[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 1591 by gezelter, Tue Jul 12 15:25:07 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	+	// 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 141 \| Line 161 \| namespace OpenMD {
161		}
162		}
163
164	<	skipsForRowAtom.clear();
165	<	skipsForRowAtom.resize(nAtomsInRow_);
164	>	excludesForAtom.clear();
165	>	excludesForAtom.resize(nAtomsInRow_);
166	>	toposForAtom.clear();
167	>	toposForAtom.resize(nAtomsInRow_);
168	>	topoDist.clear();
169	>	topoDist.resize(nAtomsInRow_);
170		for (int i = 0; i < nAtomsInRow_; i++) {
171		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	–	}
172
155	–	toposForRowAtom.clear();
156	–	toposForRowAtom.resize(nAtomsInRow_);
157	–	for (int i = 0; i < nAtomsInRow_; i++) {
158	–	int iglob = AtomRowToGlobal[i];
159	–	int nTopos = 0;
173		for (int j = 0; j < nAtomsInCol_; j++) {
174	<	int jglob = AtomColToGlobal[j];
175	<	if (oneTwo.hasPair(iglob, jglob)) {
176	<	toposForRowAtom[i].push_back(j);
177	<	topoDistRow[i][nTopos] = 1;
178	<	nTopos++;
174	>	int jglob = AtomColToGlobal[j];
175	>
176	>	if (excludes->hasPair(iglob, jglob))
177	>	excludesForAtom[i].push_back(j);
178	>
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)) {
184	>	toposForAtom[i].push_back(j);
185	>	topoDist[i].push_back(2);
186	>	} else {
187	>	if (oneFour->hasPair(iglob, jglob)) {
188	>	toposForAtom[i].push_back(j);
189	>	topoDist[i].push_back(3);
190	>	}
191	>	}
192		}
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	–	}
193		}
194		}
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 186 \| Line 209 \| namespace OpenMD {
209		int aid = AtomLocalToGlobal[j];
210		if (globalGroupMembership[aid] == gid) {
211		groupList_[i].push_back(j);
189	–
212		}
213		}
214		}
215
216	<	skipsForLocalAtom.clear();
217	<	skipsForLocalAtom.resize(nLocal_);
216	>	excludesForAtom.clear();
217	>	excludesForAtom.resize(nLocal_);
218	>	toposForAtom.clear();
219	>	toposForAtom.resize(nLocal_);
220	>	topoDist.clear();
221	>	topoDist.resize(nLocal_);
222
223		for (int i = 0; i < nLocal_; i++) {
224		int iglob = AtomLocalToGlobal[i];
225	+
226		for (int j = 0; j < nLocal_; j++) {
227	<	int jglob = AtomLocalToGlobal[j];
228	<	if (excludes.hasPair(iglob, jglob))
229	<	skipsForLocalAtom[i].push_back(j);
230	<	}
231	<	}
232	<	toposForLocalAtom.clear();
233	<	toposForLocalAtom.resize(nLocal_);
234	<	for (int i = 0; i < nLocal_; i++) {
235	<	int iglob = AtomLocalToGlobal[i];
236	<	int nTopos = 0;
237	<	for (int j = 0; j < nLocal_; j++) {
238	<	int jglob = AtomLocalToGlobal[j];
239	<	if (oneTwo.hasPair(iglob, jglob)) {
240	<	toposForLocalAtom[i].push_back(j);
241	<	topoDistLocal[i][nTopos] = 1;
242	<	nTopos++;
227	>	int jglob = AtomLocalToGlobal[j];
228	>
229	>	if (excludes->hasPair(iglob, jglob))
230	>	excludesForAtom[i].push_back(j);
231	>
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)) {
237	>	toposForAtom[i].push_back(j);
238	>	topoDist[i].push_back(2);
239	>	} else {
240	>	if (oneFour->hasPair(iglob, jglob)) {
241	>	toposForAtom[i].push_back(j);
242	>	topoDist[i].push_back(3);
243	>	}
244	>	}
245		}
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	–	}
246		}
247	<	}
247	>	}
248	>
249	>	createGtypeCutoffMap();
250
251		}
252
253		void ForceMatrixDecomposition::createGtypeCutoffMap() {
254	<
254	>
255		RealType tol = 1e-6;
256		RealType rc;
257		int atid;
258		set<AtomType*> atypes = info_->getSimulatedAtomTypes();
259	<	vector<RealType> atypeCutoff;
260	<	atypeCutoff.resize( atypes.size() );
261	<
262	<	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
242	<	rc = interactionMan_->getSuggestedCutoffRadius(*at);
259	>	map<int, RealType> atypeCutoff;
260	>
261	>	for (set<AtomType*>::iterator at = atypes.begin();
262	>	at != atypes.end(); ++at){
263		atid = (*at)->getIdent();
264	<	atypeCutoff[atid] = rc;
264	>	if (userChoseCutoff_)
265	>	atypeCutoff[atid] = userCutoff_;
266	>	else
267	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
268		}
269
270		vector<RealType> gTypeCutoffs;
248	–
271		// first we do a single loop over the cutoff groups to find the
272		// largest cutoff for any atypes present in this group.
273		#ifdef IS_MPI
274		vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
275	+	groupRowToGtype.resize(nGroupsInRow_);
276		for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
277		vector<int> atomListRow = getAtomsInGroupRow(cg1);
278		for (vector<int>::iterator ia = atomListRow.begin();
#	Line 275 \| Line 298 \| namespace OpenMD {
298
299		}
300		vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
301	+	groupColToGtype.resize(nGroupsInCol_);
302		for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
303		vector<int> atomListCol = getAtomsInGroupColumn(cg2);
304		for (vector<int>::iterator jb = atomListCol.begin();
#	Line 298 \| Line 322 \| namespace OpenMD {
322		}
323		}
324		#else
325	+
326		vector<RealType> groupCutoff(nGroups_, 0.0);
327	+	groupToGtype.resize(nGroups_);
328		for (int cg1 = 0; cg1 < nGroups_; cg1++) {
329	+
330		groupCutoff[cg1] = 0.0;
331		vector<int> atomList = getAtomsInGroupRow(cg1);
332	+
333		for (vector<int>::iterator ia = atomList.begin();
334		ia != atomList.end(); ++ia) {
335		int atom1 = (*ia);
336	<	atid = identsLocal[atom1];
336	>	atid = idents[atom1];
337		if (atypeCutoff[atid] > groupCutoff[cg1]) {
338		groupCutoff[cg1] = atypeCutoff[atid];
339		}
#	Line 327 \| Line 355 \| namespace OpenMD {
355
356		// Now we find the maximum group cutoff value present in the simulation
357
358	<	vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
359	<	RealType groupMax = *groupMaxLoc;
358	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
359	>	gTypeCutoffs.end());
360
361		#ifdef IS_MPI
362	<	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
362	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
363	>	MPI::MAX);
364		#endif
365
366		RealType tradRcut = groupMax;
367
368		for (int i = 0; i < gTypeCutoffs.size(); i++) {
369	<	for (int j = 0; j < gTypeCutoffs.size(); j++) {
341	<
369	>	for (int j = 0; j < gTypeCutoffs.size(); j++) {
370		RealType thisRcut;
371		switch(cutoffPolicy_) {
372		case TRADITIONAL:
373		thisRcut = tradRcut;
374	+	break;
375		case MIX:
376		thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
377	+	break;
378		case MAX:
379		thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
380	+	break;
381		default:
382		sprintf(painCave.errMsg,
383		"ForceMatrixDecomposition::createGtypeCutoffMap "
384		"hit an unknown cutoff policy!\n");
385		painCave.severity = OPENMD_ERROR;
386		painCave.isFatal = 1;
387	<	simError();
387	>	simError();
388	>	break;
389		}
390
391		pair<int,int> key = make_pair(i,j);
#	Line 371 \| Line 403 \| namespace OpenMD {
403		if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
404		sprintf(painCave.errMsg,
405		"ForceMatrixDecomposition::createGtypeCutoffMap "
406	<	"user-specified rCut does not match computed group Cutoff\n");
406	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
407		painCave.severity = OPENMD_ERROR;
408		painCave.isFatal = 1;
409		simError();
#	Line 383 \| Line 415 \| namespace OpenMD {
415
416
417		groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
418	<	int i, j;
387	<
418	>	int i, j;
419		#ifdef IS_MPI
420		i = groupRowToGtype[cg1];
421		j = groupColToGtype[cg2];
422		#else
423		i = groupToGtype[cg1];
424		j = groupToGtype[cg2];
425	<	#endif
395	<
425	>	#endif
426		return gTypeCutoffMap[make_pair(i,j)];
427		}
428
429	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
430	+	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
431	+	if (toposForAtom[atom1][j] == atom2)
432	+	return topoDist[atom1][j];
433	+	}
434	+	return 0;
435	+	}
436
437		void ForceMatrixDecomposition::zeroWorkArrays() {
438	+	pairwisePot = 0.0;
439	+	embeddingPot = 0.0;
440
402	–	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403	–	longRangePot_[j] = 0.0;
404	–	}
405	–
441		#ifdef IS_MPI
442		if (storageLayout_ & DataStorage::dslForce) {
443		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 418 \| Line 453 \| namespace OpenMD {
453		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
454
455		fill(pot_col.begin(), pot_col.end(),
456	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422	<
423	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
456	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
457
458		if (storageLayout_ & DataStorage::dslParticlePot) {
459	<	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
460	<	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
459	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
460	>	0.0);
461	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
462	>	0.0);
463		}
464
465		if (storageLayout_ & DataStorage::dslDensity) {
#	Line 433 \| Line 468 \| namespace OpenMD {
468		}
469
470		if (storageLayout_ & DataStorage::dslFunctional) {
471	<	fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
472	<	fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
471	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
472	>	0.0);
473	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
474	>	0.0);
475		}
476
477		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
#	Line 444 \| Line 481 \| namespace OpenMD {
481		atomColData.functionalDerivative.end(), 0.0);
482		}
483
484	<	#else
485	<
484	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
485	>	fill(atomRowData.skippedCharge.begin(),
486	>	atomRowData.skippedCharge.end(), 0.0);
487	>	fill(atomColData.skippedCharge.begin(),
488	>	atomColData.skippedCharge.end(), 0.0);
489	>	}
490	>
491	>	#endif
492	>	// even in parallel, we need to zero out the local arrays:
493	>
494		if (storageLayout_ & DataStorage::dslParticlePot) {
495		fill(snap_->atomData.particlePot.begin(),
496		snap_->atomData.particlePot.end(), 0.0);
#	Line 463 \| Line 508 \| namespace OpenMD {
508		fill(snap_->atomData.functionalDerivative.begin(),
509		snap_->atomData.functionalDerivative.end(), 0.0);
510		}
511	<	#endif
511	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
512	>	fill(snap_->atomData.skippedCharge.begin(),
513	>	snap_->atomData.skippedCharge.end(), 0.0);
514	>	}
515
516		}
517
#	Line 500 \| Line 548 \| namespace OpenMD {
548		AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
549		atomColData.electroFrame);
550		}
551	+
552		#endif
553		}
554
#	Line 566 \| Line 615 \| namespace OpenMD {
615		AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
616		for (int i = 0; i < n; i++)
617		snap_->atomData.force[i] += frc_tmp[i];
618	<
570	<
618	>
619		if (storageLayout_ & DataStorage::dslTorque) {
620
621	<	int nt = snap_->atomData.force.size();
621	>	int nt = snap_->atomData.torque.size();
622		vector<Vector3d> trq_tmp(nt, V3Zero);
623
624		AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
625	<	for (int i = 0; i < n; i++) {
625	>	for (int i = 0; i < nt; i++) {
626		snap_->atomData.torque[i] += trq_tmp[i];
627		trq_tmp[i] = 0.0;
628		}
629
630		AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
631	<	for (int i = 0; i < n; i++)
631	>	for (int i = 0; i < nt; i++)
632		snap_->atomData.torque[i] += trq_tmp[i];
633	+	}
634	+
635	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
636	+
637	+	int ns = snap_->atomData.skippedCharge.size();
638	+	vector<RealType> skch_tmp(ns, 0.0);
639	+
640	+	AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
641	+	for (int i = 0; i < ns; i++) {
642	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
643	+	skch_tmp[i] = 0.0;
644	+	}
645	+
646	+	AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
647	+	for (int i = 0; i < ns; i++)
648	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
649		}
650
651		nLocal_ = snap_->getNumberOfAtoms();
#	Line 594 \| Line 658 \| namespace OpenMD {
658		AtomCommPotRow->scatter(pot_row, pot_temp);
659
660		for (int ii = 0; ii < pot_temp.size(); ii++ )
661	<	pot_local += pot_temp[ii];
661	>	pairwisePot += pot_temp[ii];
662
663		fill(pot_temp.begin(), pot_temp.end(),
664		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
#	Line 602 \| Line 666 \| namespace OpenMD {
666		AtomCommPotColumn->scatter(pot_col, pot_temp);
667
668		for (int ii = 0; ii < pot_temp.size(); ii++ )
669	<	pot_local += pot_temp[ii];
606	<
669	>	pairwisePot += pot_temp[ii];
670		#endif
671	+
672		}
673
674		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 679 \| Line 743 \| namespace OpenMD {
743		#ifdef IS_MPI
744		return massFactorsRow[atom1];
745		#else
746	<	return massFactorsLocal[atom1];
746	>	return massFactors[atom1];
747		#endif
748		}
749
#	Line 687 \| Line 751 \| namespace OpenMD {
751		#ifdef IS_MPI
752		return massFactorsCol[atom2];
753		#else
754	<	return massFactorsLocal[atom2];
754	>	return massFactors[atom2];
755		#endif
756
757		}
#	Line 705 \| Line 769 \| namespace OpenMD {
769		return d;
770		}
771
772	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
773	<	#ifdef IS_MPI
710	<	return skipsForRowAtom[atom1];
711	<	#else
712	<	return skipsForLocalAtom[atom1];
713	<	#endif
772	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
773	>	return excludesForAtom[atom1];
774		}
775
776		/**
777	<	* 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
777	>	* We need to exclude some overcounted interactions that result from
778		* the parallel decomposition.
779		*/
780		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
#	Line 737 \| Line 794 \| namespace OpenMD {
794		} else {
795		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
796		}
740	–	#else
741	–	// in the normal loop, the atom numbers are unique
742	–	unique_id_1 = atom1;
743	–	unique_id_2 = atom2;
797		#endif
798	<
746	<	#ifdef IS_MPI
747	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748	<	i != skipsForRowAtom[atom1].end(); ++i) {
749	<	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
798	>	return false;
799		}
800
801	<	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
801	>	/**
802	>	* We need to handle the interactions for atoms who are involved in
803	>	* the same rigid body as well as some short range interactions
804	>	* (bonds, bends, torsions) differently from other interactions.
805	>	* We'll still visit the pairwise routines, but with a flag that
806	>	* tells those routines to exclude the pair from direct long range
807	>	* interactions. Some indirect interactions (notably reaction
808	>	* field) must still be handled for these pairs.
809	>	*/
810	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
811	>	int unique_id_2;
812
813		#ifdef IS_MPI
814	<	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
815	<	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
764	<	}
814	>	// in MPI, we have to look up the unique IDs for the row atom.
815	>	unique_id_2 = AtomColToGlobal[atom2];
816		#else
817	<	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
818	<	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
768	<	}
817	>	// in the normal loop, the atom numbers are unique
818	>	unique_id_2 = atom2;
819		#endif
820	+
821	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
822	+	i != excludesForAtom[atom1].end(); ++i) {
823	+	if ( (*i) == unique_id_2 ) return true;
824	+	}
825
826	<	// zero is default for unconnected (i.e. normal) pair interactions
772	<	return 0;
826	>	return false;
827		}
828
829	+
830		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
831		#ifdef IS_MPI
832		atomRowData.force[atom1] += fg;
#	Line 789 \| Line 844 \| namespace OpenMD {
844		}
845
846		// filling interaction blocks with pointers
847	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
848	<	InteractionData idat;
847	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
848	>	int atom1, int atom2) {
849
850	+	idat.excluded = excludeAtomPair(atom1, atom2);
851	+
852		#ifdef IS_MPI
853	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
854	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
855	+	// ff_->getAtomType(identsCol[atom2]) );
856
797	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
798	–	ff_->getAtomType(identsCol[atom2]) );
799	–
800	–
857		if (storageLayout_ & DataStorage::dslAmat) {
858		idat.A1 = &(atomRowData.aMat[atom1]);
859		idat.A2 = &(atomColData.aMat[atom2]);
#	Line 831 \| Line 887 \| namespace OpenMD {
887		if (storageLayout_ & DataStorage::dslParticlePot) {
888		idat.particlePot1 = &(atomRowData.particlePot[atom1]);
889		idat.particlePot2 = &(atomColData.particlePot[atom2]);
890	+	}
891	+
892	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
893	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
894	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
895		}
896
897		#else
898
899	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
900	<	ff_->getAtomType(identsLocal[atom2]) );
899	>	idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
900	>	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
901	>	// ff_->getAtomType(idents[atom2]) );
902
903		if (storageLayout_ & DataStorage::dslAmat) {
904		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 853 \| Line 915 \| namespace OpenMD {
915		idat.t2 = &(snap_->atomData.torque[atom2]);
916		}
917
918	<	if (storageLayout_ & DataStorage::dslDensity) {
918	>	if (storageLayout_ & DataStorage::dslDensity) {
919		idat.rho1 = &(snap_->atomData.density[atom1]);
920		idat.rho2 = &(snap_->atomData.density[atom2]);
921		}
#	Line 873 \| Line 935 \| namespace OpenMD {
935		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
936		}
937
938	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
939	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
940	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
941	+	}
942		#endif
877	–	return idat;
943		}
944
945
946	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
946	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
947		#ifdef IS_MPI
948		pot_row[atom1] += 0.5 * *(idat.pot);
949		pot_col[atom2] += 0.5 * *(idat.pot);
#	Line 886 \| Line 951 \| namespace OpenMD {
951		atomRowData.force[atom1] += *(idat.f1);
952		atomColData.force[atom2] -= *(idat.f1);
953		#else
954	<	longRangePot_ += *(idat.pot);
955	<
954	>	pairwisePot += *(idat.pot);
955	>
956		snap_->atomData.force[atom1] += *(idat.f1);
957		snap_->atomData.force[atom2] -= *(idat.f1);
958		#endif
959	<
959	>
960		}
961
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
926	–	}
927	–
962		/*
963		* buildNeighborList
964		*
#	Line 935 \| Line 969 \| namespace OpenMD {
969
970		vector<pair<int, int> > neighborList;
971		groupCutoffs cuts;
972	+	bool doAllPairs = false;
973	+
974		#ifdef IS_MPI
975		cellListRow_.clear();
976		cellListCol_.clear();
#	Line 954 \| Line 990 \| namespace OpenMD {
990		nCells_.y() = (int) ( Hy.length() )/ rList_;
991		nCells_.z() = (int) ( Hz.length() )/ rList_;
992
993	+	// handle small boxes where the cell offsets can end up repeating cells
994	+
995	+	if (nCells_.x() < 3) doAllPairs = true;
996	+	if (nCells_.y() < 3) doAllPairs = true;
997	+	if (nCells_.z() < 3) doAllPairs = true;
998	+
999		Mat3x3d invHmat = snap_->getInvHmat();
1000		Vector3d rs, scaled, dr;
1001		Vector3i whichCell;
1002		int cellIndex;
1003	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1004
1005		#ifdef IS_MPI
1006	<	for (int i = 0; i < nGroupsInRow_; i++) {
1007	<	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	<	}
1006	>	cellListRow_.resize(nCtot);
1007	>	cellListCol_.resize(nCtot);
1008		#else
1009	<	for (int i = 0; i < nGroups_; i++) {
1004	<	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]);
1011	<
1012	<	// find xyz-indices of cell that cutoffGroup is in.
1013	<	whichCell.x() = nCells_.x() * scaled.x();
1014	<	whichCell.y() = nCells_.y() * scaled.y();
1015	<	whichCell.z() = nCells_.z() * scaled.z();
1016	<
1017	<	// find single index of this cell:
1018	<	cellIndex = Vlinear(whichCell, nCells_);
1019	<	// add this cutoff group to the list of groups in this cell;
1020	<	cellList_[cellIndex].push_back(i);
1021	<	}
1009	>	cellList_.resize(nCtot);
1010		#endif
1011
1012	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1013	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1026	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1027	<	Vector3i m1v(m1x, m1y, m1z);
1028	<	int m1 = Vlinear(m1v, nCells_);
1012	>	if (!doAllPairs) {
1013	>	#ifdef IS_MPI
1014
1015	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1016	<	os != cellOffsets_.end(); ++os) {
1017	<
1018	<	Vector3i m2v = m1v + (*os);
1019	<
1020	<	if (m2v.x() >= nCells_.x()) {
1021	<	m2v.x() = 0;
1022	<	} else if (m2v.x() < 0) {
1023	<	m2v.x() = nCells_.x() - 1;
1024	<	}
1025	<
1026	<	if (m2v.y() >= nCells_.y()) {
1027	<	m2v.y() = 0;
1028	<	} else if (m2v.y() < 0) {
1029	<	m2v.y() = nCells_.y() - 1;
1030	<	}
1031	<
1032	<	if (m2v.z() >= nCells_.z()) {
1033	<	m2v.z() = 0;
1034	<	} else if (m2v.z() < 0) {
1035	<	m2v.z() = nCells_.z() - 1;
1036	<	}
1037	<
1038	<	int m2 = Vlinear (m2v, nCells_);
1015	>	for (int i = 0; i < nGroupsInRow_; i++) {
1016	>	rs = cgRowData.position[i];
1017	>
1018	>	// scaled positions relative to the box vectors
1019	>	scaled = invHmat * rs;
1020	>
1021	>	// wrap the vector back into the unit box by subtracting integer box
1022	>	// numbers
1023	>	for (int j = 0; j < 3; j++) {
1024	>	scaled[j] -= roundMe(scaled[j]);
1025	>	scaled[j] += 0.5;
1026	>	}
1027	>
1028	>	// find xyz-indices of cell that cutoffGroup is in.
1029	>	whichCell.x() = nCells_.x() * scaled.x();
1030	>	whichCell.y() = nCells_.y() * scaled.y();
1031	>	whichCell.z() = nCells_.z() * scaled.z();
1032	>
1033	>	// find single index of this cell:
1034	>	cellIndex = Vlinear(whichCell, nCells_);
1035	>
1036	>	// add this cutoff group to the list of groups in this cell;
1037	>	cellListRow_[cellIndex].push_back(i);
1038	>	}
1039	>
1040	>	for (int i = 0; i < nGroupsInCol_; i++) {
1041	>	rs = cgColData.position[i];
1042	>
1043	>	// scaled positions relative to the box vectors
1044	>	scaled = invHmat * rs;
1045	>
1046	>	// wrap the vector back into the unit box by subtracting integer box
1047	>	// numbers
1048	>	for (int j = 0; j < 3; j++) {
1049	>	scaled[j] -= roundMe(scaled[j]);
1050	>	scaled[j] += 0.5;
1051	>	}
1052	>
1053	>	// find xyz-indices of cell that cutoffGroup is in.
1054	>	whichCell.x() = nCells_.x() * scaled.x();
1055	>	whichCell.y() = nCells_.y() * scaled.y();
1056	>	whichCell.z() = nCells_.z() * scaled.z();
1057	>
1058	>	// find single index of this cell:
1059	>	cellIndex = Vlinear(whichCell, nCells_);
1060	>
1061	>	// add this cutoff group to the list of groups in this cell;
1062	>	cellListCol_[cellIndex].push_back(i);
1063	>	}
1064	>	#else
1065	>	for (int i = 0; i < nGroups_; i++) {
1066	>	rs = snap_->cgData.position[i];
1067	>
1068	>	// scaled positions relative to the box vectors
1069	>	scaled = invHmat * rs;
1070	>
1071	>	// wrap the vector back into the unit box by subtracting integer box
1072	>	// numbers
1073	>	for (int j = 0; j < 3; j++) {
1074	>	scaled[j] -= roundMe(scaled[j]);
1075	>	scaled[j] += 0.5;
1076	>	}
1077	>
1078	>	// find xyz-indices of cell that cutoffGroup is in.
1079	>	whichCell.x() = nCells_.x() * scaled.x();
1080	>	whichCell.y() = nCells_.y() * scaled.y();
1081	>	whichCell.z() = nCells_.z() * scaled.z();
1082	>
1083	>	// find single index of this cell:
1084	>	cellIndex = Vlinear(whichCell, nCells_);
1085	>
1086	>	// add this cutoff group to the list of groups in this cell;
1087	>	cellList_[cellIndex].push_back(i);
1088	>	}
1089	>	#endif
1090
1091	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1092	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1093	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1094	+	Vector3i m1v(m1x, m1y, m1z);
1095	+	int m1 = Vlinear(m1v, nCells_);
1096	+
1097	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1098	+	os != cellOffsets_.end(); ++os) {
1099	+
1100	+	Vector3i m2v = m1v + (*os);
1101	+
1102	+	if (m2v.x() >= nCells_.x()) {
1103	+	m2v.x() = 0;
1104	+	} else if (m2v.x() < 0) {
1105	+	m2v.x() = nCells_.x() - 1;
1106	+	}
1107	+
1108	+	if (m2v.y() >= nCells_.y()) {
1109	+	m2v.y() = 0;
1110	+	} else if (m2v.y() < 0) {
1111	+	m2v.y() = nCells_.y() - 1;
1112	+	}
1113	+
1114	+	if (m2v.z() >= nCells_.z()) {
1115	+	m2v.z() = 0;
1116	+	} else if (m2v.z() < 0) {
1117	+	m2v.z() = nCells_.z() - 1;
1118	+	}
1119	+
1120	+	int m2 = Vlinear (m2v, nCells_);
1121	+
1122		#ifdef IS_MPI
1123	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1124	<	j1 != cellListRow_[m1].end(); ++j1) {
1125	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1126	<	j2 != cellListCol_[m2].end(); ++j2) {
1127	<
1128	<	// Always do this if we're in different cells or if
1129	<	// we're in the same cell and the global index of the
1130	<	// j2 cutoff group is less than the j1 cutoff group
1131	<
1132	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1133	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1134	<	snap_->wrapVector(dr);
1135	<	cuts = getGroupCutoffs( (j1), (j2) );
1136	<	if (dr.lengthSquare() < cuts.third) {
1137	<	neighborList.push_back(make_pair((j1), (j2)));
1123	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1124	>	j1 != cellListRow_[m1].end(); ++j1) {
1125	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1126	>	j2 != cellListCol_[m2].end(); ++j2) {
1127	>
1128	>	// Always do this if we're in different cells or if
1129	>	// we're in the same cell and the global index of the
1130	>	// j2 cutoff group is less than the j1 cutoff group
1131	>
1132	>	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1133	>	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1134	>	snap_->wrapVector(dr);
1135	>	cuts = getGroupCutoffs( (j1), (j2) );
1136	>	if (dr.lengthSquare() < cuts.third) {
1137	>	neighborList.push_back(make_pair((j1), (j2)));
1138	>	}
1139		}
1140		}
1141		}
1074	–	}
1142		#else
1143	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1144	<	j1 != cellList_[m1].end(); ++j1) {
1145	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1146	<	j2 != cellList_[m2].end(); ++j2) {
1147	<
1148	<	// Always do this if we're in different cells or if
1149	<	// we're in the same cell and the global index of the
1150	<	// j2 cutoff group is less than the j1 cutoff group
1151	<
1152	<	if (m2 != m1 \|\| (j2) < (j1)) {
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)));
1143	>
1144	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1145	>	j1 != cellList_[m1].end(); ++j1) {
1146	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1147	>	j2 != cellList_[m2].end(); ++j2) {
1148	>
1149	>	// Always do this if we're in different cells or if
1150	>	// we're in the same cell and the global index of the
1151	>	// j2 cutoff group is less than the j1 cutoff group
1152	>
1153	>	if (m2 != m1 \|\| (j2) < (j1)) {
1154	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1155	>	snap_->wrapVector(dr);
1156	>	cuts = getGroupCutoffs( (j1), (j2) );
1157	>	if (dr.lengthSquare() < cuts.third) {
1158	>	neighborList.push_back(make_pair((j1), (j2)));
1159	>	}
1160		}
1161		}
1162		}
1094	–	}
1163		#endif
1164	+	}
1165		}
1166		}
1167		}
1168	+	} else {
1169	+	// branch to do all cutoff group pairs
1170	+	#ifdef IS_MPI
1171	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1172	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1173	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1174	+	snap_->wrapVector(dr);
1175	+	cuts = getGroupCutoffs( j1, j2 );
1176	+	if (dr.lengthSquare() < cuts.third) {
1177	+	neighborList.push_back(make_pair(j1, j2));
1178	+	}
1179	+	}
1180	+	}
1181	+	#else
1182	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1183	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1184	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1185	+	snap_->wrapVector(dr);
1186	+	cuts = getGroupCutoffs( j1, j2 );
1187	+	if (dr.lengthSquare() < cuts.third) {
1188	+	neighborList.push_back(make_pair(j1, j2));
1189	+	}
1190	+	}
1191	+	}
1192	+	#endif
1193		}
1194	<
1194	>
1195		// save the local cutoff group positions for the check that is
1196		// done on each loop:
1197		saved_CG_positions_.clear();
1198		for (int i = 0; i < nGroups_; i++)
1199		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1200	<
1200	>
1201		return neighborList;
1202		}
1203		} //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 1591 by gezelter, Tue Jul 12 15:25:07 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 1591 by gezelter, Tue Jul 12 15:25:07 2011 UTC