1453	>	scaled = invBox * rs;
1454
1455		// wrap the vector back into the unit box by subtracting integer box
1456		// numbers
1457		for (int j = 0; j < 3; j++) {
1458		scaled[j] -= roundMe(scaled[j]);
1459		scaled[j] += 0.5;
1460	+	// Handle the special case when an object is exactly on the
1461	+	// boundary (a scaled coordinate of 1.0 is the same as
1462	+	// scaled coordinate of 0.0)
1463	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1464		}
1465
1466		// find xyz-indices of cell that cutoffGroup is in.
1467	<	whichCell.x() = nCells_.x() * scaled.x();
1468	<	whichCell.y() = nCells_.y() * scaled.y();
1469	<	whichCell.z() = nCells_.z() * scaled.z();
1467	>	whichCell.x() = int(nCells_.x() * scaled.x());
1468	>	whichCell.y() = int(nCells_.y() * scaled.y());
1469	>	whichCell.z() = int(nCells_.z() * scaled.z());
1470
1471		// find single index of this cell:
1472		cellIndex = Vlinear(whichCell, nCells_);
#	Line 1150 | Line 1477 | namespace OpenMD {
1477
1478		#endif
1479
1153	–	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1154	–	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1155	–	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1156	–	Vector3i m1v(m1x, m1y, m1z);
1157	–	int m1 = Vlinear(m1v, nCells_);
1158	–
1159	–	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1160	–	os != cellOffsets_.end(); ++os) {
1161	–
1162	–	Vector3i m2v = m1v + (*os);
1163	–
1164	–
1165	–	if (m2v.x() >= nCells_.x()) {
1166	–	m2v.x() = 0;
1167	–	} else if (m2v.x() < 0) {
1168	–	m2v.x() = nCells_.x() - 1;
1169	–	}
1170	–
1171	–	if (m2v.y() >= nCells_.y()) {
1172	–	m2v.y() = 0;
1173	–	} else if (m2v.y() < 0) {
1174	–	m2v.y() = nCells_.y() - 1;
1175	–	}
1176	–
1177	–	if (m2v.z() >= nCells_.z()) {
1178	–	m2v.z() = 0;
1179	–	} else if (m2v.z() < 0) {
1180	–	m2v.z() = nCells_.z() - 1;
1181	–	}
1182	–
1183	–	int m2 = Vlinear (m2v, nCells_);
1184	–
1480		#ifdef IS_MPI
1481	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1482	<	j1 != cellListRow_[m1].end(); ++j1) {
1188	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1189	<	j2 != cellListCol_[m2].end(); ++j2) {
1190	<
1191	<	// In parallel, we need to visit *all* pairs of row
1192	<	// & column indicies and will divide labor in the
1193	<	// force evaluation later.
1194	<	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1195	<	snap_->wrapVector(dr);
1196	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1197	<	if (dr.lengthSquare() < cuts.third) {
1198	<	neighborList.push_back(make_pair((*j1), (*j2)));
1199	<	}
1200	<	}
1201	<	}
1481	>	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1482	>	rs = cgRowData.position[j1];
1483		#else
1203	–	for (vector<int>::iterator j1 = cellList_[m1].begin();
1204	–	j1 != cellList_[m1].end(); ++j1) {
1205	–	for (vector<int>::iterator j2 = cellList_[m2].begin();
1206	–	j2 != cellList_[m2].end(); ++j2) {
1207	–
1208	–	// Always do this if we're in different cells or if
1209	–	// we're in the same cell and the global index of
1210	–	// the j2 cutoff group is greater than or equal to
1211	–	// the j1 cutoff group.  Note that Rappaport's code
1212	–	// has a "less than" conditional here, but that
1213	–	// deals with atom-by-atom computation.  OpenMD
1214	–	// allows atoms within a single cutoff group to
1215	–	// interact with each other.
1484
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 (m2 != m1 || (*j2) >= (*j1) ) {
1518	<
1519	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1520	<	snap_->wrapVector(dr);
1521	<	cuts = getGroupCutoffs( (*j1), (*j2) );
1522	<	if (dr.lengthSquare() < cuts.third) {
1523	<	neighborList.push_back(make_pair((*j1), (*j2)));
1524	<	}
1525	<	}
1526	<	}
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 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 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];
1587	<	snap_->wrapVector(dr);
1588	<	cuts = getGroupCutoffs( j1, j2 );
1243	<	if (dr.lengthSquare() < cuts.third) {
1244	<	neighborList.push_back(make_pair(j1, j2));
1586	>	dr = cgColData.position[j2] - rs;
1587	>	if (usePeriodicBoundaryConditions_) {
1588	>	snap_->wrapVector(dr);
1589		}
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];
1604	<	snap_->wrapVector(dr);
1605	<	cuts = getGroupCutoffs( j1, j2 );
1256	<	if (dr.lengthSquare() < cuts.third) {
1257	<	neighborList.push_back(make_pair(j1, j2));
1603	>	dr = snap_->cgData.position[j2] - rs;
1604	>	if (usePeriodicBoundaryConditions_) {
1605	>	snap_->wrapVector(dr);
1606		}
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]);
1269	–
1270	–	return neighborList;
1628		}
1629		} //end namespace OpenMD

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