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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs.
Revision 1592 by gezelter, Tue Jul 12 20:33:14 2011 UTC

#	Line 57 \| Line 57 \| namespace OpenMD {
57		storageLayout_ = sman_->getStorageLayout();
58		ff_ = info_->getForceField();
59		nLocal_ = snap_->getNumberOfAtoms();
60	<
60	>
61		nGroups_ = info_->getNLocalCutoffGroups();
62	–	cerr << "in dId, nGroups = " << nGroups_ << "\n";
62		// gather the information for atomtype IDs (atids):
63	<	identsLocal = info_->getIdentArray();
63	>	idents = info_->getIdentArray();
64		AtomLocalToGlobal = info_->getGlobalAtomIndices();
65		cgLocalToGlobal = info_->getGlobalGroupIndices();
66		vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68	–	vector<RealType> massFactorsLocal = info_->getMassFactors();
69	–	PairList excludes = info_->getExcludedInteractions();
70	–	PairList oneTwo = info_->getOneTwoInteractions();
71	–	PairList oneThree = info_->getOneThreeInteractions();
72	–	PairList oneFour = info_->getOneFourInteractions();
67
68	+	massFactors = info_->getMassFactors();
69	+
70	+	PairList* excludes = info_->getExcludedInteractions();
71	+	PairList* oneTwo = info_->getOneTwoInteractions();
72	+	PairList* oneThree = info_->getOneThreeInteractions();
73	+	PairList* oneFour = info_->getOneFourInteractions();
74	+
75		#ifdef IS_MPI
76
77		AtomCommIntRow = new Communicator<Row,int>(nLocal_);
#	Line 108 \| Line 109 \| namespace OpenMD {
109		identsRow.resize(nAtomsInRow_);
110		identsCol.resize(nAtomsInCol_);
111
112	<	AtomCommIntRow->gather(identsLocal, identsRow);
113	<	AtomCommIntColumn->gather(identsLocal, identsCol);
112	>	AtomCommIntRow->gather(idents, identsRow);
113	>	AtomCommIntColumn->gather(idents, identsCol);
114
115	+	// allocate memory for the parallel objects
116	+	atypesRow.resize(nAtomsInRow_);
117	+	atypesCol.resize(nAtomsInCol_);
118	+
119	+	for (int i = 0; i < nAtomsInRow_; i++)
120	+	atypesRow[i] = ff_->getAtomType(identsRow[i]);
121	+	for (int i = 0; i < nAtomsInCol_; i++)
122	+	atypesCol[i] = ff_->getAtomType(identsCol[i]);
123	+
124	+	pot_row.resize(nAtomsInRow_);
125	+	pot_col.resize(nAtomsInCol_);
126	+
127	+	AtomRowToGlobal.resize(nAtomsInRow_);
128	+	AtomColToGlobal.resize(nAtomsInCol_);
129		AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
130		AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
131
132	+	cgRowToGlobal.resize(nGroupsInRow_);
133	+	cgColToGlobal.resize(nGroupsInCol_);
134		cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
135		cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
136
137	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
138	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
137	>	massFactorsRow.resize(nAtomsInRow_);
138	>	massFactorsCol.resize(nAtomsInCol_);
139	>	AtomCommRealRow->gather(massFactors, massFactorsRow);
140	>	AtomCommRealColumn->gather(massFactors, massFactorsCol);
141
142		groupListRow_.clear();
143		groupListRow_.resize(nGroupsInRow_);
#	Line 142 \| Line 161 \| namespace OpenMD {
161		}
162		}
163
164	<	skipsForAtom.clear();
165	<	skipsForAtom.resize(nAtomsInRow_);
164	>	excludesForAtom.clear();
165	>	excludesForAtom.resize(nAtomsInRow_);
166		toposForAtom.clear();
167		toposForAtom.resize(nAtomsInRow_);
168		topoDist.clear();
#	Line 154 \| Line 173 \| namespace OpenMD {
173		for (int j = 0; j < nAtomsInCol_; j++) {
174		int jglob = AtomColToGlobal[j];
175
176	<	if (excludes.hasPair(iglob, jglob))
177	<	skipsForAtom[i].push_back(j);
176	>	if (excludes->hasPair(iglob, jglob))
177	>	excludesForAtom[i].push_back(j);
178
179	<	if (oneTwo.hasPair(iglob, jglob)) {
179	>	if (oneTwo->hasPair(iglob, jglob)) {
180		toposForAtom[i].push_back(j);
181		topoDist[i].push_back(1);
182		} else {
183	<	if (oneThree.hasPair(iglob, jglob)) {
183	>	if (oneThree->hasPair(iglob, jglob)) {
184		toposForAtom[i].push_back(j);
185		topoDist[i].push_back(2);
186		} else {
187	<	if (oneFour.hasPair(iglob, jglob)) {
187	>	if (oneFour->hasPair(iglob, jglob)) {
188		toposForAtom[i].push_back(j);
189		topoDist[i].push_back(3);
190		}
#	Line 176 \| Line 195 \| namespace OpenMD {
195
196		#endif
197
198	+	// allocate memory for the parallel objects
199	+	atypesLocal.resize(nLocal_);
200	+
201	+	for (int i = 0; i < nLocal_; i++)
202	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
203	+
204		groupList_.clear();
205		groupList_.resize(nGroups_);
206		for (int i = 0; i < nGroups_; i++) {
#	Line 188 \| Line 213 \| namespace OpenMD {
213		}
214		}
215
216	<	skipsForAtom.clear();
217	<	skipsForAtom.resize(nLocal_);
216	>	excludesForAtom.clear();
217	>	excludesForAtom.resize(nLocal_);
218		toposForAtom.clear();
219		toposForAtom.resize(nLocal_);
220		topoDist.clear();
#	Line 201 \| Line 226 \| namespace OpenMD {
226		for (int j = 0; j < nLocal_; j++) {
227		int jglob = AtomLocalToGlobal[j];
228
229	<	if (excludes.hasPair(iglob, jglob))
230	<	skipsForAtom[i].push_back(j);
229	>	if (excludes->hasPair(iglob, jglob))
230	>	excludesForAtom[i].push_back(j);
231
232	<	if (oneTwo.hasPair(iglob, jglob)) {
232	>	if (oneTwo->hasPair(iglob, jglob)) {
233		toposForAtom[i].push_back(j);
234		topoDist[i].push_back(1);
235		} else {
236	<	if (oneThree.hasPair(iglob, jglob)) {
236	>	if (oneThree->hasPair(iglob, jglob)) {
237		toposForAtom[i].push_back(j);
238		topoDist[i].push_back(2);
239		} else {
240	<	if (oneFour.hasPair(iglob, jglob)) {
240	>	if (oneFour->hasPair(iglob, jglob)) {
241		toposForAtom[i].push_back(j);
242		topoDist[i].push_back(3);
243		}
#	Line 222 \| Line 247 \| namespace OpenMD {
247		}
248
249		createGtypeCutoffMap();
250	+
251		}
252
253		void ForceMatrixDecomposition::createGtypeCutoffMap() {
254	<
254	>
255		RealType tol = 1e-6;
256	+	largestRcut_ = 0.0;
257		RealType rc;
258		int atid;
259		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
260	<	vector<RealType> atypeCutoff;
261	<	atypeCutoff.resize( atypes.size() );
262	<
260	>
261	>	map<int, RealType> atypeCutoff;
262	>
263		for (set<AtomType*>::iterator at = atypes.begin();
264		at != atypes.end(); ++at){
238	–	rc = interactionMan_->getSuggestedCutoffRadius(*at);
265		atid = (*at)->getIdent();
266	<	atypeCutoff[atid] = rc;
266	>	if (userChoseCutoff_)
267	>	atypeCutoff[atid] = userCutoff_;
268	>	else
269	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
270		}
271	<
271	>
272		vector<RealType> gTypeCutoffs;
244	–
273		// first we do a single loop over the cutoff groups to find the
274		// largest cutoff for any atypes present in this group.
275		#ifdef IS_MPI
#	Line 299 \| Line 327 \| namespace OpenMD {
327
328		vector<RealType> groupCutoff(nGroups_, 0.0);
329		groupToGtype.resize(nGroups_);
302	–
303	–	cerr << "nGroups = " << nGroups_ << "\n";
330		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305	–
331		groupCutoff[cg1] = 0.0;
332		vector<int> atomList = getAtomsInGroupRow(cg1);
308	–
333		for (vector<int>::iterator ia = atomList.begin();
334		ia != atomList.end(); ++ia) {
335		int atom1 = (*ia);
336	<	atid = identsLocal[atom1];
337	<	if (atypeCutoff[atid] > groupCutoff[cg1]) {
336	>	atid = idents[atom1];
337	>	if (atypeCutoff[atid] > groupCutoff[cg1])
338		groupCutoff[cg1] = atypeCutoff[atid];
315	–	}
339		}
340	<
340	>
341		bool gTypeFound = false;
342		for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
343		if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
#	Line 322 \| Line 345 \| namespace OpenMD {
345		gTypeFound = true;
346		}
347		}
348	<	if (!gTypeFound) {
348	>	if (!gTypeFound) {
349		gTypeCutoffs.push_back( groupCutoff[cg1] );
350		groupToGtype[cg1] = gTypeCutoffs.size() - 1;
351		}
352		}
353		#endif
354
332	–	cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
355		// Now we find the maximum group cutoff value present in the simulation
356
357	<	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
357	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
358	>	gTypeCutoffs.end());
359
360		#ifdef IS_MPI
361	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
361	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
362	>	MPI::MAX);
363		#endif
364
365		RealType tradRcut = groupMax;
#	Line 365 \| Line 389 \| namespace OpenMD {
389
390		pair<int,int> key = make_pair(i,j);
391		gTypeCutoffMap[key].first = thisRcut;
368	–
392		if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
370	–
393		gTypeCutoffMap[key].second = thisRcut*thisRcut;
372	–
394		gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
374	–
395		// sanity check
396
397		if (userChoseCutoff_) {
398		if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
399		sprintf(painCave.errMsg,
400		"ForceMatrixDecomposition::createGtypeCutoffMap "
401	<	"user-specified rCut does not match computed group Cutoff\n");
401	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
402		painCave.severity = OPENMD_ERROR;
403		painCave.isFatal = 1;
404		simError();
#	Line 410 \| Line 430 \| namespace OpenMD {
430		}
431
432		void ForceMatrixDecomposition::zeroWorkArrays() {
433	+	pairwisePot = 0.0;
434	+	embeddingPot = 0.0;
435
414	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
415	–	longRangePot_[j] = 0.0;
416	–	}
417	–
436		#ifdef IS_MPI
437		if (storageLayout_ & DataStorage::dslForce) {
438		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 430 \| Line 448 \| namespace OpenMD {
448		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
449
450		fill(pot_col.begin(), pot_col.end(),
451	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434	<
435	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
451	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
452
453		if (storageLayout_ & DataStorage::dslParticlePot) {
454	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
455	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
454	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
455	>	0.0);
456	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
457	>	0.0);
458		}
459
460		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 445 \| Line 463 \| namespace OpenMD {
463		}
464
465		if (storageLayout_ & DataStorage::dslFunctional) {
466	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
467	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
466	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
467	>	0.0);
468	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
469	>	0.0);
470		}
471
472		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 456 \| Line 476 \| namespace OpenMD {
476		atomColData.functionalDerivative.end(), 0.0);
477		}
478
479	<	#else
480	<
479	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
480	>	fill(atomRowData.skippedCharge.begin(),
481	>	atomRowData.skippedCharge.end(), 0.0);
482	>	fill(atomColData.skippedCharge.begin(),
483	>	atomColData.skippedCharge.end(), 0.0);
484	>	}
485	>
486	>	#endif
487	>	// even in parallel, we need to zero out the local arrays:
488	>
489		if (storageLayout_ & DataStorage::dslParticlePot) {
490		fill(snap_->atomData.particlePot.begin(),
491		snap_->atomData.particlePot.end(), 0.0);
#	Line 475 \| Line 503 \| namespace OpenMD {
503		fill(snap_->atomData.functionalDerivative.begin(),
504		snap_->atomData.functionalDerivative.end(), 0.0);
505		}
506	<	#endif
506	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
507	>	fill(snap_->atomData.skippedCharge.begin(),
508	>	snap_->atomData.skippedCharge.end(), 0.0);
509	>	}
510
511		}
512
#	Line 512 \| Line 543 \| namespace OpenMD {
543		AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
544		atomColData.electroFrame);
545		}
546	+
547		#endif
548		}
549
#	Line 578 \| Line 610 \| namespace OpenMD {
610		AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
611		for (int i = 0; i < n; i++)
612		snap_->atomData.force[i] += frc_tmp[i];
613	<
582	<
613	>
614		if (storageLayout_ & DataStorage::dslTorque) {
615
616	<	int nt = snap_->atomData.force.size();
616	>	int nt = snap_->atomData.torque.size();
617		vector<Vector3d> trq_tmp(nt, V3Zero);
618
619		AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
620	<	for (int i = 0; i < n; i++) {
620	>	for (int i = 0; i < nt; i++) {
621		snap_->atomData.torque[i] += trq_tmp[i];
622		trq_tmp[i] = 0.0;
623		}
624
625		AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
626	<	for (int i = 0; i < n; i++)
626	>	for (int i = 0; i < nt; i++)
627		snap_->atomData.torque[i] += trq_tmp[i];
628		}
629	+
630	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
631	+
632	+	int ns = snap_->atomData.skippedCharge.size();
633	+	vector<RealType> skch_tmp(ns, 0.0);
634	+
635	+	AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
636	+	for (int i = 0; i < ns; i++) {
637	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
638	+	skch_tmp[i] = 0.0;
639	+	}
640	+
641	+	AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
642	+	for (int i = 0; i < ns; i++)
643	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
644	+	}
645
646		nLocal_ = snap_->getNumberOfAtoms();
647
#	Line 606 \| Line 653 \| namespace OpenMD {
653		AtomCommPotRow->scatter(pot_row, pot_temp);
654
655		for (int ii = 0; ii < pot_temp.size(); ii++ )
656	<	pot_local += pot_temp[ii];
656	>	pairwisePot += pot_temp[ii];
657
658		fill(pot_temp.begin(), pot_temp.end(),
659		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
#	Line 614 \| Line 661 \| namespace OpenMD {
661		AtomCommPotColumn->scatter(pot_col, pot_temp);
662
663		for (int ii = 0; ii < pot_temp.size(); ii++ )
664	<	pot_local += pot_temp[ii];
618	<
664	>	pairwisePot += pot_temp[ii];
665		#endif
666	+
667		}
668
669		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 691 \| Line 738 \| namespace OpenMD {
738		#ifdef IS_MPI
739		return massFactorsRow[atom1];
740		#else
741	<	return massFactorsLocal[atom1];
741	>	return massFactors[atom1];
742		#endif
743		}
744
#	Line 699 \| Line 746 \| namespace OpenMD {
746		#ifdef IS_MPI
747		return massFactorsCol[atom2];
748		#else
749	<	return massFactorsLocal[atom2];
749	>	return massFactors[atom2];
750		#endif
751
752		}
#	Line 717 \| Line 764 \| namespace OpenMD {
764		return d;
765		}
766
767	<	vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
768	<	return skipsForAtom[atom1];
767	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
768	>	return excludesForAtom[atom1];
769		}
770
771		/**
772	<	* There are a number of reasons to skip a pair or a
726	<	* particle. Mostly we do this to exclude atoms who are involved in
727	<	* short range interactions (bonds, bends, torsions), but we also
728	<	* need to exclude some overcounted interactions that result from
772	>	* We need to exclude some overcounted interactions that result from
773		* the parallel decomposition.
774		*/
775		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
#	Line 745 \| Line 789 \| namespace OpenMD {
789		} else {
790		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
791		}
792	+	#endif
793	+	return false;
794	+	}
795	+
796	+	/**
797	+	* We need to handle the interactions for atoms who are involved in
798	+	* the same rigid body as well as some short range interactions
799	+	* (bonds, bends, torsions) differently from other interactions.
800	+	* We'll still visit the pairwise routines, but with a flag that
801	+	* tells those routines to exclude the pair from direct long range
802	+	* interactions. Some indirect interactions (notably reaction
803	+	* field) must still be handled for these pairs.
804	+	*/
805	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
806	+	int unique_id_2;
807	+
808	+	#ifdef IS_MPI
809	+	// in MPI, we have to look up the unique IDs for the row atom.
810	+	unique_id_2 = AtomColToGlobal[atom2];
811		#else
812		// in the normal loop, the atom numbers are unique
750	–	unique_id_1 = atom1;
813		unique_id_2 = atom2;
814		#endif
815
816	<	for (vector<int>::iterator i = skipsForAtom[atom1].begin();
817	<	i != skipsForAtom[atom1].end(); ++i) {
818	<	if ( (*i) == unique_id_2 ) return true;
819	<	}
816	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
817	>	i != excludesForAtom[atom1].end(); ++i) {
818	>	if ( (*i) == unique_id_2 ) return true;
819	>	}
820
821	+	return false;
822		}
823
824
#	Line 776 \| Line 839 \| namespace OpenMD {
839		}
840
841		// filling interaction blocks with pointers
842	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
843	<	InteractionData idat;
842	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
843	>	int atom1, int atom2) {
844
845	+	idat.excluded = excludeAtomPair(atom1, atom2);
846	+
847		#ifdef IS_MPI
848	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
849	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
850	+	// ff_->getAtomType(identsCol[atom2]) );
851
784	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
785	–	ff_->getAtomType(identsCol[atom2]) );
786	–
787	–
852		if (storageLayout_ & DataStorage::dslAmat) {
853		idat.A1 = &(atomRowData.aMat[atom1]);
854		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 820 \| Line 884 \| namespace OpenMD {
884		idat.particlePot2 = &(atomColData.particlePot[atom2]);
885		}
886
887	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
888	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
889	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
890	+	}
891	+
892		#else
893
894	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
895	<	ff_->getAtomType(identsLocal[atom2]) );
894	>	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
895	>	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
896	>	// ff_->getAtomType(idents[atom2]) );
897
898		if (storageLayout_ & DataStorage::dslAmat) {
899		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 840 \| Line 910 \| namespace OpenMD {
910		idat.t2 = &(snap_->atomData.torque[atom2]);
911		}
912
913	<	if (storageLayout_ & DataStorage::dslDensity) {
913	>	if (storageLayout_ & DataStorage::dslDensity) {
914		idat.rho1 = &(snap_->atomData.density[atom1]);
915		idat.rho2 = &(snap_->atomData.density[atom2]);
916		}
#	Line 860 \| Line 930 \| namespace OpenMD {
930		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
931		}
932
933	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
934	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
935	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
936	+	}
937		#endif
864	–	return idat;
938		}
939
940
941	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
941	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
942		#ifdef IS_MPI
943		pot_row[atom1] += 0.5 * *(idat.pot);
944		pot_col[atom2] += 0.5 * *(idat.pot);
#	Line 873 \| Line 946 \| namespace OpenMD {
946		atomRowData.force[atom1] += *(idat.f1);
947		atomColData.force[atom2] -= *(idat.f1);
948		#else
949	<	longRangePot_ += *(idat.pot);
950	<
949	>	pairwisePot += *(idat.pot);
950	>
951		snap_->atomData.force[atom1] += *(idat.f1);
952		snap_->atomData.force[atom2] -= *(idat.f1);
953		#endif
954	<
954	>
955		}
956
884	–
885	–	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
886	–
887	–	InteractionData idat;
888	–	#ifdef IS_MPI
889	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
890	–	ff_->getAtomType(identsCol[atom2]) );
891	–
892	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
893	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
894	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
895	–	}
896	–	if (storageLayout_ & DataStorage::dslTorque) {
897	–	idat.t1 = &(atomRowData.torque[atom1]);
898	–	idat.t2 = &(atomColData.torque[atom2]);
899	–	}
900	–	#else
901	–	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
902	–	ff_->getAtomType(identsLocal[atom2]) );
903	–
904	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
905	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
906	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
907	–	}
908	–	if (storageLayout_ & DataStorage::dslTorque) {
909	–	idat.t1 = &(snap_->atomData.torque[atom1]);
910	–	idat.t2 = &(snap_->atomData.torque[atom2]);
911	–	}
912	–	#endif
913	–	}
914	–
957		/*
958		* buildNeighborList
959		*
#	Line 922 \| Line 964 \| namespace OpenMD {
964
965		vector<pair<int, int> > neighborList;
966		groupCutoffs cuts;
967	+	bool doAllPairs = false;
968	+
969		#ifdef IS_MPI
970		cellListRow_.clear();
971		cellListCol_.clear();
#	Line 941 \| Line 985 \| namespace OpenMD {
985		nCells_.y() = (int) ( Hy.length() )/ rList_;
986		nCells_.z() = (int) ( Hz.length() )/ rList_;
987
988	+	// handle small boxes where the cell offsets can end up repeating cells
989	+
990	+	if (nCells_.x() < 3) doAllPairs = true;
991	+	if (nCells_.y() < 3) doAllPairs = true;
992	+	if (nCells_.z() < 3) doAllPairs = true;
993	+
994		Mat3x3d invHmat = snap_->getInvHmat();
995		Vector3d rs, scaled, dr;
996		Vector3i whichCell;
#	Line 954 \| Line 1004 \| namespace OpenMD {
1004		cellList_.resize(nCtot);
1005		#endif
1006
1007	+	if (!doAllPairs) {
1008		#ifdef IS_MPI
958	–	for (int i = 0; i < nGroupsInRow_; i++) {
959	–	rs = cgRowData.position[i];
960	–	// scaled positions relative to the box vectors
961	–	scaled = invHmat * rs;
962	–	// wrap the vector back into the unit box by subtracting integer box
963	–	// numbers
964	–	for (int j = 0; j < 3; j++)
965	–	scaled[j] -= roundMe(scaled[j]);
966	–
967	–	// find xyz-indices of cell that cutoffGroup is in.
968	–	whichCell.x() = nCells_.x() * scaled.x();
969	–	whichCell.y() = nCells_.y() * scaled.y();
970	–	whichCell.z() = nCells_.z() * scaled.z();
1009
1010	<	// find single index of this cell:
1011	<	cellIndex = Vlinear(whichCell, nCells_);
1012	<	// add this cutoff group to the list of groups in this cell;
1013	<	cellListRow_[cellIndex].push_back(i);
1014	<	}
1015	<
1016	<	for (int i = 0; i < nGroupsInCol_; i++) {
1017	<	rs = cgColData.position[i];
1018	<	// scaled positions relative to the box vectors
1019	<	scaled = invHmat * rs;
1020	<	// wrap the vector back into the unit box by subtracting integer box
1021	<	// numbers
1022	<	for (int j = 0; j < 3; j++)
1023	<	scaled[j] -= roundMe(scaled[j]);
1024	<
1025	<	// find xyz-indices of cell that cutoffGroup is in.
1026	<	whichCell.x() = nCells_.x() * scaled.x();
1027	<	whichCell.y() = nCells_.y() * scaled.y();
1028	<	whichCell.z() = nCells_.z() * scaled.z();
1029	<
1030	<	// find single index of this cell:
1031	<	cellIndex = Vlinear(whichCell, nCells_);
1032	<	// add this cutoff group to the list of groups in this cell;
1033	<	cellListCol_[cellIndex].push_back(i);
1034	<	}
1010	>	for (int i = 0; i < nGroupsInRow_; i++) {
1011	>	rs = cgRowData.position[i];
1012	>
1013	>	// scaled positions relative to the box vectors
1014	>	scaled = invHmat * rs;
1015	>
1016	>	// wrap the vector back into the unit box by subtracting integer box
1017	>	// numbers
1018	>	for (int j = 0; j < 3; j++) {
1019	>	scaled[j] -= roundMe(scaled[j]);
1020	>	scaled[j] += 0.5;
1021	>	}
1022	>
1023	>	// find xyz-indices of cell that cutoffGroup is in.
1024	>	whichCell.x() = nCells_.x() * scaled.x();
1025	>	whichCell.y() = nCells_.y() * scaled.y();
1026	>	whichCell.z() = nCells_.z() * scaled.z();
1027	>
1028	>	// find single index of this cell:
1029	>	cellIndex = Vlinear(whichCell, nCells_);
1030	>
1031	>	// add this cutoff group to the list of groups in this cell;
1032	>	cellListRow_[cellIndex].push_back(i);
1033	>	}
1034	>
1035	>	for (int i = 0; i < nGroupsInCol_; i++) {
1036	>	rs = cgColData.position[i];
1037	>
1038	>	// scaled positions relative to the box vectors
1039	>	scaled = invHmat * rs;
1040	>
1041	>	// wrap the vector back into the unit box by subtracting integer box
1042	>	// numbers
1043	>	for (int j = 0; j < 3; j++) {
1044	>	scaled[j] -= roundMe(scaled[j]);
1045	>	scaled[j] += 0.5;
1046	>	}
1047	>
1048	>	// find xyz-indices of cell that cutoffGroup is in.
1049	>	whichCell.x() = nCells_.x() * scaled.x();
1050	>	whichCell.y() = nCells_.y() * scaled.y();
1051	>	whichCell.z() = nCells_.z() * scaled.z();
1052	>
1053	>	// find single index of this cell:
1054	>	cellIndex = Vlinear(whichCell, nCells_);
1055	>
1056	>	// add this cutoff group to the list of groups in this cell;
1057	>	cellListCol_[cellIndex].push_back(i);
1058	>	}
1059		#else
1060	<	for (int i = 0; i < nGroups_; i++) {
1061	<	rs = snap_->cgData.position[i];
1062	<	// scaled positions relative to the box vectors
1063	<	scaled = invHmat * rs;
1064	<	// wrap the vector back into the unit box by subtracting integer box
1065	<	// numbers
1066	<	for (int j = 0; j < 3; j++)
1067	<	scaled[j] -= roundMe(scaled[j]);
1068	<
1069	<	// find xyz-indices of cell that cutoffGroup is in.
1070	<	whichCell.x() = nCells_.x() * scaled.x();
1071	<	whichCell.y() = nCells_.y() * scaled.y();
1072	<	whichCell.z() = nCells_.z() * scaled.z();
1073	<
1074	<	// find single index of this cell:
1075	<	cellIndex = Vlinear(whichCell, nCells_);
1076	<	// add this cutoff group to the list of groups in this cell;
1077	<	cellList_[cellIndex].push_back(i);
1078	<	}
1060	>	for (int i = 0; i < nGroups_; i++) {
1061	>	rs = snap_->cgData.position[i];
1062	>
1063	>	// scaled positions relative to the box vectors
1064	>	scaled = invHmat * rs;
1065	>
1066	>	// wrap the vector back into the unit box by subtracting integer box
1067	>	// numbers
1068	>	for (int j = 0; j < 3; j++) {
1069	>	scaled[j] -= roundMe(scaled[j]);
1070	>	scaled[j] += 0.5;
1071	>	}
1072	>
1073	>	// find xyz-indices of cell that cutoffGroup is in.
1074	>	whichCell.x() = nCells_.x() * scaled.x();
1075	>	whichCell.y() = nCells_.y() * scaled.y();
1076	>	whichCell.z() = nCells_.z() * scaled.z();
1077	>
1078	>	// find single index of this cell:
1079	>	cellIndex = Vlinear(whichCell, nCells_);
1080	>
1081	>	// add this cutoff group to the list of groups in this cell;
1082	>	cellList_[cellIndex].push_back(i);
1083	>	}
1084		#endif
1085
1086	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1087	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1088	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1089	<	Vector3i m1v(m1x, m1y, m1z);
1090	<	int m1 = Vlinear(m1v, nCells_);
1024	<
1025	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1026	<	os != cellOffsets_.end(); ++os) {
1086	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1087	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1088	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1089	>	Vector3i m1v(m1x, m1y, m1z);
1090	>	int m1 = Vlinear(m1v, nCells_);
1091
1092	<	Vector3i m2v = m1v + (*os);
1093	<
1094	<	if (m2v.x() >= nCells_.x()) {
1095	<	m2v.x() = 0;
1096	<	} else if (m2v.x() < 0) {
1097	<	m2v.x() = nCells_.x() - 1;
1098	<	}
1099	<
1100	<	if (m2v.y() >= nCells_.y()) {
1101	<	m2v.y() = 0;
1102	<	} else if (m2v.y() < 0) {
1103	<	m2v.y() = nCells_.y() - 1;
1104	<	}
1105	<
1106	<	if (m2v.z() >= nCells_.z()) {
1107	<	m2v.z() = 0;
1108	<	} else if (m2v.z() < 0) {
1109	<	m2v.z() = nCells_.z() - 1;
1110	<	}
1111	<
1112	<	int m2 = Vlinear (m2v, nCells_);
1113	<
1092	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1093	>	os != cellOffsets_.end(); ++os) {
1094	>
1095	>	Vector3i m2v = m1v + (*os);
1096	>
1097	>	if (m2v.x() >= nCells_.x()) {
1098	>	m2v.x() = 0;
1099	>	} else if (m2v.x() < 0) {
1100	>	m2v.x() = nCells_.x() - 1;
1101	>	}
1102	>
1103	>	if (m2v.y() >= nCells_.y()) {
1104	>	m2v.y() = 0;
1105	>	} else if (m2v.y() < 0) {
1106	>	m2v.y() = nCells_.y() - 1;
1107	>	}
1108	>
1109	>	if (m2v.z() >= nCells_.z()) {
1110	>	m2v.z() = 0;
1111	>	} else if (m2v.z() < 0) {
1112	>	m2v.z() = nCells_.z() - 1;
1113	>	}
1114	>
1115	>	int m2 = Vlinear (m2v, nCells_);
1116	>
1117		#ifdef IS_MPI
1118	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1119	<	j1 != cellListRow_[m1].end(); ++j1) {
1120	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1121	<	j2 != cellListCol_[m2].end(); ++j2) {
1122	<
1123	<	// Always do this if we're in different cells or if
1124	<	// we're in the same cell and the global index of the
1125	<	// j2 cutoff group is less than the j1 cutoff group
1126	<
1127	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1128	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1129	<	snap_->wrapVector(dr);
1130	<	cuts = getGroupCutoffs( (j1), (j2) );
1131	<	if (dr.lengthSquare() < cuts.third) {
1132	<	neighborList.push_back(make_pair((j1), (j2)));
1118	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1119	>	j1 != cellListRow_[m1].end(); ++j1) {
1120	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1121	>	j2 != cellListCol_[m2].end(); ++j2) {
1122	>
1123	>	// Always do this if we're in different cells or if
1124	>	// we're in the same cell and the global index of the
1125	>	// j2 cutoff group is less than the j1 cutoff group
1126	>
1127	>	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1128	>	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1129	>	snap_->wrapVector(dr);
1130	>	cuts = getGroupCutoffs( (j1), (j2) );
1131	>	if (dr.lengthSquare() < cuts.third) {
1132	>	neighborList.push_back(make_pair((j1), (j2)));
1133	>	}
1134		}
1135		}
1136		}
1069	–	}
1137		#else
1138	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1139	<	j1 != cellList_[m1].end(); ++j1) {
1140	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1141	<	j2 != cellList_[m2].end(); ++j2) {
1142	<
1143	<	// Always do this if we're in different cells or if
1144	<	// we're in the same cell and the global index of the
1145	<	// j2 cutoff group is less than the j1 cutoff group
1146	<
1147	<	if (m2 != m1 \|\| (j2) < (j1)) {
1148	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1149	<	snap_->wrapVector(dr);
1150	<	cuts = getGroupCutoffs( (j1), (j2) );
1151	<	if (dr.lengthSquare() < cuts.third) {
1152	<	neighborList.push_back(make_pair((j1), (j2)));
1138	>
1139	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1140	>	j1 != cellList_[m1].end(); ++j1) {
1141	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1142	>	j2 != cellList_[m2].end(); ++j2) {
1143	>
1144	>	// Always do this if we're in different cells or if
1145	>	// we're in the same cell and the global index of the
1146	>	// j2 cutoff group is less than the j1 cutoff group
1147	>
1148	>	if (m2 != m1 \|\| (j2) < (j1)) {
1149	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1150	>	snap_->wrapVector(dr);
1151	>	cuts = getGroupCutoffs( (j1), (j2) );
1152	>	if (dr.lengthSquare() < cuts.third) {
1153	>	neighborList.push_back(make_pair((j1), (j2)));
1154	>	}
1155		}
1156		}
1157		}
1089	–	}
1158		#endif
1159	+	}
1160		}
1161		}
1162		}
1163	+	} else {
1164	+	// branch to do all cutoff group pairs
1165	+	#ifdef IS_MPI
1166	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1167	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1168	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1169	+	snap_->wrapVector(dr);
1170	+	cuts = getGroupCutoffs( j1, j2 );
1171	+	if (dr.lengthSquare() < cuts.third) {
1172	+	neighborList.push_back(make_pair(j1, j2));
1173	+	}
1174	+	}
1175	+	}
1176	+	#else
1177	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1178	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1179	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1180	+	snap_->wrapVector(dr);
1181	+	cuts = getGroupCutoffs( j1, j2 );
1182	+	if (dr.lengthSquare() < cuts.third) {
1183	+	neighborList.push_back(make_pair(j1, j2));
1184	+	}
1185	+	}
1186	+	}
1187	+	#endif
1188		}
1189	<
1189	>
1190		// save the local cutoff group positions for the check that is
1191		// done on each loop:
1192		saved_CG_positions_.clear();
1193		for (int i = 0; i < nGroups_; i++)
1194		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1195	<
1195	>
1196		return neighborList;
1197		}
1198		} //end namespace OpenMD

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs. Revision 1592 by gezelter, Tue Jul 12 20:33:14 2011 UTC

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs.
Revision 1592 by gezelter, Tue Jul 12 20:33:14 2011 UTC