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

Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1589 by gezelter, Sun Jul 10 16:05:34 2011 UTC

#	Line 57 \| Line 57 \| namespace OpenMD {
57		storageLayout_ = sman_->getStorageLayout();
58		ff_ = info_->getForceField();
59		nLocal_ = snap_->getNumberOfAtoms();
60	<	nGroups_ = snap_->getNumberOfCutoffGroups();
61	<
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 104 \| Line 106 \| namespace OpenMD {
106		cgColData.resize(nGroupsInCol_);
107		cgColData.setStorageLayout(DataStorage::dslPosition);
108
109	<	identsRow.reserve(nAtomsInRow_);
110	<	identsCol.reserve(nAtomsInCol_);
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	+	AtomRowToGlobal.resize(nAtomsInRow_);
117	+	AtomColToGlobal.resize(nAtomsInCol_);
118	+	cgRowToGlobal.resize(nGroupsInRow_);
119	+	cgColToGlobal.resize(nGroupsInCol_);
120	+	massFactorsRow.resize(nAtomsInRow_);
121	+	massFactorsCol.resize(nAtomsInCol_);
122	+	pot_row.resize(nAtomsInRow_);
123	+	pot_col.resize(nAtomsInCol_);
124	+
125		AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
126		AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
127
128		cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
129		cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
130
131	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
132	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
131	>	AtomCommRealRow->gather(massFactors, massFactorsRow);
132	>	AtomCommRealColumn->gather(massFactors, massFactorsCol);
133
134		groupListRow_.clear();
135	<	groupListRow_.reserve(nGroupsInRow_);
135	>	groupListRow_.resize(nGroupsInRow_);
136		for (int i = 0; i < nGroupsInRow_; i++) {
137		int gid = cgRowToGlobal[i];
138		for (int j = 0; j < nAtomsInRow_; j++) {
#	Line 131 \| Line 143 \| namespace OpenMD {
143		}
144
145		groupListCol_.clear();
146	<	groupListCol_.reserve(nGroupsInCol_);
146	>	groupListCol_.resize(nGroupsInCol_);
147		for (int i = 0; i < nGroupsInCol_; i++) {
148		int gid = cgColToGlobal[i];
149		for (int j = 0; j < nAtomsInCol_; j++) {
#	Line 141 \| Line 153 \| namespace OpenMD {
153		}
154		}
155
156	<	skipsForRowAtom.clear();
157	<	skipsForRowAtom.reserve(nAtomsInRow_);
156	>	excludesForAtom.clear();
157	>	excludesForAtom.resize(nAtomsInRow_);
158	>	toposForAtom.clear();
159	>	toposForAtom.resize(nAtomsInRow_);
160	>	topoDist.clear();
161	>	topoDist.resize(nAtomsInRow_);
162		for (int i = 0; i < nAtomsInRow_; i++) {
163		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	–	}
164
155	–	toposForRowAtom.clear();
156	–	toposForRowAtom.reserve(nAtomsInRow_);
157	–	for (int i = 0; i < nAtomsInRow_; i++) {
158	–	int iglob = AtomRowToGlobal[i];
159	–	int nTopos = 0;
165		for (int j = 0; j < nAtomsInCol_; j++) {
166	<	int jglob = AtomColToGlobal[j];
167	<	if (oneTwo.hasPair(iglob, jglob)) {
168	<	toposForRowAtom[i].push_back(j);
169	<	topoDistRow[i][nTopos] = 1;
170	<	nTopos++;
166	>	int jglob = AtomColToGlobal[j];
167	>
168	>	if (excludes->hasPair(iglob, jglob))
169	>	excludesForAtom[i].push_back(j);
170	>
171	>	if (oneTwo->hasPair(iglob, jglob)) {
172	>	toposForAtom[i].push_back(j);
173	>	topoDist[i].push_back(1);
174	>	} else {
175	>	if (oneThree->hasPair(iglob, jglob)) {
176	>	toposForAtom[i].push_back(j);
177	>	topoDist[i].push_back(2);
178	>	} else {
179	>	if (oneFour->hasPair(iglob, jglob)) {
180	>	toposForAtom[i].push_back(j);
181	>	topoDist[i].push_back(3);
182	>	}
183	>	}
184		}
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	–	}
185		}
186		}
187
188		#endif
189
190		groupList_.clear();
191	<	groupList_.reserve(nGroups_);
191	>	groupList_.resize(nGroups_);
192		for (int i = 0; i < nGroups_; i++) {
193		int gid = cgLocalToGlobal[i];
194		for (int j = 0; j < nLocal_; j++) {
195		int aid = AtomLocalToGlobal[j];
196	<	if (globalGroupMembership[aid] == gid)
196	>	if (globalGroupMembership[aid] == gid) {
197		groupList_[i].push_back(j);
198	+	}
199		}
200		}
201
202	<	skipsForLocalAtom.clear();
203	<	skipsForLocalAtom.reserve(nLocal_);
202	>	excludesForAtom.clear();
203	>	excludesForAtom.resize(nLocal_);
204	>	toposForAtom.clear();
205	>	toposForAtom.resize(nLocal_);
206	>	topoDist.clear();
207	>	topoDist.resize(nLocal_);
208
209		for (int i = 0; i < nLocal_; i++) {
210		int iglob = AtomLocalToGlobal[i];
211	+
212		for (int j = 0; j < nLocal_; j++) {
213	<	int jglob = AtomLocalToGlobal[j];
214	<	if (excludes.hasPair(iglob, jglob))
215	<	skipsForLocalAtom[i].push_back(j);
213	>	int jglob = AtomLocalToGlobal[j];
214	>
215	>	if (excludes->hasPair(iglob, jglob))
216	>	excludesForAtom[i].push_back(j);
217	>
218	>	if (oneTwo->hasPair(iglob, jglob)) {
219	>	toposForAtom[i].push_back(j);
220	>	topoDist[i].push_back(1);
221	>	} else {
222	>	if (oneThree->hasPair(iglob, jglob)) {
223	>	toposForAtom[i].push_back(j);
224	>	topoDist[i].push_back(2);
225	>	} else {
226	>	if (oneFour->hasPair(iglob, jglob)) {
227	>	toposForAtom[i].push_back(j);
228	>	topoDist[i].push_back(3);
229	>	}
230	>	}
231	>	}
232		}
233		}
234	+
235	+	createGtypeCutoffMap();
236
237	<	toposForLocalAtom.clear();
238	<	toposForLocalAtom.reserve(nLocal_);
239	<	for (int i = 0; i < nLocal_; i++) {
240	<	int iglob = AtomLocalToGlobal[i];
241	<	int nTopos = 0;
242	<	for (int j = 0; j < nLocal_; j++) {
243	<	int jglob = AtomLocalToGlobal[j];
244	<	if (oneTwo.hasPair(iglob, jglob)) {
245	<	toposForLocalAtom[i].push_back(j);
246	<	topoDistLocal[i][nTopos] = 1;
247	<	nTopos++;
237	>	}
238	>
239	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
240	>
241	>	RealType tol = 1e-6;
242	>	RealType rc;
243	>	int atid;
244	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
245	>	map<int, RealType> atypeCutoff;
246	>
247	>	for (set<AtomType*>::iterator at = atypes.begin();
248	>	at != atypes.end(); ++at){
249	>	atid = (*at)->getIdent();
250	>	if (userChoseCutoff_)
251	>	atypeCutoff[atid] = userCutoff_;
252	>	else
253	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
254	>	}
255	>
256	>	vector<RealType> gTypeCutoffs;
257	>	// first we do a single loop over the cutoff groups to find the
258	>	// largest cutoff for any atypes present in this group.
259	>	#ifdef IS_MPI
260	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
261	>	groupRowToGtype.resize(nGroupsInRow_);
262	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
263	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
264	>	for (vector<int>::iterator ia = atomListRow.begin();
265	>	ia != atomListRow.end(); ++ia) {
266	>	int atom1 = (*ia);
267	>	atid = identsRow[atom1];
268	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
269	>	groupCutoffRow[cg1] = atypeCutoff[atid];
270		}
271	<	if (oneThree.hasPair(iglob, jglob)) {
272	<	toposForLocalAtom[i].push_back(j);
273	<	topoDistLocal[i][nTopos] = 2;
274	<	nTopos++;
271	>	}
272	>
273	>	bool gTypeFound = false;
274	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
275	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
276	>	groupRowToGtype[cg1] = gt;
277	>	gTypeFound = true;
278	>	}
279	>	}
280	>	if (!gTypeFound) {
281	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
282	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
283	>	}
284	>
285	>	}
286	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
287	>	groupColToGtype.resize(nGroupsInCol_);
288	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
289	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
290	>	for (vector<int>::iterator jb = atomListCol.begin();
291	>	jb != atomListCol.end(); ++jb) {
292	>	int atom2 = (*jb);
293	>	atid = identsCol[atom2];
294	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
295	>	groupCutoffCol[cg2] = atypeCutoff[atid];
296		}
297	<	if (oneFour.hasPair(iglob, jglob)) {
298	<	toposForLocalAtom[i].push_back(j);
299	<	topoDistLocal[i][nTopos] = 3;
300	<	nTopos++;
297	>	}
298	>	bool gTypeFound = false;
299	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
300	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
301	>	groupColToGtype[cg2] = gt;
302	>	gTypeFound = true;
303	>	}
304	>	}
305	>	if (!gTypeFound) {
306	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
307	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
308	>	}
309	>	}
310	>	#else
311	>
312	>	vector<RealType> groupCutoff(nGroups_, 0.0);
313	>	groupToGtype.resize(nGroups_);
314	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
315	>
316	>	groupCutoff[cg1] = 0.0;
317	>	vector<int> atomList = getAtomsInGroupRow(cg1);
318	>
319	>	for (vector<int>::iterator ia = atomList.begin();
320	>	ia != atomList.end(); ++ia) {
321	>	int atom1 = (*ia);
322	>	atid = idents[atom1];
323	>	if (atypeCutoff[atid] > groupCutoff[cg1]) {
324	>	groupCutoff[cg1] = atypeCutoff[atid];
325		}
326	+	}
327	+
328	+	bool gTypeFound = false;
329	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
330	+	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
331	+	groupToGtype[cg1] = gt;
332	+	gTypeFound = true;
333	+	}
334	+	}
335	+	if (!gTypeFound) {
336	+	gTypeCutoffs.push_back( groupCutoff[cg1] );
337	+	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
338		}
339		}
340	+	#endif
341	+
342	+	// Now we find the maximum group cutoff value present in the simulation
343	+
344	+	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
345	+
346	+	#ifdef IS_MPI
347	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
348	+	#endif
349	+
350	+	RealType tradRcut = groupMax;
351	+
352	+	for (int i = 0; i < gTypeCutoffs.size(); i++) {
353	+	for (int j = 0; j < gTypeCutoffs.size(); j++) {
354	+	RealType thisRcut;
355	+	switch(cutoffPolicy_) {
356	+	case TRADITIONAL:
357	+	thisRcut = tradRcut;
358	+	break;
359	+	case MIX:
360	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
361	+	break;
362	+	case MAX:
363	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
364	+	break;
365	+	default:
366	+	sprintf(painCave.errMsg,
367	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
368	+	"hit an unknown cutoff policy!\n");
369	+	painCave.severity = OPENMD_ERROR;
370	+	painCave.isFatal = 1;
371	+	simError();
372	+	break;
373	+	}
374	+
375	+	pair<int,int> key = make_pair(i,j);
376	+	gTypeCutoffMap[key].first = thisRcut;
377	+
378	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
379	+
380	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
381	+
382	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
383	+
384	+	// sanity check
385	+
386	+	if (userChoseCutoff_) {
387	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
388	+	sprintf(painCave.errMsg,
389	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
390	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
391	+	painCave.severity = OPENMD_ERROR;
392	+	painCave.isFatal = 1;
393	+	simError();
394	+	}
395	+	}
396	+	}
397	+	}
398		}
230	–
231	–	void ForceMatrixDecomposition::zeroWorkArrays() {
399
400	<	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
401	<	longRangePot_[j] = 0.0;
400	>
401	>	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
402	>	int i, j;
403	>	#ifdef IS_MPI
404	>	i = groupRowToGtype[cg1];
405	>	j = groupColToGtype[cg2];
406	>	#else
407	>	i = groupToGtype[cg1];
408	>	j = groupToGtype[cg2];
409	>	#endif
410	>	return gTypeCutoffMap[make_pair(i,j)];
411	>	}
412	>
413	>	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
414	>	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
415	>	if (toposForAtom[atom1][j] == atom2)
416	>	return topoDist[atom1][j];
417		}
418	+	return 0;
419	+	}
420
421	+	void ForceMatrixDecomposition::zeroWorkArrays() {
422	+	pairwisePot = 0.0;
423	+	embeddingPot = 0.0;
424	+
425		#ifdef IS_MPI
426		if (storageLayout_ & DataStorage::dslForce) {
427		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 249 \| Line 437 \| namespace OpenMD {
437		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
438
439		fill(pot_col.begin(), pot_col.end(),
440	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
253	<
254	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
440	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
441
442		if (storageLayout_ & DataStorage::dslParticlePot) {
443		fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
#	Line 275 \| Line 461 \| namespace OpenMD {
461		atomColData.functionalDerivative.end(), 0.0);
462		}
463
464	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
465	+	fill(atomRowData.skippedCharge.begin(),
466	+	atomRowData.skippedCharge.end(), 0.0);
467	+	fill(atomColData.skippedCharge.begin(),
468	+	atomColData.skippedCharge.end(), 0.0);
469	+	}
470	+
471		#else
472
473		if (storageLayout_ & DataStorage::dslParticlePot) {
#	Line 294 \| Line 487 \| namespace OpenMD {
487		fill(snap_->atomData.functionalDerivative.begin(),
488		snap_->atomData.functionalDerivative.end(), 0.0);
489		}
490	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
491	+	fill(snap_->atomData.skippedCharge.begin(),
492	+	snap_->atomData.skippedCharge.end(), 0.0);
493	+	}
494		#endif
495
496		}
#	Line 401 \| Line 598 \| namespace OpenMD {
598
599		if (storageLayout_ & DataStorage::dslTorque) {
600
601	<	int nt = snap_->atomData.force.size();
601	>	int nt = snap_->atomData.torque.size();
602		vector<Vector3d> trq_tmp(nt, V3Zero);
603
604		AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
605	<	for (int i = 0; i < n; i++) {
605	>	for (int i = 0; i < nt; i++) {
606		snap_->atomData.torque[i] += trq_tmp[i];
607		trq_tmp[i] = 0.0;
608		}
609
610		AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
611	<	for (int i = 0; i < n; i++)
611	>	for (int i = 0; i < nt; i++)
612		snap_->atomData.torque[i] += trq_tmp[i];
613	+	}
614	+
615	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
616	+
617	+	int ns = snap_->atomData.skippedCharge.size();
618	+	vector<RealType> skch_tmp(ns, 0.0);
619	+
620	+	AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
621	+	for (int i = 0; i < ns; i++) {
622	+	snap_->atomData.skippedCharge[i] = skch_tmp[i];
623	+	skch_tmp[i] = 0.0;
624	+	}
625	+
626	+	AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
627	+	for (int i = 0; i < ns; i++)
628	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
629		}
630
631		nLocal_ = snap_->getNumberOfAtoms();
#	Line 425 \| Line 638 \| namespace OpenMD {
638		AtomCommPotRow->scatter(pot_row, pot_temp);
639
640		for (int ii = 0; ii < pot_temp.size(); ii++ )
641	<	pot_local += pot_temp[ii];
641	>	pairwisePot += pot_temp[ii];
642
643		fill(pot_temp.begin(), pot_temp.end(),
644		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
#	Line 433 \| Line 646 \| namespace OpenMD {
646		AtomCommPotColumn->scatter(pot_col, pot_temp);
647
648		for (int ii = 0; ii < pot_temp.size(); ii++ )
649	<	pot_local += pot_temp[ii];
437	<
649	>	pairwisePot += pot_temp[ii];
650		#endif
651	+
652		}
653
654		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 510 \| Line 723 \| namespace OpenMD {
723		#ifdef IS_MPI
724		return massFactorsRow[atom1];
725		#else
726	<	return massFactorsLocal[atom1];
726	>	return massFactors[atom1];
727		#endif
728		}
729
#	Line 518 \| Line 731 \| namespace OpenMD {
731		#ifdef IS_MPI
732		return massFactorsCol[atom2];
733		#else
734	<	return massFactorsLocal[atom2];
734	>	return massFactors[atom2];
735		#endif
736
737		}
#	Line 536 \| Line 749 \| namespace OpenMD {
749		return d;
750		}
751
752	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
753	<	#ifdef IS_MPI
541	<	return skipsForRowAtom[atom1];
542	<	#else
543	<	return skipsForLocalAtom[atom1];
544	<	#endif
752	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
753	>	return excludesForAtom[atom1];
754		}
755
756		/**
757	<	* There are a number of reasons to skip a pair or a
549	<	* particle. Mostly we do this to exclude atoms who are involved in
550	<	* short range interactions (bonds, bends, torsions), but we also
551	<	* need to exclude some overcounted interactions that result from
757	>	* We need to exclude some overcounted interactions that result from
758		* the parallel decomposition.
759		*/
760		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
#	Line 568 \| Line 774 \| namespace OpenMD {
774		} else {
775		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
776		}
777	+	#endif
778	+	return false;
779	+	}
780	+
781	+	/**
782	+	* We need to handle the interactions for atoms who are involved in
783	+	* the same rigid body as well as some short range interactions
784	+	* (bonds, bends, torsions) differently from other interactions.
785	+	* We'll still visit the pairwise routines, but with a flag that
786	+	* tells those routines to exclude the pair from direct long range
787	+	* interactions. Some indirect interactions (notably reaction
788	+	* field) must still be handled for these pairs.
789	+	*/
790	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
791	+	int unique_id_2;
792	+
793	+	#ifdef IS_MPI
794	+	// in MPI, we have to look up the unique IDs for the row atom.
795	+	unique_id_2 = AtomColToGlobal[atom2];
796		#else
797		// in the normal loop, the atom numbers are unique
573	–	unique_id_1 = atom1;
798		unique_id_2 = atom2;
799		#endif
800
801	<	#ifdef IS_MPI
802	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
579	<	i != skipsForRowAtom[atom1].end(); ++i) {
801	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
802	>	i != excludesForAtom[atom1].end(); ++i) {
803		if ( (*i) == unique_id_2 ) return true;
581	–	}
582	–	#else
583	–	for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
584	–	i != skipsForLocalAtom[atom1].end(); ++i) {
585	–	if ( (*i) == unique_id_2 ) return true;
586	–	}
587	–	#endif
588	–	}
589	–
590	–	int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
591	–
592	–	#ifdef IS_MPI
593	–	for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
594	–	if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
804		}
596	–	#else
597	–	for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
598	–	if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
599	–	}
600	–	#endif
805
806	<	// zero is default for unconnected (i.e. normal) pair interactions
603	<	return 0;
806	>	return false;
807		}
808
809	+
810		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
811		#ifdef IS_MPI
812		atomRowData.force[atom1] += fg;
#	Line 620 \| Line 824 \| namespace OpenMD {
824		}
825
826		// filling interaction blocks with pointers
827	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
828	<	InteractionData idat;
827	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
828	>	int atom1, int atom2) {
829
830	+	idat.excluded = excludeAtomPair(atom1, atom2);
831	+
832		#ifdef IS_MPI
833
834		idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
835		ff_->getAtomType(identsCol[atom2]) );
630	–
836
837		if (storageLayout_ & DataStorage::dslAmat) {
838		idat.A1 = &(atomRowData.aMat[atom1]);
#	Line 664 \| Line 869 \| namespace OpenMD {
869		idat.particlePot2 = &(atomColData.particlePot[atom2]);
870		}
871
872	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
873	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
874	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
875	+	}
876	+
877		#else
878
879	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
880	<	ff_->getAtomType(identsLocal[atom2]) );
879	>	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
880	>	ff_->getAtomType(idents[atom2]) );
881
882		if (storageLayout_ & DataStorage::dslAmat) {
883		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 684 \| Line 894 \| namespace OpenMD {
894		idat.t2 = &(snap_->atomData.torque[atom2]);
895		}
896
897	<	if (storageLayout_ & DataStorage::dslDensity) {
897	>	if (storageLayout_ & DataStorage::dslDensity) {
898		idat.rho1 = &(snap_->atomData.density[atom1]);
899		idat.rho2 = &(snap_->atomData.density[atom2]);
900		}
#	Line 704 \| Line 914 \| namespace OpenMD {
914		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
915		}
916
917	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
918	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
919	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
920	+	}
921		#endif
708	–	return idat;
922		}
923
924
925	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
925	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
926		#ifdef IS_MPI
927		pot_row[atom1] += 0.5 * *(idat.pot);
928		pot_col[atom2] += 0.5 * *(idat.pot);
#	Line 717 \| Line 930 \| namespace OpenMD {
930		atomRowData.force[atom1] += *(idat.f1);
931		atomColData.force[atom2] -= *(idat.f1);
932		#else
933	<	longRangePot_ += *(idat.pot);
934	<
933	>	pairwisePot += *(idat.pot);
934	>
935		snap_->atomData.force[atom1] += *(idat.f1);
936		snap_->atomData.force[atom2] -= *(idat.f1);
937		#endif
938	<
938	>
939		}
940
728	–
729	–	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
730	–
731	–	InteractionData idat;
732	–	#ifdef IS_MPI
733	–	idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
734	–	ff_->getAtomType(identsCol[atom2]) );
735	–
736	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
737	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
738	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
739	–	}
740	–	if (storageLayout_ & DataStorage::dslTorque) {
741	–	idat.t1 = &(atomRowData.torque[atom1]);
742	–	idat.t2 = &(atomColData.torque[atom2]);
743	–	}
744	–	#else
745	–	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
746	–	ff_->getAtomType(identsLocal[atom2]) );
747	–
748	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
749	–	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
750	–	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
751	–	}
752	–	if (storageLayout_ & DataStorage::dslTorque) {
753	–	idat.t1 = &(snap_->atomData.torque[atom1]);
754	–	idat.t2 = &(snap_->atomData.torque[atom2]);
755	–	}
756	–	#endif
757	–	}
758	–
941		/*
942		* buildNeighborList
943		*
#	Line 765 \| Line 947 \| namespace OpenMD {
947		vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
948
949		vector<pair<int, int> > neighborList;
950	+	groupCutoffs cuts;
951	+	bool doAllPairs = false;
952	+
953		#ifdef IS_MPI
954		cellListRow_.clear();
955		cellListCol_.clear();
#	Line 772 \| Line 957 \| namespace OpenMD {
957		cellList_.clear();
958		#endif
959
960	<	// dangerous to not do error checking.
776	<	RealType rCut_;
777	<
778	<	RealType rList_ = (rCut_ + skinThickness_);
960	>	RealType rList_ = (largestRcut_ + skinThickness_);
961		RealType rl2 = rList_ * rList_;
962		Snapshot* snap_ = sman_->getCurrentSnapshot();
963		Mat3x3d Hmat = snap_->getHmat();
#	Line 787 \| Line 969 \| namespace OpenMD {
969		nCells_.y() = (int) ( Hy.length() )/ rList_;
970		nCells_.z() = (int) ( Hz.length() )/ rList_;
971
972	+	// handle small boxes where the cell offsets can end up repeating cells
973	+
974	+	if (nCells_.x() < 3) doAllPairs = true;
975	+	if (nCells_.y() < 3) doAllPairs = true;
976	+	if (nCells_.z() < 3) doAllPairs = true;
977	+
978		Mat3x3d invHmat = snap_->getInvHmat();
979		Vector3d rs, scaled, dr;
980		Vector3i whichCell;
981		int cellIndex;
982	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
983
984		#ifdef IS_MPI
985	<	for (int i = 0; i < nGroupsInRow_; i++) {
986	<	rs = cgRowData.position[i];
798	<	// scaled positions relative to the box vectors
799	<	scaled = invHmat * rs;
800	<	// wrap the vector back into the unit box by subtracting integer box
801	<	// numbers
802	<	for (int j = 0; j < 3; j++)
803	<	scaled[j] -= roundMe(scaled[j]);
804	<
805	<	// find xyz-indices of cell that cutoffGroup is in.
806	<	whichCell.x() = nCells_.x() * scaled.x();
807	<	whichCell.y() = nCells_.y() * scaled.y();
808	<	whichCell.z() = nCells_.z() * scaled.z();
809	<
810	<	// find single index of this cell:
811	<	cellIndex = Vlinear(whichCell, nCells_);
812	<	// add this cutoff group to the list of groups in this cell;
813	<	cellListRow_[cellIndex].push_back(i);
814	<	}
815	<
816	<	for (int i = 0; i < nGroupsInCol_; i++) {
817	<	rs = cgColData.position[i];
818	<	// scaled positions relative to the box vectors
819	<	scaled = invHmat * rs;
820	<	// wrap the vector back into the unit box by subtracting integer box
821	<	// numbers
822	<	for (int j = 0; j < 3; j++)
823	<	scaled[j] -= roundMe(scaled[j]);
824	<
825	<	// find xyz-indices of cell that cutoffGroup is in.
826	<	whichCell.x() = nCells_.x() * scaled.x();
827	<	whichCell.y() = nCells_.y() * scaled.y();
828	<	whichCell.z() = nCells_.z() * scaled.z();
829	<
830	<	// find single index of this cell:
831	<	cellIndex = Vlinear(whichCell, nCells_);
832	<	// add this cutoff group to the list of groups in this cell;
833	<	cellListCol_[cellIndex].push_back(i);
834	<	}
985	>	cellListRow_.resize(nCtot);
986	>	cellListCol_.resize(nCtot);
987		#else
988	<	for (int i = 0; i < nGroups_; i++) {
837	<	rs = snap_->cgData.position[i];
838	<	// scaled positions relative to the box vectors
839	<	scaled = invHmat * rs;
840	<	// wrap the vector back into the unit box by subtracting integer box
841	<	// numbers
842	<	for (int j = 0; j < 3; j++)
843	<	scaled[j] -= roundMe(scaled[j]);
844	<
845	<	// find xyz-indices of cell that cutoffGroup is in.
846	<	whichCell.x() = nCells_.x() * scaled.x();
847	<	whichCell.y() = nCells_.y() * scaled.y();
848	<	whichCell.z() = nCells_.z() * scaled.z();
849	<
850	<	// find single index of this cell:
851	<	cellIndex = Vlinear(whichCell, nCells_);
852	<	// add this cutoff group to the list of groups in this cell;
853	<	cellList_[cellIndex].push_back(i);
854	<	}
988	>	cellList_.resize(nCtot);
989		#endif
990
991	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
992	<	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
859	<	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
860	<	Vector3i m1v(m1x, m1y, m1z);
861	<	int m1 = Vlinear(m1v, nCells_);
991	>	if (!doAllPairs) {
992	>	#ifdef IS_MPI
993
994	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
995	<	os != cellOffsets_.end(); ++os) {
996	<
997	<	Vector3i m2v = m1v + (*os);
998	<
999	<	if (m2v.x() >= nCells_.x()) {
1000	<	m2v.x() = 0;
1001	<	} else if (m2v.x() < 0) {
1002	<	m2v.x() = nCells_.x() - 1;
1003	<	}
1004	<
1005	<	if (m2v.y() >= nCells_.y()) {
1006	<	m2v.y() = 0;
1007	<	} else if (m2v.y() < 0) {
1008	<	m2v.y() = nCells_.y() - 1;
1009	<	}
1010	<
1011	<	if (m2v.z() >= nCells_.z()) {
1012	<	m2v.z() = 0;
1013	<	} else if (m2v.z() < 0) {
1014	<	m2v.z() = nCells_.z() - 1;
1015	<	}
1016	<
1017	<	int m2 = Vlinear (m2v, nCells_);
994	>	for (int i = 0; i < nGroupsInRow_; i++) {
995	>	rs = cgRowData.position[i];
996	>
997	>	// scaled positions relative to the box vectors
998	>	scaled = invHmat * rs;
999	>
1000	>	// wrap the vector back into the unit box by subtracting integer box
1001	>	// numbers
1002	>	for (int j = 0; j < 3; j++) {
1003	>	scaled[j] -= roundMe(scaled[j]);
1004	>	scaled[j] += 0.5;
1005	>	}
1006	>
1007	>	// find xyz-indices of cell that cutoffGroup is in.
1008	>	whichCell.x() = nCells_.x() * scaled.x();
1009	>	whichCell.y() = nCells_.y() * scaled.y();
1010	>	whichCell.z() = nCells_.z() * scaled.z();
1011	>
1012	>	// find single index of this cell:
1013	>	cellIndex = Vlinear(whichCell, nCells_);
1014	>
1015	>	// add this cutoff group to the list of groups in this cell;
1016	>	cellListRow_[cellIndex].push_back(i);
1017	>	}
1018	>
1019	>	for (int i = 0; i < nGroupsInCol_; i++) {
1020	>	rs = cgColData.position[i];
1021	>
1022	>	// scaled positions relative to the box vectors
1023	>	scaled = invHmat * rs;
1024	>
1025	>	// wrap the vector back into the unit box by subtracting integer box
1026	>	// numbers
1027	>	for (int j = 0; j < 3; j++) {
1028	>	scaled[j] -= roundMe(scaled[j]);
1029	>	scaled[j] += 0.5;
1030	>	}
1031	>
1032	>	// find xyz-indices of cell that cutoffGroup is in.
1033	>	whichCell.x() = nCells_.x() * scaled.x();
1034	>	whichCell.y() = nCells_.y() * scaled.y();
1035	>	whichCell.z() = nCells_.z() * scaled.z();
1036	>
1037	>	// find single index of this cell:
1038	>	cellIndex = Vlinear(whichCell, nCells_);
1039	>
1040	>	// add this cutoff group to the list of groups in this cell;
1041	>	cellListCol_[cellIndex].push_back(i);
1042	>	}
1043	>	#else
1044	>	for (int i = 0; i < nGroups_; i++) {
1045	>	rs = snap_->cgData.position[i];
1046	>
1047	>	// scaled positions relative to the box vectors
1048	>	scaled = invHmat * rs;
1049	>
1050	>	// wrap the vector back into the unit box by subtracting integer box
1051	>	// numbers
1052	>	for (int j = 0; j < 3; j++) {
1053	>	scaled[j] -= roundMe(scaled[j]);
1054	>	scaled[j] += 0.5;
1055	>	}
1056	>
1057	>	// find xyz-indices of cell that cutoffGroup is in.
1058	>	whichCell.x() = nCells_.x() * scaled.x();
1059	>	whichCell.y() = nCells_.y() * scaled.y();
1060	>	whichCell.z() = nCells_.z() * scaled.z();
1061	>
1062	>	// find single index of this cell:
1063	>	cellIndex = Vlinear(whichCell, nCells_);
1064	>
1065	>	// add this cutoff group to the list of groups in this cell;
1066	>	cellList_[cellIndex].push_back(i);
1067	>	}
1068	>	#endif
1069
1070	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1071	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1072	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1073	+	Vector3i m1v(m1x, m1y, m1z);
1074	+	int m1 = Vlinear(m1v, nCells_);
1075	+
1076	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1077	+	os != cellOffsets_.end(); ++os) {
1078	+
1079	+	Vector3i m2v = m1v + (*os);
1080	+
1081	+	if (m2v.x() >= nCells_.x()) {
1082	+	m2v.x() = 0;
1083	+	} else if (m2v.x() < 0) {
1084	+	m2v.x() = nCells_.x() - 1;
1085	+	}
1086	+
1087	+	if (m2v.y() >= nCells_.y()) {
1088	+	m2v.y() = 0;
1089	+	} else if (m2v.y() < 0) {
1090	+	m2v.y() = nCells_.y() - 1;
1091	+	}
1092	+
1093	+	if (m2v.z() >= nCells_.z()) {
1094	+	m2v.z() = 0;
1095	+	} else if (m2v.z() < 0) {
1096	+	m2v.z() = nCells_.z() - 1;
1097	+	}
1098	+
1099	+	int m2 = Vlinear (m2v, nCells_);
1100	+
1101		#ifdef IS_MPI
1102	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1103	<	j1 != cellListRow_[m1].end(); ++j1) {
1104	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1105	<	j2 != cellListCol_[m2].end(); ++j2) {
1106	<
1107	<	// Always do this if we're in different cells or if
1108	<	// we're in the same cell and the global index of the
1109	<	// j2 cutoff group is less than the j1 cutoff group
1110	<
1111	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1112	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1113	<	snap_->wrapVector(dr);
1114	<	if (dr.lengthSquare() < rl2) {
1115	<	neighborList.push_back(make_pair((j1), (j2)));
1102	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1103	>	j1 != cellListRow_[m1].end(); ++j1) {
1104	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1105	>	j2 != cellListCol_[m2].end(); ++j2) {
1106	>
1107	>	// Always do this if we're in different cells or if
1108	>	// we're in the same cell and the global index of the
1109	>	// j2 cutoff group is less than the j1 cutoff group
1110	>
1111	>	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1112	>	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1113	>	snap_->wrapVector(dr);
1114	>	cuts = getGroupCutoffs( (j1), (j2) );
1115	>	if (dr.lengthSquare() < cuts.third) {
1116	>	neighborList.push_back(make_pair((j1), (j2)));
1117	>	}
1118		}
1119		}
1120		}
906	–	}
1121		#else
1122	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1123	<	j1 != cellList_[m1].end(); ++j1) {
1124	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1125	<	j2 != cellList_[m2].end(); ++j2) {
1126	<
1127	<	// Always do this if we're in different cells or if
1128	<	// we're in the same cell and the global index of the
1129	<	// j2 cutoff group is less than the j1 cutoff group
1130	<
1131	<	if (m2 != m1 \|\| (j2) < (j1)) {
1132	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1133	<	snap_->wrapVector(dr);
1134	<	if (dr.lengthSquare() < rl2) {
1135	<	neighborList.push_back(make_pair((j1), (j2)));
1122	>
1123	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1124	>	j1 != cellList_[m1].end(); ++j1) {
1125	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1126	>	j2 != cellList_[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 \|\| (j2) < (j1)) {
1133	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.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		}
925	–	}
1142		#endif
1143	+	}
1144		}
1145		}
1146		}
1147	+	} else {
1148	+	// branch to do all cutoff group pairs
1149	+	#ifdef IS_MPI
1150	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1151	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1152	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1153	+	snap_->wrapVector(dr);
1154	+	cuts = getGroupCutoffs( j1, j2 );
1155	+	if (dr.lengthSquare() < cuts.third) {
1156	+	neighborList.push_back(make_pair(j1, j2));
1157	+	}
1158	+	}
1159	+	}
1160	+	#else
1161	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1162	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1163	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1164	+	snap_->wrapVector(dr);
1165	+	cuts = getGroupCutoffs( j1, j2 );
1166	+	if (dr.lengthSquare() < cuts.third) {
1167	+	neighborList.push_back(make_pair(j1, j2));
1168	+	}
1169	+	}
1170	+	}
1171	+	#endif
1172		}
1173	<
1173	>
1174		// save the local cutoff group positions for the check that is
1175		// done on each loop:
1176		saved_CG_positions_.clear();
1177		for (int i = 0; i < nGroups_; i++)
1178		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1179	<
1179	>
1180		return neighborList;
1181		}
1182		} //end namespace OpenMD

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs. Revision 1589 by gezelter, Sun Jul 10 16:05:34 2011 UTC

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1589 by gezelter, Sun Jul 10 16:05:34 2011 UTC