[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 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC

#	Line 57 \| Line 57 \| namespace OpenMD {
57		storageLayout_ = sman_->getStorageLayout();
58		ff_ = info_->getForceField();
59		nLocal_ = snap_->getNumberOfAtoms();
60	<	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		AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116		AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
#	Line 116 \| Line 118 \| namespace OpenMD {
118		cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119		cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120
121	<	AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
122	<	AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
121	>	AtomCommRealRow->gather(massFactors, massFactorsRow);
122	>	AtomCommRealColumn->gather(massFactors, massFactorsCol);
123
124		groupListRow_.clear();
125	<	groupListRow_.reserve(nGroupsInRow_);
125	>	groupListRow_.resize(nGroupsInRow_);
126		for (int i = 0; i < nGroupsInRow_; i++) {
127		int gid = cgRowToGlobal[i];
128		for (int j = 0; j < nAtomsInRow_; j++) {
#	Line 131 \| Line 133 \| namespace OpenMD {
133		}
134
135		groupListCol_.clear();
136	<	groupListCol_.reserve(nGroupsInCol_);
136	>	groupListCol_.resize(nGroupsInCol_);
137		for (int i = 0; i < nGroupsInCol_; i++) {
138		int gid = cgColToGlobal[i];
139		for (int j = 0; j < nAtomsInCol_; j++) {
#	Line 141 \| Line 143 \| namespace OpenMD {
143		}
144		}
145
146	<	skipsForRowAtom.clear();
147	<	skipsForRowAtom.reserve(nAtomsInRow_);
146	>	excludesForAtom.clear();
147	>	excludesForAtom.resize(nAtomsInRow_);
148	>	toposForAtom.clear();
149	>	toposForAtom.resize(nAtomsInRow_);
150	>	topoDist.clear();
151	>	topoDist.resize(nAtomsInRow_);
152		for (int i = 0; i < nAtomsInRow_; i++) {
153		int iglob = AtomRowToGlobal[i];
148	–	for (int j = 0; j < nAtomsInCol_; j++) {
149	–	int jglob = AtomColToGlobal[j];
150	–	if (excludes.hasPair(iglob, jglob))
151	–	skipsForRowAtom[i].push_back(j);
152	–	}
153	–	}
154
155	–	toposForRowAtom.clear();
156	–	toposForRowAtom.reserve(nAtomsInRow_);
157	–	for (int i = 0; i < nAtomsInRow_; i++) {
158	–	int iglob = AtomRowToGlobal[i];
159	–	int nTopos = 0;
155		for (int j = 0; j < nAtomsInCol_; j++) {
156	<	int jglob = AtomColToGlobal[j];
157	<	if (oneTwo.hasPair(iglob, jglob)) {
158	<	toposForRowAtom[i].push_back(j);
159	<	topoDistRow[i][nTopos] = 1;
160	<	nTopos++;
156	>	int jglob = AtomColToGlobal[j];
157	>
158	>	if (excludes->hasPair(iglob, jglob))
159	>	excludesForAtom[i].push_back(j);
160	>
161	>	if (oneTwo->hasPair(iglob, jglob)) {
162	>	toposForAtom[i].push_back(j);
163	>	topoDist[i].push_back(1);
164	>	} else {
165	>	if (oneThree->hasPair(iglob, jglob)) {
166	>	toposForAtom[i].push_back(j);
167	>	topoDist[i].push_back(2);
168	>	} else {
169	>	if (oneFour->hasPair(iglob, jglob)) {
170	>	toposForAtom[i].push_back(j);
171	>	topoDist[i].push_back(3);
172	>	}
173	>	}
174		}
167	–	if (oneThree.hasPair(iglob, jglob)) {
168	–	toposForRowAtom[i].push_back(j);
169	–	topoDistRow[i][nTopos] = 2;
170	–	nTopos++;
171	–	}
172	–	if (oneFour.hasPair(iglob, jglob)) {
173	–	toposForRowAtom[i].push_back(j);
174	–	topoDistRow[i][nTopos] = 3;
175	–	nTopos++;
176	–	}
175		}
176		}
177
178		#endif
179
180		groupList_.clear();
181	<	groupList_.reserve(nGroups_);
181	>	groupList_.resize(nGroups_);
182		for (int i = 0; i < nGroups_; i++) {
183		int gid = cgLocalToGlobal[i];
184		for (int j = 0; j < nLocal_; j++) {
185		int aid = AtomLocalToGlobal[j];
186	<	if (globalGroupMembership[aid] == gid)
186	>	if (globalGroupMembership[aid] == gid) {
187		groupList_[i].push_back(j);
188	+	}
189		}
190		}
191
192	<	skipsForLocalAtom.clear();
193	<	skipsForLocalAtom.reserve(nLocal_);
192	>	excludesForAtom.clear();
193	>	excludesForAtom.resize(nLocal_);
194	>	toposForAtom.clear();
195	>	toposForAtom.resize(nLocal_);
196	>	topoDist.clear();
197	>	topoDist.resize(nLocal_);
198
199		for (int i = 0; i < nLocal_; i++) {
200		int iglob = AtomLocalToGlobal[i];
201	+
202		for (int j = 0; j < nLocal_; j++) {
203	<	int jglob = AtomLocalToGlobal[j];
204	<	if (excludes.hasPair(iglob, jglob))
205	<	skipsForLocalAtom[i].push_back(j);
203	>	int jglob = AtomLocalToGlobal[j];
204	>
205	>	if (excludes->hasPair(iglob, jglob))
206	>	excludesForAtom[i].push_back(j);
207	>
208	>	if (oneTwo->hasPair(iglob, jglob)) {
209	>	toposForAtom[i].push_back(j);
210	>	topoDist[i].push_back(1);
211	>	} else {
212	>	if (oneThree->hasPair(iglob, jglob)) {
213	>	toposForAtom[i].push_back(j);
214	>	topoDist[i].push_back(2);
215	>	} else {
216	>	if (oneFour->hasPair(iglob, jglob)) {
217	>	toposForAtom[i].push_back(j);
218	>	topoDist[i].push_back(3);
219	>	}
220	>	}
221	>	}
222		}
223		}
224	+
225	+	createGtypeCutoffMap();
226
227	<	toposForLocalAtom.clear();
228	<	toposForLocalAtom.reserve(nLocal_);
229	<	for (int i = 0; i < nLocal_; i++) {
230	<	int iglob = AtomLocalToGlobal[i];
231	<	int nTopos = 0;
232	<	for (int j = 0; j < nLocal_; j++) {
233	<	int jglob = AtomLocalToGlobal[j];
234	<	if (oneTwo.hasPair(iglob, jglob)) {
235	<	toposForLocalAtom[i].push_back(j);
236	<	topoDistLocal[i][nTopos] = 1;
237	<	nTopos++;
227	>	}
228	>
229	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
230	>
231	>	RealType tol = 1e-6;
232	>	RealType rc;
233	>	int atid;
234	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
235	>	map<int, RealType> atypeCutoff;
236	>
237	>	for (set<AtomType*>::iterator at = atypes.begin();
238	>	at != atypes.end(); ++at){
239	>	atid = (*at)->getIdent();
240	>	if (userChoseCutoff_)
241	>	atypeCutoff[atid] = userCutoff_;
242	>	else
243	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
244	>	}
245	>
246	>	vector<RealType> gTypeCutoffs;
247	>	// first we do a single loop over the cutoff groups to find the
248	>	// largest cutoff for any atypes present in this group.
249	>	#ifdef IS_MPI
250	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
251	>	groupRowToGtype.resize(nGroupsInRow_);
252	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
253	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
254	>	for (vector<int>::iterator ia = atomListRow.begin();
255	>	ia != atomListRow.end(); ++ia) {
256	>	int atom1 = (*ia);
257	>	atid = identsRow[atom1];
258	>	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
259	>	groupCutoffRow[cg1] = atypeCutoff[atid];
260		}
261	<	if (oneThree.hasPair(iglob, jglob)) {
262	<	toposForLocalAtom[i].push_back(j);
263	<	topoDistLocal[i][nTopos] = 2;
264	<	nTopos++;
261	>	}
262	>
263	>	bool gTypeFound = false;
264	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
265	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
266	>	groupRowToGtype[cg1] = gt;
267	>	gTypeFound = true;
268	>	}
269	>	}
270	>	if (!gTypeFound) {
271	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
272	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
273	>	}
274	>
275	>	}
276	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
277	>	groupColToGtype.resize(nGroupsInCol_);
278	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
279	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
280	>	for (vector<int>::iterator jb = atomListCol.begin();
281	>	jb != atomListCol.end(); ++jb) {
282	>	int atom2 = (*jb);
283	>	atid = identsCol[atom2];
284	>	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
285	>	groupCutoffCol[cg2] = atypeCutoff[atid];
286		}
287	<	if (oneFour.hasPair(iglob, jglob)) {
288	<	toposForLocalAtom[i].push_back(j);
289	<	topoDistLocal[i][nTopos] = 3;
290	<	nTopos++;
287	>	}
288	>	bool gTypeFound = false;
289	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
290	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
291	>	groupColToGtype[cg2] = gt;
292	>	gTypeFound = true;
293	>	}
294	>	}
295	>	if (!gTypeFound) {
296	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
297	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
298	>	}
299	>	}
300	>	#else
301	>
302	>	vector<RealType> groupCutoff(nGroups_, 0.0);
303	>	groupToGtype.resize(nGroups_);
304	>	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305	>
306	>	groupCutoff[cg1] = 0.0;
307	>	vector<int> atomList = getAtomsInGroupRow(cg1);
308	>
309	>	for (vector<int>::iterator ia = atomList.begin();
310	>	ia != atomList.end(); ++ia) {
311	>	int atom1 = (*ia);
312	>	atid = idents[atom1];
313	>	if (atypeCutoff[atid] > groupCutoff[cg1]) {
314	>	groupCutoff[cg1] = atypeCutoff[atid];
315		}
316	+	}
317	+
318	+	bool gTypeFound = false;
319	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
320	+	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
321	+	groupToGtype[cg1] = gt;
322	+	gTypeFound = true;
323	+	}
324	+	}
325	+	if (!gTypeFound) {
326	+	gTypeCutoffs.push_back( groupCutoff[cg1] );
327	+	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
328		}
329		}
330	+	#endif
331	+
332	+	// Now we find the maximum group cutoff value present in the simulation
333	+
334	+	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
335	+
336	+	#ifdef IS_MPI
337	+	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
338	+	#endif
339	+
340	+	RealType tradRcut = groupMax;
341	+
342	+	for (int i = 0; i < gTypeCutoffs.size(); i++) {
343	+	for (int j = 0; j < gTypeCutoffs.size(); j++) {
344	+	RealType thisRcut;
345	+	switch(cutoffPolicy_) {
346	+	case TRADITIONAL:
347	+	thisRcut = tradRcut;
348	+	break;
349	+	case MIX:
350	+	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
351	+	break;
352	+	case MAX:
353	+	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
354	+	break;
355	+	default:
356	+	sprintf(painCave.errMsg,
357	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
358	+	"hit an unknown cutoff policy!\n");
359	+	painCave.severity = OPENMD_ERROR;
360	+	painCave.isFatal = 1;
361	+	simError();
362	+	break;
363	+	}
364	+
365	+	pair<int,int> key = make_pair(i,j);
366	+	gTypeCutoffMap[key].first = thisRcut;
367	+
368	+	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
369	+
370	+	gTypeCutoffMap[key].second = thisRcut*thisRcut;
371	+
372	+	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
373	+
374	+	// sanity check
375	+
376	+	if (userChoseCutoff_) {
377	+	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
378	+	sprintf(painCave.errMsg,
379	+	"ForceMatrixDecomposition::createGtypeCutoffMap "
380	+	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
381	+	painCave.severity = OPENMD_ERROR;
382	+	painCave.isFatal = 1;
383	+	simError();
384	+	}
385	+	}
386	+	}
387	+	}
388		}
230	–
231	–	void ForceMatrixDecomposition::zeroWorkArrays() {
389
390	<	for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
391	<	longRangePot_[j] = 0.0;
390	>
391	>	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
392	>	int i, j;
393	>	#ifdef IS_MPI
394	>	i = groupRowToGtype[cg1];
395	>	j = groupColToGtype[cg2];
396	>	#else
397	>	i = groupToGtype[cg1];
398	>	j = groupToGtype[cg2];
399	>	#endif
400	>	return gTypeCutoffMap[make_pair(i,j)];
401	>	}
402	>
403	>	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
404	>	for (int j = 0; j < toposForAtom[atom1].size(); j++) {
405	>	if (toposForAtom[atom1][j] == atom2)
406	>	return topoDist[atom1][j];
407		}
408	+	return 0;
409	+	}
410
411	+	void ForceMatrixDecomposition::zeroWorkArrays() {
412	+	pairwisePot = 0.0;
413	+	embeddingPot = 0.0;
414	+
415		#ifdef IS_MPI
416		if (storageLayout_ & DataStorage::dslForce) {
417		fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
#	Line 249 \| Line 427 \| namespace OpenMD {
427		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
428
429		fill(pot_col.begin(), pot_col.end(),
430	<	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
253	<
254	<	pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
430	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
431
432		if (storageLayout_ & DataStorage::dslParticlePot) {
433		fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
#	Line 275 \| Line 451 \| namespace OpenMD {
451		atomColData.functionalDerivative.end(), 0.0);
452		}
453
454	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
455	+	fill(atomRowData.skippedCharge.begin(),
456	+	atomRowData.skippedCharge.end(), 0.0);
457	+	fill(atomColData.skippedCharge.begin(),
458	+	atomColData.skippedCharge.end(), 0.0);
459	+	}
460	+
461		#else
462
463		if (storageLayout_ & DataStorage::dslParticlePot) {
#	Line 294 \| Line 477 \| namespace OpenMD {
477		fill(snap_->atomData.functionalDerivative.begin(),
478		snap_->atomData.functionalDerivative.end(), 0.0);
479		}
480	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
481	+	fill(snap_->atomData.skippedCharge.begin(),
482	+	snap_->atomData.skippedCharge.end(), 0.0);
483	+	}
484		#endif
485
486		}
#	Line 401 \| Line 588 \| namespace OpenMD {
588
589		if (storageLayout_ & DataStorage::dslTorque) {
590
591	<	int nt = snap_->atomData.force.size();
591	>	int nt = snap_->atomData.torque.size();
592		vector<Vector3d> trq_tmp(nt, V3Zero);
593
594		AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
595	<	for (int i = 0; i < n; i++) {
595	>	for (int i = 0; i < nt; i++) {
596		snap_->atomData.torque[i] += trq_tmp[i];
597		trq_tmp[i] = 0.0;
598		}
599
600		AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
601	<	for (int i = 0; i < n; i++)
601	>	for (int i = 0; i < nt; i++)
602		snap_->atomData.torque[i] += trq_tmp[i];
603		}
604	+
605	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
606	+
607	+	int ns = snap_->atomData.skippedCharge.size();
608	+	vector<RealType> skch_tmp(ns, 0.0);
609	+
610	+	AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
611	+	for (int i = 0; i < ns; i++) {
612	+	snap_->atomData.skippedCharge[i] = skch_tmp[i];
613	+	skch_tmp[i] = 0.0;
614	+	}
615	+
616	+	AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
617	+	for (int i = 0; i < ns; i++)
618	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
619	+	}
620
621		nLocal_ = snap_->getNumberOfAtoms();
622
#	Line 425 \| Line 628 \| namespace OpenMD {
628		AtomCommPotRow->scatter(pot_row, pot_temp);
629
630		for (int ii = 0; ii < pot_temp.size(); ii++ )
631	<	pot_local += pot_temp[ii];
631	>	pairwisePot += pot_temp[ii];
632
633		fill(pot_temp.begin(), pot_temp.end(),
634		Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
#	Line 433 \| Line 636 \| namespace OpenMD {
636		AtomCommPotColumn->scatter(pot_col, pot_temp);
637
638		for (int ii = 0; ii < pot_temp.size(); ii++ )
639	<	pot_local += pot_temp[ii];
437	<
639	>	pairwisePot += pot_temp[ii];
640		#endif
641	+
642		}
643
644		int ForceMatrixDecomposition::getNAtomsInRow() {
#	Line 510 \| Line 713 \| namespace OpenMD {
713		#ifdef IS_MPI
714		return massFactorsRow[atom1];
715		#else
716	<	return massFactorsLocal[atom1];
716	>	return massFactors[atom1];
717		#endif
718		}
719
#	Line 518 \| Line 721 \| namespace OpenMD {
721		#ifdef IS_MPI
722		return massFactorsCol[atom2];
723		#else
724	<	return massFactorsLocal[atom2];
724	>	return massFactors[atom2];
725		#endif
726
727		}
#	Line 536 \| Line 739 \| namespace OpenMD {
739		return d;
740		}
741
742	<	vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
743	<	#ifdef IS_MPI
541	<	return skipsForRowAtom[atom1];
542	<	#else
543	<	return skipsForLocalAtom[atom1];
544	<	#endif
742	>	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
743	>	return excludesForAtom[atom1];
744		}
745
746		/**
747	<	* There are a number of reasons to skip a pair or a
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
747	>	* We need to exclude some overcounted interactions that result from
748		* the parallel decomposition.
749		*/
750		bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
#	Line 568 \| Line 764 \| namespace OpenMD {
764		} else {
765		if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
766		}
767	+	#endif
768	+	return false;
769	+	}
770	+
771	+	/**
772	+	* We need to handle the interactions for atoms who are involved in
773	+	* the same rigid body as well as some short range interactions
774	+	* (bonds, bends, torsions) differently from other interactions.
775	+	* We'll still visit the pairwise routines, but with a flag that
776	+	* tells those routines to exclude the pair from direct long range
777	+	* interactions. Some indirect interactions (notably reaction
778	+	* field) must still be handled for these pairs.
779	+	*/
780	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
781	+	int unique_id_2;
782	+
783	+	#ifdef IS_MPI
784	+	// in MPI, we have to look up the unique IDs for the row atom.
785	+	unique_id_2 = AtomColToGlobal[atom2];
786		#else
787		// in the normal loop, the atom numbers are unique
573	–	unique_id_1 = atom1;
788		unique_id_2 = atom2;
789		#endif
790
791	<	#ifdef IS_MPI
792	<	for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
579	<	i != skipsForRowAtom[atom1].end(); ++i) {
791	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
792	>	i != excludesForAtom[atom1].end(); ++i) {
793		if ( (*i) == unique_id_2 ) return true;
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];
794		}
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
795
796	<	// zero is default for unconnected (i.e. normal) pair interactions
603	<	return 0;
796	>	return false;
797		}
798
799	+
800		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
801		#ifdef IS_MPI
802		atomRowData.force[atom1] += fg;
#	Line 620 \| Line 814 \| namespace OpenMD {
814		}
815
816		// filling interaction blocks with pointers
817	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
818	<	InteractionData idat;
817	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
818	>	int atom1, int atom2) {
819
820	+	idat.excluded = excludeAtomPair(atom1, atom2);
821	+
822		#ifdef IS_MPI
823
824		idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
825		ff_->getAtomType(identsCol[atom2]) );
630	–
826
827		if (storageLayout_ & DataStorage::dslAmat) {
828		idat.A1 = &(atomRowData.aMat[atom1]);
#	Line 664 \| Line 859 \| namespace OpenMD {
859		idat.particlePot2 = &(atomColData.particlePot[atom2]);
860		}
861
862	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
863	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
864	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
865	+	}
866	+
867		#else
868
869	<	idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
870	<	ff_->getAtomType(identsLocal[atom2]) );
869	>	idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
870	>	ff_->getAtomType(idents[atom2]) );
871
872		if (storageLayout_ & DataStorage::dslAmat) {
873		idat.A1 = &(snap_->atomData.aMat[atom1]);
#	Line 684 \| Line 884 \| namespace OpenMD {
884		idat.t2 = &(snap_->atomData.torque[atom2]);
885		}
886
887	<	if (storageLayout_ & DataStorage::dslDensity) {
887	>	if (storageLayout_ & DataStorage::dslDensity) {
888		idat.rho1 = &(snap_->atomData.density[atom1]);
889		idat.rho2 = &(snap_->atomData.density[atom2]);
890		}
#	Line 704 \| Line 904 \| namespace OpenMD {
904		idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
905		}
906
907	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
908	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
909	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
910	+	}
911		#endif
708	–	return idat;
912		}
913
914
915	<	void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {
915	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
916		#ifdef IS_MPI
917		pot_row[atom1] += 0.5 * *(idat.pot);
918		pot_col[atom2] += 0.5 * *(idat.pot);
#	Line 717 \| Line 920 \| namespace OpenMD {
920		atomRowData.force[atom1] += *(idat.f1);
921		atomColData.force[atom2] -= *(idat.f1);
922		#else
923	<	longRangePot_ += *(idat.pot);
924	<
923	>	pairwisePot += *(idat.pot);
924	>
925		snap_->atomData.force[atom1] += *(idat.f1);
926		snap_->atomData.force[atom2] -= *(idat.f1);
927		#endif
928	<
928	>
929		}
930
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	–
931		/*
932		* buildNeighborList
933		*
#	Line 765 \| Line 937 \| namespace OpenMD {
937		vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
938
939		vector<pair<int, int> > neighborList;
940	+	groupCutoffs cuts;
941	+	bool doAllPairs = false;
942	+
943		#ifdef IS_MPI
944		cellListRow_.clear();
945		cellListCol_.clear();
#	Line 772 \| Line 947 \| namespace OpenMD {
947		cellList_.clear();
948		#endif
949
950	<	// dangerous to not do error checking.
776	<	RealType rCut_;
777	<
778	<	RealType rList_ = (rCut_ + skinThickness_);
950	>	RealType rList_ = (largestRcut_ + skinThickness_);
951		RealType rl2 = rList_ * rList_;
952		Snapshot* snap_ = sman_->getCurrentSnapshot();
953		Mat3x3d Hmat = snap_->getHmat();
#	Line 787 \| Line 959 \| namespace OpenMD {
959		nCells_.y() = (int) ( Hy.length() )/ rList_;
960		nCells_.z() = (int) ( Hz.length() )/ rList_;
961
962	+	// handle small boxes where the cell offsets can end up repeating cells
963	+
964	+	if (nCells_.x() < 3) doAllPairs = true;
965	+	if (nCells_.y() < 3) doAllPairs = true;
966	+	if (nCells_.z() < 3) doAllPairs = true;
967	+
968		Mat3x3d invHmat = snap_->getInvHmat();
969		Vector3d rs, scaled, dr;
970		Vector3i whichCell;
971		int cellIndex;
972	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
973
974		#ifdef IS_MPI
975	<	for (int i = 0; i < nGroupsInRow_; i++) {
976	<	rs = cgRowData.position[i];
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	<	}
975	>	cellListRow_.resize(nCtot);
976	>	cellListCol_.resize(nCtot);
977		#else
978	<	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	<	}
978	>	cellList_.resize(nCtot);
979		#endif
980
981	<	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
982	<	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_);
981	>	if (!doAllPairs) {
982	>	#ifdef IS_MPI
983
984	<	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
985	<	os != cellOffsets_.end(); ++os) {
986	<
987	<	Vector3i m2v = m1v + (*os);
988	<
989	<	if (m2v.x() >= nCells_.x()) {
990	<	m2v.x() = 0;
991	<	} else if (m2v.x() < 0) {
992	<	m2v.x() = nCells_.x() - 1;
993	<	}
994	<
995	<	if (m2v.y() >= nCells_.y()) {
996	<	m2v.y() = 0;
997	<	} else if (m2v.y() < 0) {
998	<	m2v.y() = nCells_.y() - 1;
999	<	}
1000	<
1001	<	if (m2v.z() >= nCells_.z()) {
1002	<	m2v.z() = 0;
1003	<	} else if (m2v.z() < 0) {
1004	<	m2v.z() = nCells_.z() - 1;
1005	<	}
1006	<
1007	<	int m2 = Vlinear (m2v, nCells_);
984	>	for (int i = 0; i < nGroupsInRow_; i++) {
985	>	rs = cgRowData.position[i];
986	>
987	>	// scaled positions relative to the box vectors
988	>	scaled = invHmat * rs;
989	>
990	>	// wrap the vector back into the unit box by subtracting integer box
991	>	// numbers
992	>	for (int j = 0; j < 3; j++) {
993	>	scaled[j] -= roundMe(scaled[j]);
994	>	scaled[j] += 0.5;
995	>	}
996	>
997	>	// find xyz-indices of cell that cutoffGroup is in.
998	>	whichCell.x() = nCells_.x() * scaled.x();
999	>	whichCell.y() = nCells_.y() * scaled.y();
1000	>	whichCell.z() = nCells_.z() * scaled.z();
1001	>
1002	>	// find single index of this cell:
1003	>	cellIndex = Vlinear(whichCell, nCells_);
1004	>
1005	>	// add this cutoff group to the list of groups in this cell;
1006	>	cellListRow_[cellIndex].push_back(i);
1007	>	}
1008	>
1009	>	for (int i = 0; i < nGroupsInCol_; i++) {
1010	>	rs = cgColData.position[i];
1011	>
1012	>	// scaled positions relative to the box vectors
1013	>	scaled = invHmat * rs;
1014	>
1015	>	// wrap the vector back into the unit box by subtracting integer box
1016	>	// numbers
1017	>	for (int j = 0; j < 3; j++) {
1018	>	scaled[j] -= roundMe(scaled[j]);
1019	>	scaled[j] += 0.5;
1020	>	}
1021	>
1022	>	// find xyz-indices of cell that cutoffGroup is in.
1023	>	whichCell.x() = nCells_.x() * scaled.x();
1024	>	whichCell.y() = nCells_.y() * scaled.y();
1025	>	whichCell.z() = nCells_.z() * scaled.z();
1026	>
1027	>	// find single index of this cell:
1028	>	cellIndex = Vlinear(whichCell, nCells_);
1029	>
1030	>	// add this cutoff group to the list of groups in this cell;
1031	>	cellListCol_[cellIndex].push_back(i);
1032	>	}
1033	>	#else
1034	>	for (int i = 0; i < nGroups_; i++) {
1035	>	rs = snap_->cgData.position[i];
1036	>
1037	>	// scaled positions relative to the box vectors
1038	>	scaled = invHmat * rs;
1039	>
1040	>	// wrap the vector back into the unit box by subtracting integer box
1041	>	// numbers
1042	>	for (int j = 0; j < 3; j++) {
1043	>	scaled[j] -= roundMe(scaled[j]);
1044	>	scaled[j] += 0.5;
1045	>	}
1046	>
1047	>	// find xyz-indices of cell that cutoffGroup is in.
1048	>	whichCell.x() = nCells_.x() * scaled.x();
1049	>	whichCell.y() = nCells_.y() * scaled.y();
1050	>	whichCell.z() = nCells_.z() * scaled.z();
1051	>
1052	>	// find single index of this cell:
1053	>	cellIndex = Vlinear(whichCell, nCells_);
1054	>
1055	>	// add this cutoff group to the list of groups in this cell;
1056	>	cellList_[cellIndex].push_back(i);
1057	>	}
1058	>	#endif
1059
1060	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1061	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1062	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1063	+	Vector3i m1v(m1x, m1y, m1z);
1064	+	int m1 = Vlinear(m1v, nCells_);
1065	+
1066	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1067	+	os != cellOffsets_.end(); ++os) {
1068	+
1069	+	Vector3i m2v = m1v + (*os);
1070	+
1071	+	if (m2v.x() >= nCells_.x()) {
1072	+	m2v.x() = 0;
1073	+	} else if (m2v.x() < 0) {
1074	+	m2v.x() = nCells_.x() - 1;
1075	+	}
1076	+
1077	+	if (m2v.y() >= nCells_.y()) {
1078	+	m2v.y() = 0;
1079	+	} else if (m2v.y() < 0) {
1080	+	m2v.y() = nCells_.y() - 1;
1081	+	}
1082	+
1083	+	if (m2v.z() >= nCells_.z()) {
1084	+	m2v.z() = 0;
1085	+	} else if (m2v.z() < 0) {
1086	+	m2v.z() = nCells_.z() - 1;
1087	+	}
1088	+
1089	+	int m2 = Vlinear (m2v, nCells_);
1090	+
1091		#ifdef IS_MPI
1092	<	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1093	<	j1 != cellListRow_[m1].end(); ++j1) {
1094	<	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1095	<	j2 != cellListCol_[m2].end(); ++j2) {
1096	<
1097	<	// Always do this if we're in different cells or if
1098	<	// we're in the same cell and the global index of the
1099	<	// j2 cutoff group is less than the j1 cutoff group
1100	<
1101	<	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1102	<	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1103	<	snap_->wrapVector(dr);
1104	<	if (dr.lengthSquare() < rl2) {
1105	<	neighborList.push_back(make_pair((j1), (j2)));
1092	>	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1093	>	j1 != cellListRow_[m1].end(); ++j1) {
1094	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1095	>	j2 != cellListCol_[m2].end(); ++j2) {
1096	>
1097	>	// Always do this if we're in different cells or if
1098	>	// we're in the same cell and the global index of the
1099	>	// j2 cutoff group is less than the j1 cutoff group
1100	>
1101	>	if (m2 != m1 \|\| cgColToGlobal[(j2)] < cgRowToGlobal[(j1)]) {
1102	>	dr = cgColData.position[(j2)] - cgRowData.position[(j1)];
1103	>	snap_->wrapVector(dr);
1104	>	cuts = getGroupCutoffs( (j1), (j2) );
1105	>	if (dr.lengthSquare() < cuts.third) {
1106	>	neighborList.push_back(make_pair((j1), (j2)));
1107	>	}
1108		}
1109		}
1110		}
906	–	}
1111		#else
1112	<	for (vector<int>::iterator j1 = cellList_[m1].begin();
1113	<	j1 != cellList_[m1].end(); ++j1) {
1114	<	for (vector<int>::iterator j2 = cellList_[m2].begin();
1115	<	j2 != cellList_[m2].end(); ++j2) {
1116	<
1117	<	// Always do this if we're in different cells or if
1118	<	// we're in the same cell and the global index of the
1119	<	// j2 cutoff group is less than the j1 cutoff group
1120	<
1121	<	if (m2 != m1 \|\| (j2) < (j1)) {
1122	<	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1123	<	snap_->wrapVector(dr);
1124	<	if (dr.lengthSquare() < rl2) {
1125	<	neighborList.push_back(make_pair((j1), (j2)));
1112	>
1113	>	for (vector<int>::iterator j1 = cellList_[m1].begin();
1114	>	j1 != cellList_[m1].end(); ++j1) {
1115	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1116	>	j2 != cellList_[m2].end(); ++j2) {
1117	>
1118	>	// Always do this if we're in different cells or if
1119	>	// we're in the same cell and the global index of the
1120	>	// j2 cutoff group is less than the j1 cutoff group
1121	>
1122	>	if (m2 != m1 \|\| (j2) < (j1)) {
1123	>	dr = snap_->cgData.position[(j2)] - snap_->cgData.position[(j1)];
1124	>	snap_->wrapVector(dr);
1125	>	cuts = getGroupCutoffs( (j1), (j2) );
1126	>	if (dr.lengthSquare() < cuts.third) {
1127	>	neighborList.push_back(make_pair((j1), (j2)));
1128	>	}
1129		}
1130		}
1131		}
925	–	}
1132		#endif
1133	+	}
1134		}
1135		}
1136		}
1137	+	} else {
1138	+	// branch to do all cutoff group pairs
1139	+	#ifdef IS_MPI
1140	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1141	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1142	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1143	+	snap_->wrapVector(dr);
1144	+	cuts = getGroupCutoffs( j1, j2 );
1145	+	if (dr.lengthSquare() < cuts.third) {
1146	+	neighborList.push_back(make_pair(j1, j2));
1147	+	}
1148	+	}
1149	+	}
1150	+	#else
1151	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1152	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1153	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1154	+	snap_->wrapVector(dr);
1155	+	cuts = getGroupCutoffs( j1, j2 );
1156	+	if (dr.lengthSquare() < cuts.third) {
1157	+	neighborList.push_back(make_pair(j1, j2));
1158	+	}
1159	+	}
1160	+	}
1161	+	#endif
1162		}
1163	<
1163	>
1164		// save the local cutoff group positions for the check that is
1165		// done on each loop:
1166		saved_CG_positions_.clear();
1167		for (int i = 0; i < nGroups_; i++)
1168		saved_CG_positions_.push_back(snap_->cgData.position[i]);
1169	<
1169	>
1170		return neighborList;
1171		}
1172		} //end namespace OpenMD

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents): Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs. Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC

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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC