[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 1588 by gezelter, Sat Jul 9 15:05:59 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	+	vector<int>::iterator it;
116	+	for (it = AtomLocalToGlobal.begin(); it != AtomLocalToGlobal.end(); ++it) {
117	+	cerr << "my AtomLocalToGlobal = " << (*it) << "\n";
118	+	}
119		AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
120		AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
121
122		cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
123		cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
124
125	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
126	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
125	>	AtomCommRealRow->gather(massFactors, massFactorsRow);
126	>	AtomCommRealColumn->gather(massFactors, massFactorsCol);
127
128		groupListRow_.clear();
129	<	groupListRow_.reserve(nGroupsInRow_);
129	>	groupListRow_.resize(nGroupsInRow_);
130		for (int i = 0; i < nGroupsInRow_; i++) {
131		int gid = cgRowToGlobal[i];
132		for (int j = 0; j < nAtomsInRow_; j++) {
#	Line 131 \| Line 137 \| namespace OpenMD {
137		}
138
139		groupListCol_.clear();
140	<	groupListCol_.reserve(nGroupsInCol_);
140	>	groupListCol_.resize(nGroupsInCol_);
141		for (int i = 0; i < nGroupsInCol_; i++) {
142		int gid = cgColToGlobal[i];
143		for (int j = 0; j < nAtomsInCol_; j++) {
#	Line 141 \| Line 147 \| namespace OpenMD {
147		}
148		}
149
150	<	skipsForRowAtom.clear();
151	<	skipsForRowAtom.reserve(nAtomsInRow_);
150	>	excludesForAtom.clear();
151	>	excludesForAtom.resize(nAtomsInRow_);
152	>	toposForAtom.clear();
153	>	toposForAtom.resize(nAtomsInRow_);
154	>	topoDist.clear();
155	>	topoDist.resize(nAtomsInRow_);
156		for (int i = 0; i < nAtomsInRow_; i++) {
157		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	–	}
158
155	–	toposForRowAtom.clear();
156	–	toposForRowAtom.reserve(nAtomsInRow_);
157	–	for (int i = 0; i < nAtomsInRow_; i++) {
158	–	int iglob = AtomRowToGlobal[i];
159	–	int nTopos = 0;
159		for (int j = 0; j < nAtomsInCol_; j++) {
160	<	int jglob = AtomColToGlobal[j];
161	<	if (oneTwo.hasPair(iglob, jglob)) {
162	<	toposForRowAtom[i].push_back(j);
163	<	topoDistRow[i][nTopos] = 1;
164	<	nTopos++;
160	>	int jglob = AtomColToGlobal[j];
161	>
162	>	if (excludes->hasPair(iglob, jglob))
163	>	excludesForAtom[i].push_back(j);
164	>
165	>	if (oneTwo->hasPair(iglob, jglob)) {
166	>	toposForAtom[i].push_back(j);
167	>	topoDist[i].push_back(1);
168	>	} else {
169	>	if (oneThree->hasPair(iglob, jglob)) {
170	>	toposForAtom[i].push_back(j);
171	>	topoDist[i].push_back(2);
172	>	} else {
173	>	if (oneFour->hasPair(iglob, jglob)) {
174	>	toposForAtom[i].push_back(j);
175	>	topoDist[i].push_back(3);
176	>	}
177	>	}
178		}
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	–	}
179		}
180		}
181
182		#endif
183
184		groupList_.clear();
185	<	groupList_.reserve(nGroups_);
185	>	groupList_.resize(nGroups_);
186		for (int i = 0; i < nGroups_; i++) {
187		int gid = cgLocalToGlobal[i];
188		for (int j = 0; j < nLocal_; j++) {
189		int aid = AtomLocalToGlobal[j];
190	<	if (globalGroupMembership[aid] == gid)
190	>	if (globalGroupMembership[aid] == gid) {
191		groupList_[i].push_back(j);
192	+	}
193		}
194		}
195
196	<	skipsForLocalAtom.clear();
197	<	skipsForLocalAtom.reserve(nLocal_);
196	>	excludesForAtom.clear();
197	>	excludesForAtom.resize(nLocal_);
198	>	toposForAtom.clear();
199	>	toposForAtom.resize(nLocal_);
200	>	topoDist.clear();
201	>	topoDist.resize(nLocal_);
202
203		for (int i = 0; i < nLocal_; i++) {
204		int iglob = AtomLocalToGlobal[i];
205	+
206		for (int j = 0; j < nLocal_; j++) {
207	<	int jglob = AtomLocalToGlobal[j];
208	<	if (excludes.hasPair(iglob, jglob))
209	<	skipsForLocalAtom[i].push_back(j);
207	>	int jglob = AtomLocalToGlobal[j];
208	>
209	>	if (excludes->hasPair(iglob, jglob))
210	>	excludesForAtom[i].push_back(j);
211	>
212	>	if (oneTwo->hasPair(iglob, jglob)) {
213	>	toposForAtom[i].push_back(j);
214	>	topoDist[i].push_back(1);
215	>	} else {
216	>	if (oneThree->hasPair(iglob, jglob)) {
217	>	toposForAtom[i].push_back(j);
218	>	topoDist[i].push_back(2);
219	>	} else {
220	>	if (oneFour->hasPair(iglob, jglob)) {
221	>	toposForAtom[i].push_back(j);
222	>	topoDist[i].push_back(3);
223	>	}
224	>	}
225	>	}
226		}
227		}
228	+
229	+	createGtypeCutoffMap();
230
231	<	toposForLocalAtom.clear();
232	<	toposForLocalAtom.reserve(nLocal_);
233	<	for (int i = 0; i < nLocal_; i++) {
234	<	int iglob = AtomLocalToGlobal[i];
235	<	int nTopos = 0;
236	<	for (int j = 0; j < nLocal_; j++) {
237	<	int jglob = AtomLocalToGlobal[j];
238	<	if (oneTwo.hasPair(iglob, jglob)) {
239	<	toposForLocalAtom[i].push_back(j);
240	<	topoDistLocal[i][nTopos] = 1;
241	<	nTopos++;
231	>	}
232	>
233	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
234	>
235	>	RealType tol = 1e-6;
236	>	RealType rc;
237	>	int atid;
238	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
239	>	map<int, RealType> atypeCutoff;
240	>
241	>	for (set<AtomType*>::iterator at = atypes.begin();
242	>	at != atypes.end(); ++at){
243	>	atid = (*at)->getIdent();
244	>	if (userChoseCutoff_)
245	>	atypeCutoff[atid] = userCutoff_;
246	>	else
247	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
248	>	}
249	>
250	>	vector<RealType> gTypeCutoffs;
251	>	// first we do a single loop over the cutoff groups to find the
252	>	// largest cutoff for any atypes present in this group.
253	>	#ifdef IS_MPI
254	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
255	>	groupRowToGtype.resize(nGroupsInRow_);
256	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
257	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
258	>	for (vector<int>::iterator ia = atomListRow.begin();
259	>	ia != atomListRow.end(); ++ia) {
260	>	int atom1 = (*ia);
261	>	atid = identsRow[atom1];
262	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
263	>	groupCutoffRow[cg1] = atypeCutoff[atid];
264		}
265	<	if (oneThree.hasPair(iglob, jglob)) {
266	<	toposForLocalAtom[i].push_back(j);
267	<	topoDistLocal[i][nTopos] = 2;
268	<	nTopos++;
265	>	}
266	>
267	>	bool gTypeFound = false;
268	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
269	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
270	>	groupRowToGtype[cg1] = gt;
271	>	gTypeFound = true;
272	>	}
273	>	}
274	>	if (!gTypeFound) {
275	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
276	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
277	>	}
278	>
279	>	}
280	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
281	>	groupColToGtype.resize(nGroupsInCol_);
282	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
283	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
284	>	for (vector<int>::iterator jb = atomListCol.begin();
285	>	jb != atomListCol.end(); ++jb) {
286	>	int atom2 = (*jb);
287	>	atid = identsCol[atom2];
288	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
289	>	groupCutoffCol[cg2] = atypeCutoff[atid];
290		}
291	<	if (oneFour.hasPair(iglob, jglob)) {
292	<	toposForLocalAtom[i].push_back(j);
293	<	topoDistLocal[i][nTopos] = 3;
294	<	nTopos++;
291	>	}
292	>	bool gTypeFound = false;
293	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
294	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
295	>	groupColToGtype[cg2] = gt;
296	>	gTypeFound = true;
297	>	}
298	>	}
299	>	if (!gTypeFound) {
300	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
301	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
302	>	}
303	>	}
304	>	#else
305	>
306	>	vector<RealType> groupCutoff(nGroups_, 0.0);
307	>	groupToGtype.resize(nGroups_);
308	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
309	>
310	>	groupCutoff[cg1] = 0.0;
311	>	vector<int> atomList = getAtomsInGroupRow(cg1);
312	>
313	>	for (vector<int>::iterator ia = atomList.begin();
314	>	ia != atomList.end(); ++ia) {
315	>	int atom1 = (*ia);
316	>	atid = idents[atom1];
317	>	if (atypeCutoff[atid] > groupCutoff[cg1]) {
318	>	groupCutoff[cg1] = atypeCutoff[atid];
319		}
320	+	}
321	+
322	+	bool gTypeFound = false;
323	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
324	+	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
325	+	groupToGtype[cg1] = gt;
326	+	gTypeFound = true;
327	+	}
328	+	}
329	+	if (!gTypeFound) {
330	+	gTypeCutoffs.push_back( groupCutoff[cg1] );
331	+	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
332		}
333		}
334	+	#endif
335	+
336	+	// Now we find the maximum group cutoff value present in the simulation
337	+
338	+	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
339	+
340	+	#ifdef IS_MPI
341	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
342	+	#endif
343	+
344	+	RealType tradRcut = groupMax;
345	+
346	+	for (int i = 0; i < gTypeCutoffs.size(); i++) {
347	+	for (int j = 0; j < gTypeCutoffs.size(); j++) {
348	+	RealType thisRcut;
349	+	switch(cutoffPolicy_) {
350	+	case TRADITIONAL:
351	+	thisRcut = tradRcut;
352	+	break;
353	+	case MIX:
354	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
355	+	break;
356	+	case MAX:
357	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
358	+	break;
359	+	default:
360	+	sprintf(painCave.errMsg,
361	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
362	+	"hit an unknown cutoff policy!\n");
363	+	painCave.severity = OPENMD_ERROR;
364	+	painCave.isFatal = 1;
365	+	simError();
366	+	break;
367	+	}
368	+
369	+	pair<int,int> key = make_pair(i,j);
370	+	gTypeCutoffMap[key].first = thisRcut;
371	+
372	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
373	+
374	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
375	+
376	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
377	+
378	+	// sanity check
379	+
380	+	if (userChoseCutoff_) {
381	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
382	+	sprintf(painCave.errMsg,
383	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
384	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
385	+	painCave.severity = OPENMD_ERROR;
386	+	painCave.isFatal = 1;
387	+	simError();
388	+	}
389	+	}
390	+	}
391	+	}
392		}
230	–
231	–	void ForceMatrixDecomposition::zeroWorkArrays() {
393
394	<	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
395	<	longRangePot_[j] = 0.0;
394	>
395	>	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
396	>	int i, j;
397	>	#ifdef IS_MPI
398	>	i = groupRowToGtype[cg1];
399	>	j = groupColToGtype[cg2];
400	>	#else
401	>	i = groupToGtype[cg1];
402	>	j = groupToGtype[cg2];
403	>	#endif
404	>	return gTypeCutoffMap[make_pair(i,j)];
405	>	}
406	>
407	>	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
408	>	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
409	>	if (toposForAtom[atom1][j] == atom2)
410	>	return topoDist[atom1][j];
411		}
412	+	return 0;
413	+	}
414
415	+	void ForceMatrixDecomposition::zeroWorkArrays() {
416	+	pairwisePot = 0.0;
417	+	embeddingPot = 0.0;
418	+
419		#ifdef IS_MPI
420		if (storageLayout_ & DataStorage::dslForce) {
421		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 249 \| Line 431 \| namespace OpenMD {
431		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
432
433		fill(pot_col.begin(), pot_col.end(),
434	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
253	<
254	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
434	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
435
436		if (storageLayout_ & DataStorage::dslParticlePot) {
437		fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
#	Line 275 \| Line 455 \| namespace OpenMD {
455		atomColData.functionalDerivative.end(), 0.0);
456		}
457
458	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
459	+	fill(atomRowData.skippedCharge.begin(),
460	+	atomRowData.skippedCharge.end(), 0.0);
461	+	fill(atomColData.skippedCharge.begin(),
462	+	atomColData.skippedCharge.end(), 0.0);
463	+	}
464	+
465		#else
466
467		if (storageLayout_ & DataStorage::dslParticlePot) {
#	Line 294 \| Line 481 \| namespace OpenMD {
481		fill(snap_->atomData.functionalDerivative.begin(),
482		snap_->atomData.functionalDerivative.end(), 0.0);
483		}
484	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
485	+	fill(snap_->atomData.skippedCharge.begin(),
486	+	snap_->atomData.skippedCharge.end(), 0.0);
487	+	}
488		#endif
489
490		}
#	Line 401 \| Line 592 \| namespace OpenMD {
592
593		if (storageLayout_ & DataStorage::dslTorque) {
594
595	<	int nt = snap_->atomData.force.size();
595	>	int nt = snap_->atomData.torque.size();
596		vector<Vector3d> trq_tmp(nt, V3Zero);
597
598		AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
599	<	for (int i = 0; i < n; i++) {
599	>	for (int i = 0; i < nt; i++) {
600		snap_->atomData.torque[i] += trq_tmp[i];
601		trq_tmp[i] = 0.0;
602		}
603
604		AtomCommVectorColumn->scatter(atomColData.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	+	}
608	+
609	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
610	+
611	+	int ns = snap_->atomData.skippedCharge.size();
612	+	vector<RealType> skch_tmp(ns, 0.0);
613	+
614	+	AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
615	+	for (int i = 0; i < ns; i++) {
616	+	snap_->atomData.skippedCharge[i] = skch_tmp[i];
617	+	skch_tmp[i] = 0.0;
618	+	}
619	+
620	+	AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
621	+	for (int i = 0; i < ns; i++)
622	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
623		}
624
625		nLocal_ = snap_->getNumberOfAtoms();
#	Line 425 \| Line 632 \| namespace OpenMD {
632		AtomCommPotRow->scatter(pot_row, pot_temp);
633
634		for (int ii = 0; ii < pot_temp.size(); ii++ )
635	<	pot_local += pot_temp[ii];
635	>	pairwisePot += pot_temp[ii];
636
637		fill(pot_temp.begin(), pot_temp.end(),
638		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
#	Line 433 \| Line 640 \| namespace OpenMD {
640		AtomCommPotColumn->scatter(pot_col, pot_temp);
641
642		for (int ii = 0; ii < pot_temp.size(); ii++ )
643	<	pot_local += pot_temp[ii];
437	<
643	>	pairwisePot += pot_temp[ii];
644		#endif
645	+
646		}
647
648		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 510 \| Line 717 \| namespace OpenMD {
717		#ifdef IS_MPI
718		return massFactorsRow[atom1];
719		#else
720	<	return massFactorsLocal[atom1];
720	>	return massFactors[atom1];
721		#endif
722		}
723
#	Line 518 \| Line 725 \| namespace OpenMD {
725		#ifdef IS_MPI
726		return massFactorsCol[atom2];
727		#else
728	<	return massFactorsLocal[atom2];
728	>	return massFactors[atom2];
729		#endif
730
731		}
#	Line 536 \| Line 743 \| namespace OpenMD {
743		return d;
744		}
745
746	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
747	<	#ifdef IS_MPI
541	<	return skipsForRowAtom[atom1];
542	<	#else
543	<	return skipsForLocalAtom[atom1];
544	<	#endif
746	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
747	>	return excludesForAtom[atom1];
748		}
749
750		/**
751	<	* 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
751	>	* We need to exclude some overcounted interactions that result from
752		* the parallel decomposition.
753		*/
754		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
#	Line 568 \| Line 768 \| namespace OpenMD {
768		} else {
769		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
770		}
771	+	#endif
772	+	return false;
773	+	}
774	+
775	+	/**
776	+	* We need to handle the interactions for atoms who are involved in
777	+	* the same rigid body as well as some short range interactions
778	+	* (bonds, bends, torsions) differently from other interactions.
779	+	* We'll still visit the pairwise routines, but with a flag that
780	+	* tells those routines to exclude the pair from direct long range
781	+	* interactions. Some indirect interactions (notably reaction
782	+	* field) must still be handled for these pairs.
783	+	*/
784	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
785	+	int unique_id_2;
786	+
787	+	#ifdef IS_MPI
788	+	// in MPI, we have to look up the unique IDs for the row atom.
789	+	unique_id_2 = AtomColToGlobal[atom2];
790		#else
791		// in the normal loop, the atom numbers are unique
573	–	unique_id_1 = atom1;
792		unique_id_2 = atom2;
793		#endif
794
795	<	#ifdef IS_MPI
796	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
579	<	i != skipsForRowAtom[atom1].end(); ++i) {
795	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
796	>	i != excludesForAtom[atom1].end(); ++i) {
797		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];
798		}
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
799
800	<	// zero is default for unconnected (i.e. normal) pair interactions
603	<	return 0;
800	>	return false;
801		}
802
803	+
804		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
805		#ifdef IS_MPI
806		atomRowData.force[atom1] += fg;
#	Line 620 \| Line 818 \| namespace OpenMD {
818		}
819
820		// filling interaction blocks with pointers
821	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
822	<	InteractionData idat;
821	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
822	>	int atom1, int atom2) {
823
824	+	idat.excluded = excludeAtomPair(atom1, atom2);
825	+
826		#ifdef IS_MPI
827
828		idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
829		ff_->getAtomType(identsCol[atom2]) );
630	–
830
831		if (storageLayout_ & DataStorage::dslAmat) {
832		idat.A1 = &(atomRowData.aMat[atom1]);
#	Line 664 \| Line 863 \| namespace OpenMD {
863		idat.particlePot2 = &(atomColData.particlePot[atom2]);
864		}
865
866	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
867	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
868	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
869	+	}
870	+
871		#else
872
873	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
874	<	ff_->getAtomType(identsLocal[atom2]) );
873	>	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
874	>	ff_->getAtomType(idents[atom2]) );
875
876		if (storageLayout_ & DataStorage::dslAmat) {
877		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 684 \| Line 888 \| namespace OpenMD {
888		idat.t2 = &(snap_->atomData.torque[atom2]);
889		}
890
891	<	if (storageLayout_ & DataStorage::dslDensity) {
891	>	if (storageLayout_ & DataStorage::dslDensity) {
892		idat.rho1 = &(snap_->atomData.density[atom1]);
893		idat.rho2 = &(snap_->atomData.density[atom2]);
894		}
#	Line 704 \| Line 908 \| namespace OpenMD {
908		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
909		}
910
911	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
912	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
913	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
914	+	}
915		#endif
708	–	return idat;
916		}
917
918
919	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
919	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
920		#ifdef IS_MPI
921		pot_row[atom1] += 0.5 * *(idat.pot);
922		pot_col[atom2] += 0.5 * *(idat.pot);
#	Line 717 \| Line 924 \| namespace OpenMD {
924		atomRowData.force[atom1] += *(idat.f1);
925		atomColData.force[atom2] -= *(idat.f1);
926		#else
927	<	longRangePot_ += *(idat.pot);
928	<
927	>	pairwisePot += *(idat.pot);
928	>
929		snap_->atomData.force[atom1] += *(idat.f1);
930		snap_->atomData.force[atom2] -= *(idat.f1);
931		#endif
932	<
932	>
933		}
934
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	–
935		/*
936		* buildNeighborList
937		*
#	Line 765 \| Line 941 \| namespace OpenMD {
941		vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
942
943		vector<pair<int, int> > neighborList;
944	+	groupCutoffs cuts;
945	+	bool doAllPairs = false;
946	+
947		#ifdef IS_MPI
948		cellListRow_.clear();
949		cellListCol_.clear();
#	Line 772 \| Line 951 \| namespace OpenMD {
951		cellList_.clear();
952		#endif
953
954	<	// dangerous to not do error checking.
776	<	RealType rCut_;
777	<
778	<	RealType rList_ = (rCut_ + skinThickness_);
954	>	RealType rList_ = (largestRcut_ + skinThickness_);
955		RealType rl2 = rList_ * rList_;
956		Snapshot* snap_ = sman_->getCurrentSnapshot();
957		Mat3x3d Hmat = snap_->getHmat();
#	Line 787 \| Line 963 \| namespace OpenMD {
963		nCells_.y() = (int) ( Hy.length() )/ rList_;
964		nCells_.z() = (int) ( Hz.length() )/ rList_;
965
966	+	// handle small boxes where the cell offsets can end up repeating cells
967	+
968	+	if (nCells_.x() < 3) doAllPairs = true;
969	+	if (nCells_.y() < 3) doAllPairs = true;
970	+	if (nCells_.z() < 3) doAllPairs = true;
971	+
972		Mat3x3d invHmat = snap_->getInvHmat();
973		Vector3d rs, scaled, dr;
974		Vector3i whichCell;
975		int cellIndex;
976	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
977
978		#ifdef IS_MPI
979	<	for (int i = 0; i < nGroupsInRow_; i++) {
980	<	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	<	}
979	>	cellListRow_.resize(nCtot);
980	>	cellListCol_.resize(nCtot);
981		#else
982	<	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	<	}
982	>	cellList_.resize(nCtot);
983		#endif
984
985	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
986	<	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_);
985	>	if (!doAllPairs) {
986	>	#ifdef IS_MPI
987
988	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
989	<	os != cellOffsets_.end(); ++os) {
990	<
991	<	Vector3i m2v = m1v + (*os);
992	<
993	<	if (m2v.x() >= nCells_.x()) {
994	<	m2v.x() = 0;
995	<	} else if (m2v.x() < 0) {
996	<	m2v.x() = nCells_.x() - 1;
997	<	}
998	<
999	<	if (m2v.y() >= nCells_.y()) {
1000	<	m2v.y() = 0;
1001	<	} else if (m2v.y() < 0) {
1002	<	m2v.y() = nCells_.y() - 1;
1003	<	}
1004	<
1005	<	if (m2v.z() >= nCells_.z()) {
1006	<	m2v.z() = 0;
1007	<	} else if (m2v.z() < 0) {
1008	<	m2v.z() = nCells_.z() - 1;
1009	<	}
1010	<
1011	<	int m2 = Vlinear (m2v, nCells_);
988	>	for (int i = 0; i < nGroupsInRow_; i++) {
989	>	rs = cgRowData.position[i];
990	>
991	>	// scaled positions relative to the box vectors
992	>	scaled = invHmat * rs;
993	>
994	>	// wrap the vector back into the unit box by subtracting integer box
995	>	// numbers
996	>	for (int j = 0; j < 3; j++) {
997	>	scaled[j] -= roundMe(scaled[j]);
998	>	scaled[j] += 0.5;
999	>	}
1000	>
1001	>	// find xyz-indices of cell that cutoffGroup is in.
1002	>	whichCell.x() = nCells_.x() * scaled.x();
1003	>	whichCell.y() = nCells_.y() * scaled.y();
1004	>	whichCell.z() = nCells_.z() * scaled.z();
1005	>
1006	>	// find single index of this cell:
1007	>	cellIndex = Vlinear(whichCell, nCells_);
1008	>
1009	>	// add this cutoff group to the list of groups in this cell;
1010	>	cellListRow_[cellIndex].push_back(i);
1011	>	}
1012	>
1013	>	for (int i = 0; i < nGroupsInCol_; i++) {
1014	>	rs = cgColData.position[i];
1015	>
1016	>	// scaled positions relative to the box vectors
1017	>	scaled = invHmat * rs;
1018	>
1019	>	// wrap the vector back into the unit box by subtracting integer box
1020	>	// numbers
1021	>	for (int j = 0; j < 3; j++) {
1022	>	scaled[j] -= roundMe(scaled[j]);
1023	>	scaled[j] += 0.5;
1024	>	}
1025	>
1026	>	// find xyz-indices of cell that cutoffGroup is in.
1027	>	whichCell.x() = nCells_.x() * scaled.x();
1028	>	whichCell.y() = nCells_.y() * scaled.y();
1029	>	whichCell.z() = nCells_.z() * scaled.z();
1030	>
1031	>	// find single index of this cell:
1032	>	cellIndex = Vlinear(whichCell, nCells_);
1033	>
1034	>	// add this cutoff group to the list of groups in this cell;
1035	>	cellListCol_[cellIndex].push_back(i);
1036	>	}
1037	>	#else
1038	>	for (int i = 0; i < nGroups_; i++) {
1039	>	rs = snap_->cgData.position[i];
1040	>
1041	>	// scaled positions relative to the box vectors
1042	>	scaled = invHmat * rs;
1043	>
1044	>	// wrap the vector back into the unit box by subtracting integer box
1045	>	// numbers
1046	>	for (int j = 0; j < 3; j++) {
1047	>	scaled[j] -= roundMe(scaled[j]);
1048	>	scaled[j] += 0.5;
1049	>	}
1050	>
1051	>	// find xyz-indices of cell that cutoffGroup is in.
1052	>	whichCell.x() = nCells_.x() * scaled.x();
1053	>	whichCell.y() = nCells_.y() * scaled.y();
1054	>	whichCell.z() = nCells_.z() * scaled.z();
1055	>
1056	>	// find single index of this cell:
1057	>	cellIndex = Vlinear(whichCell, nCells_);
1058	>
1059	>	// add this cutoff group to the list of groups in this cell;
1060	>	cellList_[cellIndex].push_back(i);
1061	>	}
1062	>	#endif
1063
1064	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1065	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1066	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1067	+	Vector3i m1v(m1x, m1y, m1z);
1068	+	int m1 = Vlinear(m1v, nCells_);
1069	+
1070	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1071	+	os != cellOffsets_.end(); ++os) {
1072	+
1073	+	Vector3i m2v = m1v + (*os);
1074	+
1075	+	if (m2v.x() >= nCells_.x()) {
1076	+	m2v.x() = 0;
1077	+	} else if (m2v.x() < 0) {
1078	+	m2v.x() = nCells_.x() - 1;
1079	+	}
1080	+
1081	+	if (m2v.y() >= nCells_.y()) {
1082	+	m2v.y() = 0;
1083	+	} else if (m2v.y() < 0) {
1084	+	m2v.y() = nCells_.y() - 1;
1085	+	}
1086	+
1087	+	if (m2v.z() >= nCells_.z()) {
1088	+	m2v.z() = 0;
1089	+	} else if (m2v.z() < 0) {
1090	+	m2v.z() = nCells_.z() - 1;
1091	+	}
1092	+
1093	+	int m2 = Vlinear (m2v, nCells_);
1094	+
1095		#ifdef IS_MPI
1096	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1097	<	j1 != cellListRow_[m1].end(); ++j1) {
1098	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1099	<	j2 != cellListCol_[m2].end(); ++j2) {
1100	<
1101	<	// Always do this if we're in different cells or if
1102	<	// we're in the same cell and the global index of the
1103	<	// j2 cutoff group is less than the j1 cutoff group
1104	<
1105	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1106	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1107	<	snap_->wrapVector(dr);
1108	<	if (dr.lengthSquare() < rl2) {
1109	<	neighborList.push_back(make_pair((j1), (j2)));
1096	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1097	>	j1 != cellListRow_[m1].end(); ++j1) {
1098	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1099	>	j2 != cellListCol_[m2].end(); ++j2) {
1100	>
1101	>	// Always do this if we're in different cells or if
1102	>	// we're in the same cell and the global index of the
1103	>	// j2 cutoff group is less than the j1 cutoff group
1104	>
1105	>	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1106	>	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1107	>	snap_->wrapVector(dr);
1108	>	cuts = getGroupCutoffs( (j1), (j2) );
1109	>	if (dr.lengthSquare() < cuts.third) {
1110	>	neighborList.push_back(make_pair((j1), (j2)));
1111	>	}
1112		}
1113		}
1114		}
906	–	}
1115		#else
1116	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1117	<	j1 != cellList_[m1].end(); ++j1) {
1118	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1119	<	j2 != cellList_[m2].end(); ++j2) {
1120	<
1121	<	// Always do this if we're in different cells or if
1122	<	// we're in the same cell and the global index of the
1123	<	// j2 cutoff group is less than the j1 cutoff group
1124	<
1125	<	if (m2 != m1 \|\| (j2) < (j1)) {
1126	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1127	<	snap_->wrapVector(dr);
1128	<	if (dr.lengthSquare() < rl2) {
1129	<	neighborList.push_back(make_pair((j1), (j2)));
1116	>
1117	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1118	>	j1 != cellList_[m1].end(); ++j1) {
1119	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1120	>	j2 != cellList_[m2].end(); ++j2) {
1121	>
1122	>	// Always do this if we're in different cells or if
1123	>	// we're in the same cell and the global index of the
1124	>	// j2 cutoff group is less than the j1 cutoff group
1125	>
1126	>	if (m2 != m1 \|\| (j2) < (j1)) {
1127	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1128	>	snap_->wrapVector(dr);
1129	>	cuts = getGroupCutoffs( (j1), (j2) );
1130	>	if (dr.lengthSquare() < cuts.third) {
1131	>	neighborList.push_back(make_pair((j1), (j2)));
1132	>	}
1133		}
1134		}
1135		}
925	–	}
1136		#endif
1137	+	}
1138		}
1139		}
1140		}
1141	+	} else {
1142	+	// branch to do all cutoff group pairs
1143	+	#ifdef IS_MPI
1144	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1145	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1146	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1147	+	snap_->wrapVector(dr);
1148	+	cuts = getGroupCutoffs( j1, j2 );
1149	+	if (dr.lengthSquare() < cuts.third) {
1150	+	neighborList.push_back(make_pair(j1, j2));
1151	+	}
1152	+	}
1153	+	}
1154	+	#else
1155	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1156	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1157	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1158	+	snap_->wrapVector(dr);
1159	+	cuts = getGroupCutoffs( j1, j2 );
1160	+	if (dr.lengthSquare() < cuts.third) {
1161	+	neighborList.push_back(make_pair(j1, j2));
1162	+	}
1163	+	}
1164	+	}
1165	+	#endif
1166		}
1167	<
1167	>
1168		// save the local cutoff group positions for the check that is
1169		// done on each loop:
1170		saved_CG_positions_.clear();
1171		for (int i = 0; i < nGroups_; i++)
1172		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1173	<
1173	>
1174		return neighborList;
1175		}
1176		} //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 1588 by gezelter, Sat Jul 9 15:05:59 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 1588 by gezelter, Sat Jul 9 15:05:59 2011 UTC