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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs.
Revision 1587 by gezelter, Fri Jul 8 20:25:32 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		// 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();
67	–	vector<RealType> massFactorsLocal = info_->getMassFactors();
68	–	PairList excludes = info_->getExcludedInteractions();
69	–	PairList oneTwo = info_->getOneTwoInteractions();
70	–	PairList oneThree = info_->getOneThreeInteractions();
71	–	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 107 \| 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		AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116		AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
#	Line 116 \| Line 118 \| namespace OpenMD {
118		cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119		cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120
121	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
122	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
121	>	AtomCommRealRow->gather(massFactors, massFactorsRow);
122	>	AtomCommRealColumn->gather(massFactors, massFactorsCol);
123
124		groupListRow_.clear();
125		groupListRow_.resize(nGroupsInRow_);
#	Line 141 \| Line 143 \| namespace OpenMD {
143		}
144		}
145
146	<	skipsForRowAtom.clear();
147	<	skipsForRowAtom.resize(nAtomsInRow_);
146	>	excludesForAtom.clear();
147	>	excludesForAtom.resize(nAtomsInRow_);
148	>	toposForAtom.clear();
149	>	toposForAtom.resize(nAtomsInRow_);
150	>	topoDist.clear();
151	>	topoDist.resize(nAtomsInRow_);
152		for (int i = 0; i < nAtomsInRow_; i++) {
153		int iglob = AtomRowToGlobal[i];
148	–	for (int j = 0; j < nAtomsInCol_; j++) {
149	–	int jglob = AtomColToGlobal[j];
150	–	if (excludes.hasPair(iglob, jglob))
151	–	skipsForRowAtom[i].push_back(j);
152	–	}
153	–	}
154
155	–	toposForRowAtom.clear();
156	–	toposForRowAtom.resize(nAtomsInRow_);
157	–	for (int i = 0; i < nAtomsInRow_; i++) {
158	–	int iglob = AtomRowToGlobal[i];
159	–	int nTopos = 0;
155		for (int j = 0; j < nAtomsInCol_; j++) {
156	<	int jglob = AtomColToGlobal[j];
157	<	if (oneTwo.hasPair(iglob, jglob)) {
158	<	toposForRowAtom[i].push_back(j);
159	<	topoDistRow[i][nTopos] = 1;
160	<	nTopos++;
156	>	int jglob = AtomColToGlobal[j];
157	>
158	>	if (excludes->hasPair(iglob, jglob))
159	>	excludesForAtom[i].push_back(j);
160	>
161	>	if (oneTwo->hasPair(iglob, jglob)) {
162	>	toposForAtom[i].push_back(j);
163	>	topoDist[i].push_back(1);
164	>	} else {
165	>	if (oneThree->hasPair(iglob, jglob)) {
166	>	toposForAtom[i].push_back(j);
167	>	topoDist[i].push_back(2);
168	>	} else {
169	>	if (oneFour->hasPair(iglob, jglob)) {
170	>	toposForAtom[i].push_back(j);
171	>	topoDist[i].push_back(3);
172	>	}
173	>	}
174		}
167	–	if (oneThree.hasPair(iglob, jglob)) {
168	–	toposForRowAtom[i].push_back(j);
169	–	topoDistRow[i][nTopos] = 2;
170	–	nTopos++;
171	–	}
172	–	if (oneFour.hasPair(iglob, jglob)) {
173	–	toposForRowAtom[i].push_back(j);
174	–	topoDistRow[i][nTopos] = 3;
175	–	nTopos++;
176	–	}
175		}
176		}
177
178		#endif
179	+
180		groupList_.clear();
181		groupList_.resize(nGroups_);
182		for (int i = 0; i < nGroups_; i++) {
#	Line 186 \| Line 185 \| namespace OpenMD {
185		int aid = AtomLocalToGlobal[j];
186		if (globalGroupMembership[aid] == gid) {
187		groupList_[i].push_back(j);
189	–
188		}
189		}
190		}
191
192	<	skipsForLocalAtom.clear();
193	<	skipsForLocalAtom.resize(nLocal_);
192	>	excludesForAtom.clear();
193	>	excludesForAtom.resize(nLocal_);
194	>	toposForAtom.clear();
195	>	toposForAtom.resize(nLocal_);
196	>	topoDist.clear();
197	>	topoDist.resize(nLocal_);
198
199		for (int i = 0; i < nLocal_; i++) {
200		int iglob = AtomLocalToGlobal[i];
201	+
202		for (int j = 0; j < nLocal_; j++) {
203	<	int jglob = AtomLocalToGlobal[j];
204	<	if (excludes.hasPair(iglob, jglob))
205	<	skipsForLocalAtom[i].push_back(j);
206	<	}
207	<	}
208	<	toposForLocalAtom.clear();
209	<	toposForLocalAtom.resize(nLocal_);
210	<	for (int i = 0; i < nLocal_; i++) {
211	<	int iglob = AtomLocalToGlobal[i];
212	<	int nTopos = 0;
213	<	for (int j = 0; j < nLocal_; j++) {
214	<	int jglob = AtomLocalToGlobal[j];
215	<	if (oneTwo.hasPair(iglob, jglob)) {
216	<	toposForLocalAtom[i].push_back(j);
217	<	topoDistLocal[i][nTopos] = 1;
218	<	nTopos++;
203	>	int jglob = AtomLocalToGlobal[j];
204	>
205	>	if (excludes->hasPair(iglob, jglob))
206	>	excludesForAtom[i].push_back(j);
207	>
208	>	if (oneTwo->hasPair(iglob, jglob)) {
209	>	toposForAtom[i].push_back(j);
210	>	topoDist[i].push_back(1);
211	>	} else {
212	>	if (oneThree->hasPair(iglob, jglob)) {
213	>	toposForAtom[i].push_back(j);
214	>	topoDist[i].push_back(2);
215	>	} else {
216	>	if (oneFour->hasPair(iglob, jglob)) {
217	>	toposForAtom[i].push_back(j);
218	>	topoDist[i].push_back(3);
219	>	}
220	>	}
221		}
217	–	if (oneThree.hasPair(iglob, jglob)) {
218	–	toposForLocalAtom[i].push_back(j);
219	–	topoDistLocal[i][nTopos] = 2;
220	–	nTopos++;
221	–	}
222	–	if (oneFour.hasPair(iglob, jglob)) {
223	–	toposForLocalAtom[i].push_back(j);
224	–	topoDistLocal[i][nTopos] = 3;
225	–	nTopos++;
226	–	}
222		}
223	<	}
223	>	}
224	>
225	>	createGtypeCutoffMap();
226
227		}
228
229		void ForceMatrixDecomposition::createGtypeCutoffMap() {
230	<
230	>
231		RealType tol = 1e-6;
232		RealType rc;
233		int atid;
234		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
235	<	vector<RealType> atypeCutoff;
236	<	atypeCutoff.resize( atypes.size() );
237	<
238	<	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
242	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
235	>	map<int, RealType> atypeCutoff;
236	>
237	>	for (set<AtomType*>::iterator at = atypes.begin();
238	>	at != atypes.end(); ++at){
239		atid = (*at)->getIdent();
240	<	atypeCutoff[atid] = rc;
240	>	if (userChoseCutoff_)
241	>	atypeCutoff[atid] = userCutoff_;
242	>	else
243	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
244		}
245
246		vector<RealType> gTypeCutoffs;
248	–
247		// first we do a single loop over the cutoff groups to find the
248		// largest cutoff for any atypes present in this group.
249		#ifdef IS_MPI
250		vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
251	+	groupRowToGtype.resize(nGroupsInRow_);
252		for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
253		vector<int> atomListRow = getAtomsInGroupRow(cg1);
254		for (vector<int>::iterator ia = atomListRow.begin();
#	Line 275 \| Line 274 \| namespace OpenMD {
274
275		}
276		vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
277	+	groupColToGtype.resize(nGroupsInCol_);
278		for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
279		vector<int> atomListCol = getAtomsInGroupColumn(cg2);
280		for (vector<int>::iterator jb = atomListCol.begin();
#	Line 298 \| Line 298 \| namespace OpenMD {
298		}
299		}
300		#else
301	+
302		vector<RealType> groupCutoff(nGroups_, 0.0);
303	+	groupToGtype.resize(nGroups_);
304		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305	+
306		groupCutoff[cg1] = 0.0;
307		vector<int> atomList = getAtomsInGroupRow(cg1);
308	+
309		for (vector<int>::iterator ia = atomList.begin();
310		ia != atomList.end(); ++ia) {
311		int atom1 = (*ia);
312	<	atid = identsLocal[atom1];
312	>	atid = idents[atom1];
313		if (atypeCutoff[atid] > groupCutoff[cg1]) {
314		groupCutoff[cg1] = atypeCutoff[atid];
315		}
#	Line 327 \| Line 331 \| namespace OpenMD {
331
332		// Now we find the maximum group cutoff value present in the simulation
333
334	<	vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
331	<	RealType groupMax = *groupMaxLoc;
334	>	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
335
336		#ifdef IS_MPI
337		MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
#	Line 337 \| Line 340 \| namespace OpenMD {
340		RealType tradRcut = groupMax;
341
342		for (int i = 0; i < gTypeCutoffs.size(); i++) {
343	<	for (int j = 0; j < gTypeCutoffs.size(); j++) {
341	<
343	>	for (int j = 0; j < gTypeCutoffs.size(); j++) {
344		RealType thisRcut;
345		switch(cutoffPolicy_) {
346		case TRADITIONAL:
347		thisRcut = tradRcut;
348	+	break;
349		case MIX:
350		thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
351	+	break;
352		case MAX:
353		thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
354	+	break;
355		default:
356		sprintf(painCave.errMsg,
357		"ForceMatrixDecomposition::createGtypeCutoffMap "
358		"hit an unknown cutoff policy!\n");
359		painCave.severity = OPENMD_ERROR;
360		painCave.isFatal = 1;
361	<	simError();
361	>	simError();
362	>	break;
363		}
364
365		pair<int,int> key = make_pair(i,j);
#	Line 371 \| Line 377 \| namespace OpenMD {
377		if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
378		sprintf(painCave.errMsg,
379		"ForceMatrixDecomposition::createGtypeCutoffMap "
380	<	"user-specified rCut does not match computed group Cutoff\n");
380	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
381		painCave.severity = OPENMD_ERROR;
382		painCave.isFatal = 1;
383		simError();
#	Line 383 \| Line 389 \| namespace OpenMD {
389
390
391		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
392	<	int i, j;
387	<
392	>	int i, j;
393		#ifdef IS_MPI
394		i = groupRowToGtype[cg1];
395		j = groupColToGtype[cg2];
396		#else
397		i = groupToGtype[cg1];
398		j = groupToGtype[cg2];
399	<	#endif
395	<
399	>	#endif
400		return gTypeCutoffMap[make_pair(i,j)];
401		}
402
403	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
404	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
405	+	if (toposForAtom[atom1][j] == atom2)
406	+	return topoDist[atom1][j];
407	+	}
408	+	return 0;
409	+	}
410
411		void ForceMatrixDecomposition::zeroWorkArrays() {
412	+	pairwisePot = 0.0;
413	+	embeddingPot = 0.0;
414
402	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403	–	longRangePot_[j] = 0.0;
404	–	}
405	–
415		#ifdef IS_MPI
416		if (storageLayout_ & DataStorage::dslForce) {
417		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 418 \| Line 427 \| namespace OpenMD {
427		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
428
429		fill(pot_col.begin(), pot_col.end(),
430	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422	<
423	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
430	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
431
432		if (storageLayout_ & DataStorage::dslParticlePot) {
433		fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
#	Line 444 \| Line 451 \| namespace OpenMD {
451		atomColData.functionalDerivative.end(), 0.0);
452		}
453
454	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
455	+	fill(atomRowData.skippedCharge.begin(),
456	+	atomRowData.skippedCharge.end(), 0.0);
457	+	fill(atomColData.skippedCharge.begin(),
458	+	atomColData.skippedCharge.end(), 0.0);
459	+	}
460	+
461		#else
462
463		if (storageLayout_ & DataStorage::dslParticlePot) {
#	Line 463 \| Line 477 \| namespace OpenMD {
477		fill(snap_->atomData.functionalDerivative.begin(),
478		snap_->atomData.functionalDerivative.end(), 0.0);
479		}
480	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
481	+	fill(snap_->atomData.skippedCharge.begin(),
482	+	snap_->atomData.skippedCharge.end(), 0.0);
483	+	}
484		#endif
485
486		}
#	Line 570 \| Line 588 \| namespace OpenMD {
588
589		if (storageLayout_ & DataStorage::dslTorque) {
590
591	<	int nt = snap_->atomData.force.size();
591	>	int nt = snap_->atomData.torque.size();
592		vector<Vector3d> trq_tmp(nt, V3Zero);
593
594		AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
595	<	for (int i = 0; i < n; i++) {
595	>	for (int i = 0; i < nt; i++) {
596		snap_->atomData.torque[i] += trq_tmp[i];
597		trq_tmp[i] = 0.0;
598		}
599
600		AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
601	<	for (int i = 0; i < n; i++)
601	>	for (int i = 0; i < nt; i++)
602		snap_->atomData.torque[i] += trq_tmp[i];
603	+	}
604	+
605	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
606	+
607	+	int ns = snap_->atomData.skippedCharge.size();
608	+	vector<RealType> skch_tmp(ns, 0.0);
609	+
610	+	AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
611	+	for (int i = 0; i < ns; i++) {
612	+	snap_->atomData.skippedCharge[i] = skch_tmp[i];
613	+	skch_tmp[i] = 0.0;
614	+	}
615	+
616	+	AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
617	+	for (int i = 0; i < ns; i++)
618	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
619		}
620
621		nLocal_ = snap_->getNumberOfAtoms();
#	Line 594 \| Line 628 \| namespace OpenMD {
628		AtomCommPotRow->scatter(pot_row, pot_temp);
629
630		for (int ii = 0; ii < pot_temp.size(); ii++ )
631	<	pot_local += pot_temp[ii];
631	>	pairwisePot += pot_temp[ii];
632
633		fill(pot_temp.begin(), pot_temp.end(),
634		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
#	Line 602 \| Line 636 \| namespace OpenMD {
636		AtomCommPotColumn->scatter(pot_col, pot_temp);
637
638		for (int ii = 0; ii < pot_temp.size(); ii++ )
639	<	pot_local += pot_temp[ii];
606	<
639	>	pairwisePot += pot_temp[ii];
640		#endif
641	+
642		}
643
644		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 679 \| Line 713 \| namespace OpenMD {
713		#ifdef IS_MPI
714		return massFactorsRow[atom1];
715		#else
716	<	return massFactorsLocal[atom1];
716	>	return massFactors[atom1];
717		#endif
718		}
719
#	Line 687 \| Line 721 \| namespace OpenMD {
721		#ifdef IS_MPI
722		return massFactorsCol[atom2];
723		#else
724	<	return massFactorsLocal[atom2];
724	>	return massFactors[atom2];
725		#endif
726
727		}
#	Line 705 \| Line 739 \| namespace OpenMD {
739		return d;
740		}
741
742	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
743	<	#ifdef IS_MPI
710	<	return skipsForRowAtom[atom1];
711	<	#else
712	<	return skipsForLocalAtom[atom1];
713	<	#endif
742	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
743	>	return excludesForAtom[atom1];
744		}
745
746		/**
747	<	* There are a number of reasons to skip a pair or a
718	<	* particle. Mostly we do this to exclude atoms who are involved in
719	<	* short range interactions (bonds, bends, torsions), but we also
720	<	* need to exclude some overcounted interactions that result from
747	>	* We need to exclude some overcounted interactions that result from
748		* the parallel decomposition.
749		*/
750		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
#	Line 737 \| Line 764 \| namespace OpenMD {
764		} else {
765		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
766		}
767	+	#endif
768	+	return false;
769	+	}
770	+
771	+	/**
772	+	* We need to handle the interactions for atoms who are involved in
773	+	* the same rigid body as well as some short range interactions
774	+	* (bonds, bends, torsions) differently from other interactions.
775	+	* We'll still visit the pairwise routines, but with a flag that
776	+	* tells those routines to exclude the pair from direct long range
777	+	* interactions. Some indirect interactions (notably reaction
778	+	* field) must still be handled for these pairs.
779	+	*/
780	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
781	+	int unique_id_2;
782	+
783	+	#ifdef IS_MPI
784	+	// in MPI, we have to look up the unique IDs for the row atom.
785	+	unique_id_2 = AtomColToGlobal[atom2];
786		#else
787		// in the normal loop, the atom numbers are unique
742	–	unique_id_1 = atom1;
788		unique_id_2 = atom2;
789		#endif
790
791	<	#ifdef IS_MPI
792	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748	<	i != skipsForRowAtom[atom1].end(); ++i) {
791	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
792	>	i != excludesForAtom[atom1].end(); ++i) {
793		if ( (*i) == unique_id_2 ) return true;
750	–	}
751	–	#else
752	–	for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
753	–	i != skipsForLocalAtom[atom1].end(); ++i) {
754	–	if ( (*i) == unique_id_2 ) return true;
755	–	}
756	–	#endif
757	–	}
758	–
759	–	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
760	–
761	–	#ifdef IS_MPI
762	–	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
763	–	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
794		}
765	–	#else
766	–	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
767	–	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
768	–	}
769	–	#endif
795
796	<	// zero is default for unconnected (i.e. normal) pair interactions
772	<	return 0;
796	>	return false;
797		}
798
799	+
800		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
801		#ifdef IS_MPI
802		atomRowData.force[atom1] += fg;
#	Line 789 \| Line 814 \| namespace OpenMD {
814		}
815
816		// filling interaction blocks with pointers
817	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
818	<	InteractionData idat;
817	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
818	>	int atom1, int atom2) {
819
820	+	idat.excluded = excludeAtomPair(atom1, atom2);
821	+
822		#ifdef IS_MPI
823
824		idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
825		ff_->getAtomType(identsCol[atom2]) );
799	–
826
827		if (storageLayout_ & DataStorage::dslAmat) {
828		idat.A1 = &(atomRowData.aMat[atom1]);
#	Line 833 \| Line 859 \| namespace OpenMD {
859		idat.particlePot2 = &(atomColData.particlePot[atom2]);
860		}
861
862	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
863	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
864	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
865	+	}
866	+
867		#else
868
869	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
870	<	ff_->getAtomType(identsLocal[atom2]) );
869	>	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
870	>	ff_->getAtomType(idents[atom2]) );
871
872		if (storageLayout_ & DataStorage::dslAmat) {
873		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 853 \| Line 884 \| namespace OpenMD {
884		idat.t2 = &(snap_->atomData.torque[atom2]);
885		}
886
887	<	if (storageLayout_ & DataStorage::dslDensity) {
887	>	if (storageLayout_ & DataStorage::dslDensity) {
888		idat.rho1 = &(snap_->atomData.density[atom1]);
889		idat.rho2 = &(snap_->atomData.density[atom2]);
890		}
#	Line 873 \| Line 904 \| namespace OpenMD {
904		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
905		}
906
907	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
908	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
909	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
910	+	}
911		#endif
877	–	return idat;
912		}
913
914
915	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
915	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
916		#ifdef IS_MPI
917		pot_row[atom1] += 0.5 * *(idat.pot);
918		pot_col[atom2] += 0.5 * *(idat.pot);
#	Line 886 \| Line 920 \| namespace OpenMD {
920		atomRowData.force[atom1] += *(idat.f1);
921		atomColData.force[atom2] -= *(idat.f1);
922		#else
923	<	longRangePot_ += *(idat.pot);
924	<
923	>	pairwisePot += *(idat.pot);
924	>
925		snap_->atomData.force[atom1] += *(idat.f1);
926		snap_->atomData.force[atom2] -= *(idat.f1);
927		#endif
928	<
895	<	}
896	<
897	<
898	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
899	<
900	<	InteractionData idat;
901	<	#ifdef IS_MPI
902	<	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
903	<	ff_->getAtomType(identsCol[atom2]) );
904	<
905	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
906	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
907	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
908	<	}
909	<	if (storageLayout_ & DataStorage::dslTorque) {
910	<	idat.t1 = &(atomRowData.torque[atom1]);
911	<	idat.t2 = &(atomColData.torque[atom2]);
912	<	}
913	<	#else
914	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
915	<	ff_->getAtomType(identsLocal[atom2]) );
916	<
917	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
918	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
919	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
920	<	}
921	<	if (storageLayout_ & DataStorage::dslTorque) {
922	<	idat.t1 = &(snap_->atomData.torque[atom1]);
923	<	idat.t2 = &(snap_->atomData.torque[atom2]);
924	<	}
925	<	#endif
928	>
929		}
930
931		/*
#	Line 935 \| Line 938 \| namespace OpenMD {
938
939		vector<pair<int, int> > neighborList;
940		groupCutoffs cuts;
941	+	bool doAllPairs = false;
942	+
943		#ifdef IS_MPI
944		cellListRow_.clear();
945		cellListCol_.clear();
#	Line 954 \| Line 959 \| namespace OpenMD {
959		nCells_.y() = (int) ( Hy.length() )/ rList_;
960		nCells_.z() = (int) ( Hz.length() )/ rList_;
961
962	+	// handle small boxes where the cell offsets can end up repeating cells
963	+
964	+	if (nCells_.x() < 3) doAllPairs = true;
965	+	if (nCells_.y() < 3) doAllPairs = true;
966	+	if (nCells_.z() < 3) doAllPairs = true;
967	+
968		Mat3x3d invHmat = snap_->getInvHmat();
969		Vector3d rs, scaled, dr;
970		Vector3i whichCell;
971		int cellIndex;
972	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
973
974		#ifdef IS_MPI
975	<	for (int i = 0; i < nGroupsInRow_; i++) {
976	<	rs = cgRowData.position[i];
965	<	// scaled positions relative to the box vectors
966	<	scaled = invHmat * rs;
967	<	// wrap the vector back into the unit box by subtracting integer box
968	<	// numbers
969	<	for (int j = 0; j < 3; j++)
970	<	scaled[j] -= roundMe(scaled[j]);
971	<
972	<	// find xyz-indices of cell that cutoffGroup is in.
973	<	whichCell.x() = nCells_.x() * scaled.x();
974	<	whichCell.y() = nCells_.y() * scaled.y();
975	<	whichCell.z() = nCells_.z() * scaled.z();
976	<
977	<	// find single index of this cell:
978	<	cellIndex = Vlinear(whichCell, nCells_);
979	<	// add this cutoff group to the list of groups in this cell;
980	<	cellListRow_[cellIndex].push_back(i);
981	<	}
982	<
983	<	for (int i = 0; i < nGroupsInCol_; i++) {
984	<	rs = cgColData.position[i];
985	<	// scaled positions relative to the box vectors
986	<	scaled = invHmat * rs;
987	<	// wrap the vector back into the unit box by subtracting integer box
988	<	// numbers
989	<	for (int j = 0; j < 3; j++)
990	<	scaled[j] -= roundMe(scaled[j]);
991	<
992	<	// find xyz-indices of cell that cutoffGroup is in.
993	<	whichCell.x() = nCells_.x() * scaled.x();
994	<	whichCell.y() = nCells_.y() * scaled.y();
995	<	whichCell.z() = nCells_.z() * scaled.z();
996	<
997	<	// find single index of this cell:
998	<	cellIndex = Vlinear(whichCell, nCells_);
999	<	// add this cutoff group to the list of groups in this cell;
1000	<	cellListCol_[cellIndex].push_back(i);
1001	<	}
975	>	cellListRow_.resize(nCtot);
976	>	cellListCol_.resize(nCtot);
977		#else
978	<	for (int i = 0; i < nGroups_; i++) {
979	<	rs = snap_->cgData.position[i];
1005	<	// scaled positions relative to the box vectors
1006	<	scaled = invHmat * rs;
1007	<	// wrap the vector back into the unit box by subtracting integer box
1008	<	// numbers
1009	<	for (int j = 0; j < 3; j++)
1010	<	scaled[j] -= roundMe(scaled[j]);
978	>	cellList_.resize(nCtot);
979	>	#endif
980
981	<	// find xyz-indices of cell that cutoffGroup is in.
982	<	whichCell.x() = nCells_.x() * scaled.x();
1014	<	whichCell.y() = nCells_.y() * scaled.y();
1015	<	whichCell.z() = nCells_.z() * scaled.z();
981	>	if (!doAllPairs) {
982	>	#ifdef IS_MPI
983
984	<	// find single index of this cell:
985	<	cellIndex = Vlinear(whichCell, nCells_);
986	<	// add this cutoff group to the list of groups in this cell;
987	<	cellList_[cellIndex].push_back(i);
988	<	}
984	>	for (int i = 0; i < nGroupsInRow_; i++) {
985	>	rs = cgRowData.position[i];
986	>
987	>	// scaled positions relative to the box vectors
988	>	scaled = invHmat * rs;
989	>
990	>	// wrap the vector back into the unit box by subtracting integer box
991	>	// numbers
992	>	for (int j = 0; j < 3; j++) {
993	>	scaled[j] -= roundMe(scaled[j]);
994	>	scaled[j] += 0.5;
995	>	}
996	>
997	>	// find xyz-indices of cell that cutoffGroup is in.
998	>	whichCell.x() = nCells_.x() * scaled.x();
999	>	whichCell.y() = nCells_.y() * scaled.y();
1000	>	whichCell.z() = nCells_.z() * scaled.z();
1001	>
1002	>	// find single index of this cell:
1003	>	cellIndex = Vlinear(whichCell, nCells_);
1004	>
1005	>	// add this cutoff group to the list of groups in this cell;
1006	>	cellListRow_[cellIndex].push_back(i);
1007	>	}
1008	>
1009	>	for (int i = 0; i < nGroupsInCol_; i++) {
1010	>	rs = cgColData.position[i];
1011	>
1012	>	// scaled positions relative to the box vectors
1013	>	scaled = invHmat * rs;
1014	>
1015	>	// wrap the vector back into the unit box by subtracting integer box
1016	>	// numbers
1017	>	for (int j = 0; j < 3; j++) {
1018	>	scaled[j] -= roundMe(scaled[j]);
1019	>	scaled[j] += 0.5;
1020	>	}
1021	>
1022	>	// find xyz-indices of cell that cutoffGroup is in.
1023	>	whichCell.x() = nCells_.x() * scaled.x();
1024	>	whichCell.y() = nCells_.y() * scaled.y();
1025	>	whichCell.z() = nCells_.z() * scaled.z();
1026	>
1027	>	// find single index of this cell:
1028	>	cellIndex = Vlinear(whichCell, nCells_);
1029	>
1030	>	// add this cutoff group to the list of groups in this cell;
1031	>	cellListCol_[cellIndex].push_back(i);
1032	>	}
1033	>	#else
1034	>	for (int i = 0; i < nGroups_; i++) {
1035	>	rs = snap_->cgData.position[i];
1036	>
1037	>	// scaled positions relative to the box vectors
1038	>	scaled = invHmat * rs;
1039	>
1040	>	// wrap the vector back into the unit box by subtracting integer box
1041	>	// numbers
1042	>	for (int j = 0; j < 3; j++) {
1043	>	scaled[j] -= roundMe(scaled[j]);
1044	>	scaled[j] += 0.5;
1045	>	}
1046	>
1047	>	// find xyz-indices of cell that cutoffGroup is in.
1048	>	whichCell.x() = nCells_.x() * scaled.x();
1049	>	whichCell.y() = nCells_.y() * scaled.y();
1050	>	whichCell.z() = nCells_.z() * scaled.z();
1051	>
1052	>	// find single index of this cell:
1053	>	cellIndex = Vlinear(whichCell, nCells_);
1054	>
1055	>	// add this cutoff group to the list of groups in this cell;
1056	>	cellList_[cellIndex].push_back(i);
1057	>	}
1058		#endif
1059
1060	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1061	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1062	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1063	<	Vector3i m1v(m1x, m1y, m1z);
1064	<	int m1 = Vlinear(m1v, nCells_);
1029	<
1030	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1031	<	os != cellOffsets_.end(); ++os) {
1060	>	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1061	>	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1062	>	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1063	>	Vector3i m1v(m1x, m1y, m1z);
1064	>	int m1 = Vlinear(m1v, nCells_);
1065
1066	<	Vector3i m2v = m1v + (*os);
1067	<
1068	<	if (m2v.x() >= nCells_.x()) {
1069	<	m2v.x() = 0;
1070	<	} else if (m2v.x() < 0) {
1071	<	m2v.x() = nCells_.x() - 1;
1072	<	}
1073	<
1074	<	if (m2v.y() >= nCells_.y()) {
1075	<	m2v.y() = 0;
1076	<	} else if (m2v.y() < 0) {
1077	<	m2v.y() = nCells_.y() - 1;
1078	<	}
1079	<
1080	<	if (m2v.z() >= nCells_.z()) {
1081	<	m2v.z() = 0;
1082	<	} else if (m2v.z() < 0) {
1083	<	m2v.z() = nCells_.z() - 1;
1084	<	}
1085	<
1086	<	int m2 = Vlinear (m2v, nCells_);
1087	<
1066	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1067	>	os != cellOffsets_.end(); ++os) {
1068	>
1069	>	Vector3i m2v = m1v + (*os);
1070	>
1071	>	if (m2v.x() >= nCells_.x()) {
1072	>	m2v.x() = 0;
1073	>	} else if (m2v.x() < 0) {
1074	>	m2v.x() = nCells_.x() - 1;
1075	>	}
1076	>
1077	>	if (m2v.y() >= nCells_.y()) {
1078	>	m2v.y() = 0;
1079	>	} else if (m2v.y() < 0) {
1080	>	m2v.y() = nCells_.y() - 1;
1081	>	}
1082	>
1083	>	if (m2v.z() >= nCells_.z()) {
1084	>	m2v.z() = 0;
1085	>	} else if (m2v.z() < 0) {
1086	>	m2v.z() = nCells_.z() - 1;
1087	>	}
1088	>
1089	>	int m2 = Vlinear (m2v, nCells_);
1090	>
1091		#ifdef IS_MPI
1092	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1093	<	j1 != cellListRow_[m1].end(); ++j1) {
1094	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1095	<	j2 != cellListCol_[m2].end(); ++j2) {
1096	<
1097	<	// Always do this if we're in different cells or if
1098	<	// we're in the same cell and the global index of the
1099	<	// j2 cutoff group is less than the j1 cutoff group
1100	<
1101	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1102	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1103	<	snap_->wrapVector(dr);
1104	<	cuts = getGroupCutoffs( (j1), (j2) );
1105	<	if (dr.lengthSquare() < cuts.third) {
1106	<	neighborList.push_back(make_pair((j1), (j2)));
1092	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1093	>	j1 != cellListRow_[m1].end(); ++j1) {
1094	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1095	>	j2 != cellListCol_[m2].end(); ++j2) {
1096	>
1097	>	// Always do this if we're in different cells or if
1098	>	// we're in the same cell and the global index of the
1099	>	// j2 cutoff group is less than the j1 cutoff group
1100	>
1101	>	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1102	>	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1103	>	snap_->wrapVector(dr);
1104	>	cuts = getGroupCutoffs( (j1), (j2) );
1105	>	if (dr.lengthSquare() < cuts.third) {
1106	>	neighborList.push_back(make_pair((j1), (j2)));
1107	>	}
1108		}
1109		}
1110		}
1074	–	}
1111		#else
1112	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1113	<	j1 != cellList_[m1].end(); ++j1) {
1114	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1115	<	j2 != cellList_[m2].end(); ++j2) {
1116	<
1117	<	// Always do this if we're in different cells or if
1118	<	// we're in the same cell and the global index of the
1119	<	// j2 cutoff group is less than the j1 cutoff group
1120	<
1121	<	if (m2 != m1 \|\| (j2) < (j1)) {
1122	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1123	<	snap_->wrapVector(dr);
1124	<	cuts = getGroupCutoffs( (j1), (j2) );
1125	<	if (dr.lengthSquare() < cuts.third) {
1126	<	neighborList.push_back(make_pair((j1), (j2)));
1112	>
1113	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1114	>	j1 != cellList_[m1].end(); ++j1) {
1115	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1116	>	j2 != cellList_[m2].end(); ++j2) {
1117	>
1118	>	// Always do this if we're in different cells or if
1119	>	// we're in the same cell and the global index of the
1120	>	// j2 cutoff group is less than the j1 cutoff group
1121	>
1122	>	if (m2 != m1 \|\| (j2) < (j1)) {
1123	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1124	>	snap_->wrapVector(dr);
1125	>	cuts = getGroupCutoffs( (j1), (j2) );
1126	>	if (dr.lengthSquare() < cuts.third) {
1127	>	neighborList.push_back(make_pair((j1), (j2)));
1128	>	}
1129		}
1130		}
1131		}
1094	–	}
1132		#endif
1133	+	}
1134		}
1135		}
1136		}
1137	+	} else {
1138	+	// branch to do all cutoff group pairs
1139	+	#ifdef IS_MPI
1140	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1141	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1142	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1143	+	snap_->wrapVector(dr);
1144	+	cuts = getGroupCutoffs( j1, j2 );
1145	+	if (dr.lengthSquare() < cuts.third) {
1146	+	neighborList.push_back(make_pair(j1, j2));
1147	+	}
1148	+	}
1149	+	}
1150	+	#else
1151	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1152	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1153	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1154	+	snap_->wrapVector(dr);
1155	+	cuts = getGroupCutoffs( j1, j2 );
1156	+	if (dr.lengthSquare() < cuts.third) {
1157	+	neighborList.push_back(make_pair(j1, j2));
1158	+	}
1159	+	}
1160	+	}
1161	+	#endif
1162		}
1163	<
1163	>
1164		// save the local cutoff group positions for the check that is
1165		// done on each loop:
1166		saved_CG_positions_.clear();
1167		for (int i = 0; i < nGroups_; i++)
1168		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1169	<
1169	>
1170		return neighborList;
1171		}
1172		} //end namespace OpenMD

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs. Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC vs.
Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC