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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp

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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1567 by gezelter, Tue May 24 21:24:45 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 2062 by gezelter, Tue Mar 3 16:40:39 2015 UTC

#	Line 35 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42		#include "parallel/ForceMatrixDecomposition.hpp"
43		#include "math/SquareMatrix3.hpp"
44		#include "nonbonded/NonBondedInteraction.hpp"
45		#include "brains/SnapshotManager.hpp"
46	+	#include "brains/PairList.hpp"
47
48		using namespace std;
49		namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52	+
53	+	// Row and colum scans must visit all surrounding cells
54	+	cellOffsets_.clear();
55	+	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
56	+	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
57	+	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
58	+	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
59	+	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
60	+	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
61	+	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
62	+	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
63	+	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
64	+	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
65	+	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
66	+	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
67	+	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
68	+	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
69	+	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
70	+	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
71	+	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
72	+	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
73	+	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
74	+	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
75	+	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
76	+	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
77	+	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
78	+	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
79	+	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
80	+	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
81	+	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
82	+	}
83	+
84	+
85		/**
86		* distributeInitialData is essentially a copy of the older fortran
87		* SimulationSetup
88		*/
53	–
89		void ForceMatrixDecomposition::distributeInitialData() {
90		snap_ = sman_->getCurrentSnapshot();
91		storageLayout_ = sman_->getStorageLayout();
92	+	ff_ = info_->getForceField();
93		nLocal_ = snap_->getNumberOfAtoms();
94	<	nGroups_ = snap_->getNumberOfCutoffGroups();
94	>
95	>	nGroups_ = info_->getNLocalCutoffGroups();
96	>	// gather the information for atomtype IDs (atids):
97	>	idents = info_->getIdentArray();
98	>	regions = info_->getRegions();
99	>	AtomLocalToGlobal = info_->getGlobalAtomIndices();
100	>	cgLocalToGlobal = info_->getGlobalGroupIndices();
101	>	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
102
103	+	massFactors = info_->getMassFactors();
104	+
105	+	PairList* excludes = info_->getExcludedInteractions();
106	+	PairList* oneTwo = info_->getOneTwoInteractions();
107	+	PairList* oneThree = info_->getOneThreeInteractions();
108	+	PairList* oneFour = info_->getOneFourInteractions();
109	+
110	+	if (needVelocities_)
111	+	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
112	+	DataStorage::dslVelocity);
113	+	else
114	+	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
115	+
116		#ifdef IS_MPI
117
118	<	AtomCommIntRow = new Communicator<Row,int>(nLocal_);
119	<	AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
64	<	AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
65	<	AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
118	>	MPI_Comm row = rowComm.getComm();
119	>	MPI_Comm col = colComm.getComm();
120
121	<	AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
122	<	AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
123	<	AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
124	<	AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
121	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
122	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
123	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
124	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
125	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
126
127	<	cgCommIntRow = new Communicator<Row,int>(nGroups_);
128	<	cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
129	<	cgCommIntColumn = new Communicator<Column,int>(nGroups_);
130	<	cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
127	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
128	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
129	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
130	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
131	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
132
133	<	nAtomsInRow_ = AtomCommIntRow->getSize();
134	<	nAtomsInCol_ = AtomCommIntColumn->getSize();
135	<	nGroupsInRow_ = cgCommIntRow->getSize();
136	<	nGroupsInCol_ = cgCommIntColumn->getSize();
133	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
134	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
135	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
136	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
137
138	+	nAtomsInRow_ = AtomPlanIntRow->getSize();
139	+	nAtomsInCol_ = AtomPlanIntColumn->getSize();
140	+	nGroupsInRow_ = cgPlanIntRow->getSize();
141	+	nGroupsInCol_ = cgPlanIntColumn->getSize();
142	+
143		// Modify the data storage objects with the correct layouts and sizes:
144		atomRowData.resize(nAtomsInRow_);
145		atomRowData.setStorageLayout(storageLayout_);
#	Line 87 | Line 148 | namespace OpenMD {
148		cgRowData.resize(nGroupsInRow_);
149		cgRowData.setStorageLayout(DataStorage::dslPosition);
150		cgColData.resize(nGroupsInCol_);
151	<	cgColData.setStorageLayout(DataStorage::dslPosition);
151	>	if (needVelocities_)
152	>	// we only need column velocities if we need them.
153	>	cgColData.setStorageLayout(DataStorage::dslPosition |
154	>	DataStorage::dslVelocity);
155	>	else
156	>	cgColData.setStorageLayout(DataStorage::dslPosition);
157	>
158	>	identsRow.resize(nAtomsInRow_);
159	>	identsCol.resize(nAtomsInCol_);
160
161	<	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
162	<	vector<RealType> (nAtomsInRow_, 0.0));
94	<	vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
95	<	vector<RealType> (nAtomsInCol_, 0.0));
161	>	AtomPlanIntRow->gather(idents, identsRow);
162	>	AtomPlanIntColumn->gather(idents, identsCol);
163
164	<
165	<	vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
164	>	regionsRow.resize(nAtomsInRow_);
165	>	regionsCol.resize(nAtomsInCol_);
166
167	<	// gather the information for atomtype IDs (atids):
168	<	vector<int> identsLocal = info_->getIdentArray();
102	<	identsRow.reserve(nAtomsInRow_);
103	<	identsCol.reserve(nAtomsInCol_);
167	>	AtomPlanIntRow->gather(regions, regionsRow);
168	>	AtomPlanIntColumn->gather(regions, regionsCol);
169
170	<	AtomCommIntRow->gather(identsLocal, identsRow);
171	<	AtomCommIntColumn->gather(identsLocal, identsCol);
172	<
108	<	AtomLocalToGlobal = info_->getGlobalAtomIndices();
109	<	AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
110	<	AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
111	<
112	<	cgLocalToGlobal = info_->getGlobalGroupIndices();
113	<	cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
114	<	cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
170	>	// allocate memory for the parallel objects
171	>	atypesRow.resize(nAtomsInRow_);
172	>	atypesCol.resize(nAtomsInCol_);
173
174	<	// still need:
175	<	// topoDist
176	<	// exclude
174	>	for (int i = 0; i < nAtomsInRow_; i++)
175	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
176	>	for (int i = 0; i < nAtomsInCol_; i++)
177	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
178	>
179	>	pot_row.resize(nAtomsInRow_);
180	>	pot_col.resize(nAtomsInCol_);
181	>
182	>	expot_row.resize(nAtomsInRow_);
183	>	expot_col.resize(nAtomsInCol_);
184	>
185	>	AtomRowToGlobal.resize(nAtomsInRow_);
186	>	AtomColToGlobal.resize(nAtomsInCol_);
187	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
188	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
189	>
190	>	cgRowToGlobal.resize(nGroupsInRow_);
191	>	cgColToGlobal.resize(nGroupsInCol_);
192	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
193	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
194	>
195	>	massFactorsRow.resize(nAtomsInRow_);
196	>	massFactorsCol.resize(nAtomsInCol_);
197	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
198	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
199	>
200	>	groupListRow_.clear();
201	>	groupListRow_.resize(nGroupsInRow_);
202	>	for (int i = 0; i < nGroupsInRow_; i++) {
203	>	int gid = cgRowToGlobal[i];
204	>	for (int j = 0; j < nAtomsInRow_; j++) {
205	>	int aid = AtomRowToGlobal[j];
206	>	if (globalGroupMembership[aid] == gid)
207	>	groupListRow_[i].push_back(j);
208	>	}
209	>	}
210	>
211	>	groupListCol_.clear();
212	>	groupListCol_.resize(nGroupsInCol_);
213	>	for (int i = 0; i < nGroupsInCol_; i++) {
214	>	int gid = cgColToGlobal[i];
215	>	for (int j = 0; j < nAtomsInCol_; j++) {
216	>	int aid = AtomColToGlobal[j];
217	>	if (globalGroupMembership[aid] == gid)
218	>	groupListCol_[i].push_back(j);
219	>	}
220	>	}
221	>
222	>	excludesForAtom.clear();
223	>	excludesForAtom.resize(nAtomsInRow_);
224	>	toposForAtom.clear();
225	>	toposForAtom.resize(nAtomsInRow_);
226	>	topoDist.clear();
227	>	topoDist.resize(nAtomsInRow_);
228	>	for (int i = 0; i < nAtomsInRow_; i++) {
229	>	int iglob = AtomRowToGlobal[i];
230	>
231	>	for (int j = 0; j < nAtomsInCol_; j++) {
232	>	int jglob = AtomColToGlobal[j];
233	>
234	>	if (excludes->hasPair(iglob, jglob))
235	>	excludesForAtom[i].push_back(j);
236	>
237	>	if (oneTwo->hasPair(iglob, jglob)) {
238	>	toposForAtom[i].push_back(j);
239	>	topoDist[i].push_back(1);
240	>	} else {
241	>	if (oneThree->hasPair(iglob, jglob)) {
242	>	toposForAtom[i].push_back(j);
243	>	topoDist[i].push_back(2);
244	>	} else {
245	>	if (oneFour->hasPair(iglob, jglob)) {
246	>	toposForAtom[i].push_back(j);
247	>	topoDist[i].push_back(3);
248	>	}
249	>	}
250	>	}
251	>	}
252	>	}
253	>
254	>	#else
255	>	excludesForAtom.clear();
256	>	excludesForAtom.resize(nLocal_);
257	>	toposForAtom.clear();
258	>	toposForAtom.resize(nLocal_);
259	>	topoDist.clear();
260	>	topoDist.resize(nLocal_);
261	>
262	>	for (int i = 0; i < nLocal_; i++) {
263	>	int iglob = AtomLocalToGlobal[i];
264	>
265	>	for (int j = 0; j < nLocal_; j++) {
266	>	int jglob = AtomLocalToGlobal[j];
267	>
268	>	if (excludes->hasPair(iglob, jglob))
269	>	excludesForAtom[i].push_back(j);
270	>
271	>	if (oneTwo->hasPair(iglob, jglob)) {
272	>	toposForAtom[i].push_back(j);
273	>	topoDist[i].push_back(1);
274	>	} else {
275	>	if (oneThree->hasPair(iglob, jglob)) {
276	>	toposForAtom[i].push_back(j);
277	>	topoDist[i].push_back(2);
278	>	} else {
279	>	if (oneFour->hasPair(iglob, jglob)) {
280	>	toposForAtom[i].push_back(j);
281	>	topoDist[i].push_back(3);
282	>	}
283	>	}
284	>	}
285	>	}
286	>	}
287		#endif
288	+
289	+	// allocate memory for the parallel objects
290	+	atypesLocal.resize(nLocal_);
291	+
292	+	for (int i = 0; i < nLocal_; i++)
293	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
294	+
295	+	groupList_.clear();
296	+	groupList_.resize(nGroups_);
297	+	for (int i = 0; i < nGroups_; i++) {
298	+	int gid = cgLocalToGlobal[i];
299	+	for (int j = 0; j < nLocal_; j++) {
300	+	int aid = AtomLocalToGlobal[j];
301	+	if (globalGroupMembership[aid] == gid) {
302	+	groupList_[i].push_back(j);
303	+	}
304	+	}
305	+	}
306		}
307
308	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
309	+	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
310	+	if (toposForAtom[atom1][j] == atom2)
311	+	return topoDist[atom1][j];
312	+	}
313	+	return 0;
314	+	}
315
316	+	void ForceMatrixDecomposition::zeroWorkArrays() {
317	+	pairwisePot = 0.0;
318	+	embeddingPot = 0.0;
319	+	excludedPot = 0.0;
320	+	excludedSelfPot = 0.0;
321
322	+	#ifdef IS_MPI
323	+	if (storageLayout_ & DataStorage::dslForce) {
324	+	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
325	+	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
326	+	}
327	+
328	+	if (storageLayout_ & DataStorage::dslTorque) {
329	+	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
330	+	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
331	+	}
332	+
333	+	fill(pot_row.begin(), pot_row.end(),
334	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
335	+
336	+	fill(pot_col.begin(), pot_col.end(),
337	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
338	+
339	+	fill(expot_row.begin(), expot_row.end(),
340	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
341	+
342	+	fill(expot_col.begin(), expot_col.end(),
343	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
344	+
345	+	if (storageLayout_ & DataStorage::dslParticlePot) {
346	+	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
347	+	0.0);
348	+	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
349	+	0.0);
350	+	}
351	+
352	+	if (storageLayout_ & DataStorage::dslDensity) {
353	+	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
354	+	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
355	+	}
356	+
357	+	if (storageLayout_ & DataStorage::dslFunctional) {
358	+	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
359	+	0.0);
360	+	fill(atomColData.functional.begin(), atomColData.functional.end(),
361	+	0.0);
362	+	}
363	+
364	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
365	+	fill(atomRowData.functionalDerivative.begin(),
366	+	atomRowData.functionalDerivative.end(), 0.0);
367	+	fill(atomColData.functionalDerivative.begin(),
368	+	atomColData.functionalDerivative.end(), 0.0);
369	+	}
370	+
371	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
372	+	fill(atomRowData.skippedCharge.begin(),
373	+	atomRowData.skippedCharge.end(), 0.0);
374	+	fill(atomColData.skippedCharge.begin(),
375	+	atomColData.skippedCharge.end(), 0.0);
376	+	}
377	+
378	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
379	+	fill(atomRowData.flucQFrc.begin(),
380	+	atomRowData.flucQFrc.end(), 0.0);
381	+	fill(atomColData.flucQFrc.begin(),
382	+	atomColData.flucQFrc.end(), 0.0);
383	+	}
384	+
385	+	if (storageLayout_ & DataStorage::dslElectricField) {
386	+	fill(atomRowData.electricField.begin(),
387	+	atomRowData.electricField.end(), V3Zero);
388	+	fill(atomColData.electricField.begin(),
389	+	atomColData.electricField.end(), V3Zero);
390	+	}
391	+
392	+	if (storageLayout_ & DataStorage::dslSitePotential) {
393	+	fill(atomRowData.sitePotential.begin(),
394	+	atomRowData.sitePotential.end(), 0.0);
395	+	fill(atomColData.sitePotential.begin(),
396	+	atomColData.sitePotential.end(), 0.0);
397	+	}
398	+
399	+	#endif
400	+	// even in parallel, we need to zero out the local arrays:
401	+
402	+	if (storageLayout_ & DataStorage::dslParticlePot) {
403	+	fill(snap_->atomData.particlePot.begin(),
404	+	snap_->atomData.particlePot.end(), 0.0);
405	+	}
406	+
407	+	if (storageLayout_ & DataStorage::dslDensity) {
408	+	fill(snap_->atomData.density.begin(),
409	+	snap_->atomData.density.end(), 0.0);
410	+	}
411	+
412	+	if (storageLayout_ & DataStorage::dslFunctional) {
413	+	fill(snap_->atomData.functional.begin(),
414	+	snap_->atomData.functional.end(), 0.0);
415	+	}
416	+
417	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
418	+	fill(snap_->atomData.functionalDerivative.begin(),
419	+	snap_->atomData.functionalDerivative.end(), 0.0);
420	+	}
421	+
422	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
423	+	fill(snap_->atomData.skippedCharge.begin(),
424	+	snap_->atomData.skippedCharge.end(), 0.0);
425	+	}
426	+
427	+	if (storageLayout_ & DataStorage::dslElectricField) {
428	+	fill(snap_->atomData.electricField.begin(),
429	+	snap_->atomData.electricField.end(), V3Zero);
430	+	}
431	+	if (storageLayout_ & DataStorage::dslSitePotential) {
432	+	fill(snap_->atomData.sitePotential.begin(),
433	+	snap_->atomData.sitePotential.end(), 0.0);
434	+	}
435	+	}
436	+
437	+
438		void ForceMatrixDecomposition::distributeData()  {
439	+
440	+	#ifdef IS_MPI
441	+
442		snap_ = sman_->getCurrentSnapshot();
443		storageLayout_ = sman_->getStorageLayout();
127	–	#ifdef IS_MPI
444
445	+	bool needsCG = true;
446	+	if(info_->getNCutoffGroups() != info_->getNAtoms())
447	+	needsCG = false;
448	+
449		// gather up the atomic positions
450	<	AtomCommVectorRow->gather(snap_->atomData.position,
450	>	AtomPlanVectorRow->gather(snap_->atomData.position,
451		atomRowData.position);
452	<	AtomCommVectorColumn->gather(snap_->atomData.position,
452	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
453		atomColData.position);
454
455		// gather up the cutoff group positions
456	<	cgCommVectorRow->gather(snap_->cgData.position,
457	<	cgRowData.position);
458	<	cgCommVectorColumn->gather(snap_->cgData.position,
459	<	cgColData.position);
456	>
457	>	if (needsCG) {
458	>	cgPlanVectorRow->gather(snap_->cgData.position,
459	>	cgRowData.position);
460	>
461	>	cgPlanVectorColumn->gather(snap_->cgData.position,
462	>	cgColData.position);
463	>	}
464	>
465	>
466	>	if (needVelocities_) {
467	>	// gather up the atomic velocities
468	>	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
469	>	atomColData.velocity);
470	>
471	>	if (needsCG) {
472	>	cgPlanVectorColumn->gather(snap_->cgData.velocity,
473	>	cgColData.velocity);
474	>	}
475	>	}
476	>
477
478		// if needed, gather the atomic rotation matrices
479		if (storageLayout_ & DataStorage::dslAmat) {
480	<	AtomCommMatrixRow->gather(snap_->atomData.aMat,
480	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
481		atomRowData.aMat);
482	<	AtomCommMatrixColumn->gather(snap_->atomData.aMat,
482	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
483		atomColData.aMat);
484		}
485	<
486	<	// if needed, gather the atomic eletrostatic frames
487	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
488	<	AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
489	<	atomRowData.electroFrame);
490	<	AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
491	<	atomColData.electroFrame);
485	>
486	>	// if needed, gather the atomic eletrostatic information
487	>	if (storageLayout_ & DataStorage::dslDipole) {
488	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
489	>	atomRowData.dipole);
490	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
491	>	atomColData.dipole);
492		}
493	+
494	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
495	+	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
496	+	atomRowData.quadrupole);
497	+	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
498	+	atomColData.quadrupole);
499	+	}
500	+
501	+	// if needed, gather the atomic fluctuating charge values
502	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
503	+	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
504	+	atomRowData.flucQPos);
505	+	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
506	+	atomColData.flucQPos);
507	+	}
508	+
509		#endif
510		}
511
512	+	/* collects information obtained during the pre-pair loop onto local
513	+	* data structures.
514	+	*/
515		void ForceMatrixDecomposition::collectIntermediateData() {
516	+	#ifdef IS_MPI
517	+
518		snap_ = sman_->getCurrentSnapshot();
519		storageLayout_ = sman_->getStorageLayout();
520	<	#ifdef IS_MPI
163	<
520	>
521		if (storageLayout_ & DataStorage::dslDensity) {
522
523	<	AtomCommRealRow->scatter(atomRowData.density,
523	>	AtomPlanRealRow->scatter(atomRowData.density,
524		snap_->atomData.density);
525
526		int n = snap_->atomData.density.size();
527	<	std::vector<RealType> rho_tmp(n, 0.0);
528	<	AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
527	>	vector<RealType> rho_tmp(n, 0.0);
528	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
529		for (int i = 0; i < n; i++)
530		snap_->atomData.density[i] += rho_tmp[i];
531		}
532	+
533	+	// this isn't necessary if we don't have polarizable atoms, but
534	+	// we'll leave it here for now.
535	+	if (storageLayout_ & DataStorage::dslElectricField) {
536	+
537	+	AtomPlanVectorRow->scatter(atomRowData.electricField,
538	+	snap_->atomData.electricField);
539	+
540	+	int n = snap_->atomData.electricField.size();
541	+	vector<Vector3d> field_tmp(n, V3Zero);
542	+	AtomPlanVectorColumn->scatter(atomColData.electricField,
543	+	field_tmp);
544	+	for (int i = 0; i < n; i++)
545	+	snap_->atomData.electricField[i] += field_tmp[i];
546	+	}
547		#endif
548		}
549	<
549	>
550	>	/*
551	>	* redistributes information obtained during the pre-pair loop out to
552	>	* row and column-indexed data structures
553	>	*/
554		void ForceMatrixDecomposition::distributeIntermediateData() {
555	+	#ifdef IS_MPI
556		snap_ = sman_->getCurrentSnapshot();
557		storageLayout_ = sman_->getStorageLayout();
558	<	#ifdef IS_MPI
558	>
559		if (storageLayout_ & DataStorage::dslFunctional) {
560	<	AtomCommRealRow->gather(snap_->atomData.functional,
560	>	AtomPlanRealRow->gather(snap_->atomData.functional,
561		atomRowData.functional);
562	<	AtomCommRealColumn->gather(snap_->atomData.functional,
562	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
563		atomColData.functional);
564		}
565
566		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
567	<	AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
567	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
568		atomRowData.functionalDerivative);
569	<	AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
569	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
570		atomColData.functionalDerivative);
571		}
572		#endif
#	Line 197 | Line 574 | namespace OpenMD {
574
575
576		void ForceMatrixDecomposition::collectData() {
577	+	#ifdef IS_MPI
578		snap_ = sman_->getCurrentSnapshot();
579		storageLayout_ = sman_->getStorageLayout();
580	<	#ifdef IS_MPI
580	>
581		int n = snap_->atomData.force.size();
582		vector<Vector3d> frc_tmp(n, V3Zero);
583
584	<	AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
584	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
585		for (int i = 0; i < n; i++) {
586		snap_->atomData.force[i] += frc_tmp[i];
587		frc_tmp[i] = 0.0;
588		}
589
590	<	AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
591	<	for (int i = 0; i < n; i++)
590	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
591	>	for (int i = 0; i < n; i++) {
592		snap_->atomData.force[i] += frc_tmp[i];
593	<
594	<
593	>	}
594	>
595		if (storageLayout_ & DataStorage::dslTorque) {
596
597	<	int nt = snap_->atomData.force.size();
597	>	int nt = snap_->atomData.torque.size();
598		vector<Vector3d> trq_tmp(nt, V3Zero);
599
600	<	AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
601	<	for (int i = 0; i < n; i++) {
600	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
601	>	for (int i = 0; i < nt; i++) {
602		snap_->atomData.torque[i] += trq_tmp[i];
603		trq_tmp[i] = 0.0;
604		}
605
606	<	AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
607	<	for (int i = 0; i < n; i++)
606	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
607	>	for (int i = 0; i < nt; i++)
608		snap_->atomData.torque[i] += trq_tmp[i];
609		}
610	+
611	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
612	+
613	+	int ns = snap_->atomData.skippedCharge.size();
614	+	vector<RealType> skch_tmp(ns, 0.0);
615	+
616	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
617	+	for (int i = 0; i < ns; i++) {
618	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
619	+	skch_tmp[i] = 0.0;
620	+	}
621	+
622	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
623	+	for (int i = 0; i < ns; i++)
624	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
625	+
626	+	}
627
628	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
629	+
630	+	int nq = snap_->atomData.flucQFrc.size();
631	+	vector<RealType> fqfrc_tmp(nq, 0.0);
632	+
633	+	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
634	+	for (int i = 0; i < nq; i++) {
635	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
636	+	fqfrc_tmp[i] = 0.0;
637	+	}
638	+
639	+	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
640	+	for (int i = 0; i < nq; i++)
641	+	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
642	+
643	+	}
644	+
645	+	if (storageLayout_ & DataStorage::dslElectricField) {
646	+
647	+	int nef = snap_->atomData.electricField.size();
648	+	vector<Vector3d> efield_tmp(nef, V3Zero);
649	+
650	+	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
651	+	for (int i = 0; i < nef; i++) {
652	+	snap_->atomData.electricField[i] += efield_tmp[i];
653	+	efield_tmp[i] = 0.0;
654	+	}
655	+
656	+	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
657	+	for (int i = 0; i < nef; i++)
658	+	snap_->atomData.electricField[i] += efield_tmp[i];
659	+	}
660	+
661	+	if (storageLayout_ & DataStorage::dslSitePotential) {
662	+
663	+	int nsp = snap_->atomData.sitePotential.size();
664	+	vector<RealType> sp_tmp(nsp, 0.0);
665	+
666	+	AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
667	+	for (int i = 0; i < nsp; i++) {
668	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
669	+	sp_tmp[i] = 0.0;
670	+	}
671	+
672	+	AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
673	+	for (int i = 0; i < nsp; i++)
674	+	snap_->atomData.sitePotential[i] += sp_tmp[i];
675	+	}
676	+
677		nLocal_ = snap_->getNumberOfAtoms();
678
679	<	vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
680	<	vector<RealType> (nLocal_, 0.0));
679	>	vector<potVec> pot_temp(nLocal_,
680	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
681	>	vector<potVec> expot_temp(nLocal_,
682	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
683	>
684	>	// scatter/gather pot_row into the members of my column
685	>
686	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
687	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
688	>
689	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
690	>	pairwisePot += pot_temp[ii];
691	>
692	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
693	>	excludedPot += expot_temp[ii];
694	>
695	>	if (storageLayout_ & DataStorage::dslParticlePot) {
696	>	// This is the pairwise contribution to the particle pot.  The
697	>	// embedding contribution is added in each of the low level
698	>	// non-bonded routines.  In single processor, this is done in
699	>	// unpackInteractionData, not in collectData.
700	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
701	>	for (int i = 0; i < nLocal_; i++) {
702	>	// factor of two is because the total potential terms are divided
703	>	// by 2 in parallel due to row/ column scatter
704	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
705	>	}
706	>	}
707	>	}
708	>
709	>	fill(pot_temp.begin(), pot_temp.end(),
710	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
711	>	fill(expot_temp.begin(), expot_temp.end(),
712	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
713	>
714	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
715	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
716
717	<	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
718	<	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
719	<	for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
720	<	pot_local[i] += pot_temp[i][ii];
717	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
718	>	pairwisePot += pot_temp[ii];
719	>
720	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
721	>	excludedPot += expot_temp[ii];
722	>
723	>	if (storageLayout_ & DataStorage::dslParticlePot) {
724	>	// This is the pairwise contribution to the particle pot.  The
725	>	// embedding contribution is added in each of the low level
726	>	// non-bonded routines.  In single processor, this is done in
727	>	// unpackInteractionData, not in collectData.
728	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
729	>	for (int i = 0; i < nLocal_; i++) {
730	>	// factor of two is because the total potential terms are divided
731	>	// by 2 in parallel due to row/ column scatter
732	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
733	>	}
734		}
735		}
736	+
737	+	if (storageLayout_ & DataStorage::dslParticlePot) {
738	+	int npp = snap_->atomData.particlePot.size();
739	+	vector<RealType> ppot_temp(npp, 0.0);
740	+
741	+	// This is the direct or embedding contribution to the particle
742	+	// pot.
743	+
744	+	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
745	+	for (int i = 0; i < npp; i++) {
746	+	snap_->atomData.particlePot[i] += ppot_temp[i];
747	+	}
748	+
749	+	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
750	+
751	+	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
752	+	for (int i = 0; i < npp; i++) {
753	+	snap_->atomData.particlePot[i] += ppot_temp[i];
754	+	}
755	+	}
756	+
757	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
758	+	RealType ploc1 = pairwisePot[ii];
759	+	RealType ploc2 = 0.0;
760	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
761	+	pairwisePot[ii] = ploc2;
762	+	}
763	+
764	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
765	+	RealType ploc1 = excludedPot[ii];
766	+	RealType ploc2 = 0.0;
767	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
768	+	excludedPot[ii] = ploc2;
769	+	}
770	+
771	+	// Here be dragons.
772	+	MPI_Comm col = colComm.getComm();
773	+
774	+	MPI_Allreduce(MPI_IN_PLACE,
775	+	&snap_->frameData.conductiveHeatFlux[0], 3,
776	+	MPI_REALTYPE, MPI_SUM, col);
777	+
778	+
779		#endif
780	+
781		}
782
783	+	/**
784	+	* Collects information obtained during the post-pair (and embedding
785	+	* functional) loops onto local data structures.
786	+	*/
787	+	void ForceMatrixDecomposition::collectSelfData() {
788	+
789	+	#ifdef IS_MPI
790	+	snap_ = sman_->getCurrentSnapshot();
791	+	storageLayout_ = sman_->getStorageLayout();
792	+
793	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
794	+	RealType ploc1 = embeddingPot[ii];
795	+	RealType ploc2 = 0.0;
796	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
797	+	embeddingPot[ii] = ploc2;
798	+	}
799	+	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
800	+	RealType ploc1 = excludedSelfPot[ii];
801	+	RealType ploc2 = 0.0;
802	+	MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
803	+	excludedSelfPot[ii] = ploc2;
804	+	}
805	+	#endif
806	+
807	+	}
808	+
809	+	int& ForceMatrixDecomposition::getNAtomsInRow() {
810	+	#ifdef IS_MPI
811	+	return nAtomsInRow_;
812	+	#else
813	+	return nLocal_;
814	+	#endif
815	+	}
816	+
817	+	/**
818	+	* returns the list of atoms belonging to this group.
819	+	*/
820	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
821	+	#ifdef IS_MPI
822	+	return groupListRow_[cg1];
823	+	#else
824	+	return groupList_[cg1];
825	+	#endif
826	+	}
827	+
828	+	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
829	+	#ifdef IS_MPI
830	+	return groupListCol_[cg2];
831	+	#else
832	+	return groupList_[cg2];
833	+	#endif
834	+	}
835
836	<	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
836	>	inline Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1,
837	>	int cg2){
838	>
839		Vector3d d;
250	–
840		#ifdef IS_MPI
841		d = cgColData.position[cg2] - cgRowData.position[cg1];
842		#else
843		d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
844		#endif
845
846	<	snap_->wrapVector(d);
846	>	if (usePeriodicBoundaryConditions_) {
847	>	snap_->wrapVector(d);
848	>	}
849		return d;
850		}
851
852	+	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
853	+	#ifdef IS_MPI
854	+	return cgColData.velocity[cg2];
855	+	#else
856	+	return snap_->cgData.velocity[cg2];
857	+	#endif
858	+	}
859
860	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
860	>	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
861	>	#ifdef IS_MPI
862	>	return atomColData.velocity[atom2];
863	>	#else
864	>	return snap_->atomData.velocity[atom2];
865	>	#endif
866	>	}
867
868	+
869	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1,
870	+	int cg1) {
871		Vector3d d;
872
873		#ifdef IS_MPI
#	Line 268 | Line 875 | namespace OpenMD {
875		#else
876		d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
877		#endif
878	<
879	<	snap_->wrapVector(d);
878	>	if (usePeriodicBoundaryConditions_) {
879	>	snap_->wrapVector(d);
880	>	}
881		return d;
882		}
883
884	<	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
884	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2,
885	>	int cg2) {
886		Vector3d d;
887
888		#ifdef IS_MPI
#	Line 281 | Line 890 | namespace OpenMD {
890		#else
891		d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
892		#endif
893	<
894	<	snap_->wrapVector(d);
893	>	if (usePeriodicBoundaryConditions_) {
894	>	snap_->wrapVector(d);
895	>	}
896		return d;
897		}
898	+
899	+	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
900	+	#ifdef IS_MPI
901	+	return massFactorsRow[atom1];
902	+	#else
903	+	return massFactors[atom1];
904	+	#endif
905	+	}
906	+
907	+	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
908	+	#ifdef IS_MPI
909	+	return massFactorsCol[atom2];
910	+	#else
911	+	return massFactors[atom2];
912	+	#endif
913	+
914	+	}
915
916	<	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
916	>	inline Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1,
917	>	int atom2){
918		Vector3d d;
919
920		#ifdef IS_MPI
#	Line 294 | Line 922 | namespace OpenMD {
922		#else
923		d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
924		#endif
925	<
926	<	snap_->wrapVector(d);
925	>	if (usePeriodicBoundaryConditions_) {
926	>	snap_->wrapVector(d);
927	>	}
928		return d;
929		}
930
931	+	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
932	+	return excludesForAtom[atom1];
933	+	}
934	+
935	+	/**
936	+	* We need to exclude some overcounted interactions that result from
937	+	* the parallel decomposition.
938	+	*/
939	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2,
940	+	int cg1, int cg2) {
941	+	int unique_id_1, unique_id_2;
942	+
943	+	#ifdef IS_MPI
944	+	// in MPI, we have to look up the unique IDs for each atom
945	+	unique_id_1 = AtomRowToGlobal[atom1];
946	+	unique_id_2 = AtomColToGlobal[atom2];
947	+	// group1 = cgRowToGlobal[cg1];
948	+	// group2 = cgColToGlobal[cg2];
949	+	#else
950	+	unique_id_1 = AtomLocalToGlobal[atom1];
951	+	unique_id_2 = AtomLocalToGlobal[atom2];
952	+	int group1 = cgLocalToGlobal[cg1];
953	+	int group2 = cgLocalToGlobal[cg2];
954	+	#endif
955	+
956	+	if (unique_id_1 == unique_id_2) return true;
957	+
958	+	#ifdef IS_MPI
959	+	// this prevents us from doing the pair on multiple processors
960	+	if (unique_id_1 < unique_id_2) {
961	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
962	+	} else {
963	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
964	+	}
965	+	#endif
966	+
967	+	#ifndef IS_MPI
968	+	if (group1 == group2) {
969	+	if (unique_id_1 < unique_id_2) return true;
970	+	}
971	+	#endif
972	+
973	+	return false;
974	+	}
975	+
976	+	/**
977	+	* We need to handle the interactions for atoms who are involved in
978	+	* the same rigid body as well as some short range interactions
979	+	* (bonds, bends, torsions) differently from other interactions.
980	+	* We'll still visit the pairwise routines, but with a flag that
981	+	* tells those routines to exclude the pair from direct long range
982	+	* interactions.  Some indirect interactions (notably reaction
983	+	* field) must still be handled for these pairs.
984	+	*/
985	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
986	+
987	+	// excludesForAtom was constructed to use row/column indices in the MPI
988	+	// version, and to use local IDs in the non-MPI version:
989	+
990	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
991	+	i != excludesForAtom[atom1].end(); ++i) {
992	+	if ( (*i) == atom2 ) return true;
993	+	}
994	+
995	+	return false;
996	+	}
997	+
998	+
999		void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1000		#ifdef IS_MPI
1001		atomRowData.force[atom1] += fg;
#	Line 316 | Line 1013 | namespace OpenMD {
1013		}
1014
1015		// filling interaction blocks with pointers
1016	<	InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {
1017	<	InteractionData idat;
1016	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1017	>	int atom1, int atom2,
1018	>	bool newAtom1) {
1019
1020	+	idat.excluded = excludeAtomPair(atom1, atom2);
1021	+
1022	+	if (newAtom1) {
1023	+
1024		#ifdef IS_MPI
1025	+	idat.atid1 = identsRow[atom1];
1026	+	idat.atid2 = identsCol[atom2];
1027	+
1028	+	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1029	+	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1030	+	} else {
1031	+	idat.sameRegion = false;
1032	+	}
1033	+
1034	+	if (storageLayout_ & DataStorage::dslAmat) {
1035	+	idat.A1 = &(atomRowData.aMat[atom1]);
1036	+	idat.A2 = &(atomColData.aMat[atom2]);
1037	+	}
1038	+
1039	+	if (storageLayout_ & DataStorage::dslTorque) {
1040	+	idat.t1 = &(atomRowData.torque[atom1]);
1041	+	idat.t2 = &(atomColData.torque[atom2]);
1042	+	}
1043	+
1044	+	if (storageLayout_ & DataStorage::dslDipole) {
1045	+	idat.dipole1 = &(atomRowData.dipole[atom1]);
1046	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1047	+	}
1048	+
1049	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1050	+	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1051	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1052	+	}
1053	+
1054	+	if (storageLayout_ & DataStorage::dslDensity) {
1055	+	idat.rho1 = &(atomRowData.density[atom1]);
1056	+	idat.rho2 = &(atomColData.density[atom2]);
1057	+	}
1058	+
1059	+	if (storageLayout_ & DataStorage::dslFunctional) {
1060	+	idat.frho1 = &(atomRowData.functional[atom1]);
1061	+	idat.frho2 = &(atomColData.functional[atom2]);
1062	+	}
1063	+
1064	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1065	+	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1066	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1067	+	}
1068	+
1069	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1070	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1071	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1072	+	}
1073	+
1074	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1075	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1076	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1077	+	}
1078	+
1079	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1080	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1081	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1082	+	}
1083	+
1084	+	#else
1085	+
1086	+	idat.atid1 = idents[atom1];
1087	+	idat.atid2 = idents[atom2];
1088	+
1089	+	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1090	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1091	+	} else {
1092	+	idat.sameRegion = false;
1093	+	}
1094	+
1095	+	if (storageLayout_ & DataStorage::dslAmat) {
1096	+	idat.A1 = &(snap_->atomData.aMat[atom1]);
1097	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1098	+	}
1099	+
1100	+	if (storageLayout_ & DataStorage::dslTorque) {
1101	+	idat.t1 = &(snap_->atomData.torque[atom1]);
1102	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1103	+	}
1104	+
1105	+	if (storageLayout_ & DataStorage::dslDipole) {
1106	+	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1107	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1108	+	}
1109	+
1110	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1111	+	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1112	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1113	+	}
1114	+
1115	+	if (storageLayout_ & DataStorage::dslDensity) {
1116	+	idat.rho1 = &(snap_->atomData.density[atom1]);
1117	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1118	+	}
1119	+
1120	+	if (storageLayout_ & DataStorage::dslFunctional) {
1121	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1122	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1123	+	}
1124	+
1125	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1126	+	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1127	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1128	+	}
1129	+
1130	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1131	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1132	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1133	+	}
1134	+
1135	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1136	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1137	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1138	+	}
1139	+
1140	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1141	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1142	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1143	+	}
1144	+	#endif
1145	+
1146	+	} else {
1147	+	// atom1 is not new, so don't bother updating properties of that atom:
1148	+	#ifdef IS_MPI
1149	+	idat.atid2 = identsCol[atom2];
1150	+
1151	+	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1152	+	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1153	+	} else {
1154	+	idat.sameRegion = false;
1155	+	}
1156	+
1157		if (storageLayout_ & DataStorage::dslAmat) {
324	–	idat.A1 = &(atomRowData.aMat[atom1]);
1158		idat.A2 = &(atomColData.aMat[atom2]);
1159		}
1160
328	–	if (storageLayout_ & DataStorage::dslElectroFrame) {
329	–	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
330	–	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
331	–	}
332	–
1161		if (storageLayout_ & DataStorage::dslTorque) {
334	–	idat.t1 = &(atomRowData.torque[atom1]);
1162		idat.t2 = &(atomColData.torque[atom2]);
1163		}
1164
1165	+	if (storageLayout_ & DataStorage::dslDipole) {
1166	+	idat.dipole2 = &(atomColData.dipole[atom2]);
1167	+	}
1168	+
1169	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1170	+	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1171	+	}
1172	+
1173		if (storageLayout_ & DataStorage::dslDensity) {
339	–	idat.rho1 = &(atomRowData.density[atom1]);
1174		idat.rho2 = &(atomColData.density[atom2]);
1175		}
1176
1177	+	if (storageLayout_ & DataStorage::dslFunctional) {
1178	+	idat.frho2 = &(atomColData.functional[atom2]);
1179	+	}
1180	+
1181		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
344	–	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1182		idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1183		}
1184	<	#else
1185	<	if (storageLayout_ & DataStorage::dslAmat) {
1186	<	idat.A1 = &(snap_->atomData.aMat[atom1]);
350	<	idat.A2 = &(snap_->atomData.aMat[atom2]);
1184	>
1185	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1186	>	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1187		}
1188
1189	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1190	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
355	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1189	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1190	>	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1191		}
1192
1193	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1194	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1195	+	}
1196	+
1197	+	#else
1198	+	idat.atid2 = idents[atom2];
1199	+
1200	+	if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1201	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1202	+	} else {
1203	+	idat.sameRegion = false;
1204	+	}
1205	+
1206	+	if (storageLayout_ & DataStorage::dslAmat) {
1207	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1208	+	}
1209	+
1210		if (storageLayout_ & DataStorage::dslTorque) {
359	–	idat.t1 = &(snap_->atomData.torque[atom1]);
1211		idat.t2 = &(snap_->atomData.torque[atom2]);
1212		}
1213
1214	<	if (storageLayout_ & DataStorage::dslDensity) {
1215	<	idat.rho1 = &(snap_->atomData.density[atom1]);
1214	>	if (storageLayout_ & DataStorage::dslDipole) {
1215	>	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1216	>	}
1217	>
1218	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1219	>	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1220	>	}
1221	>
1222	>	if (storageLayout_ & DataStorage::dslDensity) {
1223		idat.rho2 = &(snap_->atomData.density[atom2]);
1224		}
1225
1226	+	if (storageLayout_ & DataStorage::dslFunctional) {
1227	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1228	+	}
1229	+
1230		if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
369	–	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1231		idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1232		}
372	–	#endif
373	–	return idat;
374	–	}
1233
1234	<	InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
1234	>	if (storageLayout_ & DataStorage::dslParticlePot) {
1235	>	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1236	>	}
1237
1238	<	InteractionData idat;
1239	<	#ifdef IS_MPI
380	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
381	<	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
382	<	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1238	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1239	>	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1240		}
1241	<	if (storageLayout_ & DataStorage::dslTorque) {
1242	<	idat.t1 = &(atomRowData.torque[atom1]);
1243	<	idat.t2 = &(atomColData.torque[atom2]);
1241	>
1242	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1243	>	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1244		}
1245	<	if (storageLayout_ & DataStorage::dslForce) {
1246	<	idat.t1 = &(atomRowData.force[atom1]);
390	<	idat.t2 = &(atomColData.force[atom2]);
1245	>
1246	>	#endif
1247		}
1248	<	#else
1249	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1250	<	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1251	<	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1248	>	}
1249	>
1250	>	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat,
1251	>	int atom1, int atom2) {
1252	>	#ifdef IS_MPI
1253	>	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1254	>	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1255	>	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1256	>	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1257	>
1258	>	atomRowData.force[atom1] += *(idat.f1);
1259	>	atomColData.force[atom2] -= *(idat.f1);
1260	>
1261	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1262	>	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1263	>	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1264		}
1265	<	if (storageLayout_ & DataStorage::dslTorque) {
1266	<	idat.t1 = &(snap_->atomData.torque[atom1]);
1267	<	idat.t2 = &(snap_->atomData.torque[atom2]);
1265	>
1266	>	if (storageLayout_ & DataStorage::dslElectricField) {
1267	>	atomRowData.electricField[atom1] += *(idat.eField1);
1268	>	atomColData.electricField[atom2] += *(idat.eField2);
1269		}
1270	<	if (storageLayout_ & DataStorage::dslForce) {
1271	<	idat.t1 = &(snap_->atomData.force[atom1]);
1272	<	idat.t2 = &(snap_->atomData.force[atom2]);
1270	>
1271	>	if (storageLayout_ & DataStorage::dslSitePotential) {
1272	>	atomRowData.sitePotential[atom1] += *(idat.sPot1);
1273	>	atomColData.sitePotential[atom2] += *(idat.sPot2);
1274		}
405	–	#endif
406	–
407	–	}
1275
1276	<	SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
1277	<	SelfData sdat;
1278	<	// Still Missing atype, skippedCharge, potVec pot,
1279	<	if (storageLayout_ & DataStorage::dslElectroFrame) {
1280	<	sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
1276	>	#else
1277	>	pairwisePot += *(idat.pot);
1278	>	excludedPot += *(idat.excludedPot);
1279	>
1280	>	snap_->atomData.force[atom1] += *(idat.f1);
1281	>	snap_->atomData.force[atom2] -= *(idat.f1);
1282	>
1283	>	if (idat.doParticlePot) {
1284	>	// This is the pairwise contribution to the particle pot.  The
1285	>	// embedding contribution is added in each of the low level
1286	>	// non-bonded routines.  In parallel, this calculation is done
1287	>	// in collectData, not in unpackInteractionData.
1288	>	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1289	>	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1290		}
1291
1292	<	if (storageLayout_ & DataStorage::dslTorque) {
1293	<	sdat.t = &(snap_->atomData.torque[atom1]);
1292	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
1293	>	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1294	>	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1295		}
1296	<
1297	<	if (storageLayout_ & DataStorage::dslDensity) {
1298	<	sdat.rho = &(snap_->atomData.density[atom1]);
1296	>
1297	>	if (storageLayout_ & DataStorage::dslElectricField) {
1298	>	snap_->atomData.electricField[atom1] += *(idat.eField1);
1299	>	snap_->atomData.electricField[atom2] += *(idat.eField2);
1300		}
1301	<
1302	<	if (storageLayout_ & DataStorage::dslFunctional) {
1303	<	sdat.frho = &(snap_->atomData.functional[atom1]);
1301	>
1302	>	if (storageLayout_ & DataStorage::dslSitePotential) {
1303	>	snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1304	>	snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1305		}
427	–
428	–	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
429	–	sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
430	–	}
1306
1307	<	return sdat;
1307	>	#endif
1308	>
1309		}
1310
435	–
436	–
1311		/*
1312		* buildNeighborList
1313		*
1314	<	* first element of pair is row-indexed CutoffGroup
1315	<	* second element of pair is column-indexed CutoffGroup
1314	>	* Constructs the Verlet neighbor list for a force-matrix
1315	>	* decomposition.  In this case, each processor is responsible for
1316	>	* row-site interactions with column-sites.
1317	>	*
1318	>	* neighborList is returned as a packed array of neighboring
1319	>	* column-ordered CutoffGroups.  The starting position in
1320	>	* neighborList for each row-ordered CutoffGroup is given by the
1321	>	* returned vector point.
1322		*/
1323	<	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1324	<
1325	<	vector<pair<int, int> > neighborList;
1326	<	#ifdef IS_MPI
1327	<	CellListRow.clear();
1328	<	CellListCol.clear();
1329	<	#else
450	<	CellList.clear();
451	<	#endif
1323	>	void ForceMatrixDecomposition::buildNeighborList(vector<int>& neighborList,
1324	>	vector<int>& point) {
1325	>	neighborList.clear();
1326	>	point.clear();
1327	>	int len = 0;
1328	>
1329	>	bool doAllPairs = false;
1330
453	–	// dangerous to not do error checking.
454	–	RealType skinThickness_ = info_->getSimParams()->getSkinThickness();
455	–	RealType rCut_;
456	–
457	–	RealType rList_ = (rCut_ + skinThickness_);
458	–	RealType rl2 = rList_ * rList_;
1331		Snapshot* snap_ = sman_->getCurrentSnapshot();
1332	<	Mat3x3d Hmat = snap_->getHmat();
1333	<	Vector3d Hx = Hmat.getColumn(0);
462	<	Vector3d Hy = Hmat.getColumn(1);
463	<	Vector3d Hz = Hmat.getColumn(2);
464	<	Vector3i nCells;
1332	>	Mat3x3d box;
1333	>	Mat3x3d invBox;
1334
466	–	nCells.x() = (int) ( Hx.length() )/ rList_;
467	–	nCells.y() = (int) ( Hy.length() )/ rList_;
468	–	nCells.z() = (int) ( Hz.length() )/ rList_;
469	–
470	–	Mat3x3d invHmat = snap_->getInvHmat();
1335		Vector3d rs, scaled, dr;
1336		Vector3i whichCell;
1337		int cellIndex;
1338
1339		#ifdef IS_MPI
1340	<	for (int i = 0; i < nGroupsInRow_; i++) {
1341	<	rs = cgRowData.position[i];
1342	<	// scaled positions relative to the box vectors
1343	<	scaled = invHmat * rs;
1344	<	// wrap the vector back into the unit box by subtracting integer box
1345	<	// numbers
1346	<	for (int j = 0; j < 3; j++)
1347	<	scaled[j] -= roundMe(scaled[j]);
1348	<
1349	<	// find xyz-indices of cell that cutoffGroup is in.
1350	<	whichCell.x() = nCells.x() * scaled.x();
1351	<	whichCell.y() = nCells.y() * scaled.y();
1352	<	whichCell.z() = nCells.z() * scaled.z();
1353	<
490	<	// find single index of this cell:
491	<	cellIndex = Vlinear(whichCell, nCells);
492	<	// add this cutoff group to the list of groups in this cell;
493	<	CellListRow[cellIndex].push_back(i);
1340	>	cellListRow_.clear();
1341	>	cellListCol_.clear();
1342	>	point.resize(nGroupsInRow_+1);
1343	>	#else
1344	>	cellList_.clear();
1345	>	point.resize(nGroups_+1);
1346	>	#endif
1347	>
1348	>	if (!usePeriodicBoundaryConditions_) {
1349	>	box = snap_->getBoundingBox();
1350	>	invBox = snap_->getInvBoundingBox();
1351	>	} else {
1352	>	box = snap_->getHmat();
1353	>	invBox = snap_->getInvHmat();
1354		}
1355	+
1356	+	Vector3d A = box.getColumn(0);
1357	+	Vector3d B = box.getColumn(1);
1358	+	Vector3d C = box.getColumn(2);
1359
1360	<	for (int i = 0; i < nGroupsInCol_; i++) {
1361	<	rs = cgColData.position[i];
1362	<	// scaled positions relative to the box vectors
1363	<	scaled = invHmat * rs;
500	<	// wrap the vector back into the unit box by subtracting integer box
501	<	// numbers
502	<	for (int j = 0; j < 3; j++)
503	<	scaled[j] -= roundMe(scaled[j]);
1360	>	// Required for triclinic cells
1361	>	Vector3d AxB = cross(A, B);
1362	>	Vector3d BxC = cross(B, C);
1363	>	Vector3d CxA = cross(C, A);
1364
1365	<	// find xyz-indices of cell that cutoffGroup is in.
1366	<	whichCell.x() = nCells.x() * scaled.x();
1367	<	whichCell.y() = nCells.y() * scaled.y();
1368	<	whichCell.z() = nCells.z() * scaled.z();
1365	>	// unit vectors perpendicular to the faces of the triclinic cell:
1366	>	AxB.normalize();
1367	>	BxC.normalize();
1368	>	CxA.normalize();
1369
1370	<	// find single index of this cell:
1371	<	cellIndex = Vlinear(whichCell, nCells);
1372	<	// add this cutoff group to the list of groups in this cell;
1373	<	CellListCol[cellIndex].push_back(i);
1374	<	}
1370	>	// A set of perpendicular lengths in triclinic cells:
1371	>	RealType Wa = abs(dot(A, BxC));
1372	>	RealType Wb = abs(dot(B, CxA));
1373	>	RealType Wc = abs(dot(C, AxB));
1374	>
1375	>	nCells_.x() = int( Wa / rList_ );
1376	>	nCells_.y() = int( Wb / rList_ );
1377	>	nCells_.z() = int( Wc / rList_ );
1378	>
1379	>	// handle small boxes where the cell offsets can end up repeating cells
1380	>	if (nCells_.x() < 3) doAllPairs = true;
1381	>	if (nCells_.y() < 3) doAllPairs = true;
1382	>	if (nCells_.z() < 3) doAllPairs = true;
1383	>
1384	>	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1385	>
1386	>	#ifdef IS_MPI
1387	>	cellListRow_.resize(nCtot);
1388	>	cellListCol_.resize(nCtot);
1389		#else
1390	<	for (int i = 0; i < nGroups_; i++) {
1391	<	rs = snap_->cgData.position[i];
1392	<	// scaled positions relative to the box vectors
1393	<	scaled = invHmat * rs;
1394	<	// wrap the vector back into the unit box by subtracting integer box
1395	<	// numbers
1396	<	for (int j = 0; j < 3; j++)
1397	<	scaled[j] -= roundMe(scaled[j]);
1390	>	cellList_.resize(nCtot);
1391	>	#endif
1392	>
1393	>	if (!doAllPairs) {
1394	>
1395	>	#ifdef IS_MPI
1396	>
1397	>	for (int i = 0; i < nGroupsInRow_; i++) {
1398	>	rs = cgRowData.position[i];
1399	>
1400	>	// scaled positions relative to the box vectors
1401	>	scaled = invBox * rs;
1402	>
1403	>	// wrap the vector back into the unit box by subtracting integer box
1404	>	// numbers
1405	>	for (int j = 0; j < 3; j++) {
1406	>	scaled[j] -= roundMe(scaled[j]);
1407	>	scaled[j] += 0.5;
1408	>	// Handle the special case when an object is exactly on the
1409	>	// boundary (a scaled coordinate of 1.0 is the same as
1410	>	// scaled coordinate of 0.0)
1411	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1412	>	}
1413	>
1414	>	// find xyz-indices of cell that cutoffGroup is in.
1415	>	whichCell.x() = nCells_.x() * scaled.x();
1416	>	whichCell.y() = nCells_.y() * scaled.y();
1417	>	whichCell.z() = nCells_.z() * scaled.z();
1418	>
1419	>	// find single index of this cell:
1420	>	cellIndex = Vlinear(whichCell, nCells_);
1421	>
1422	>	// add this cutoff group to the list of groups in this cell;
1423	>	cellListRow_[cellIndex].push_back(i);
1424	>	}
1425	>	for (int i = 0; i < nGroupsInCol_; i++) {
1426	>	rs = cgColData.position[i];
1427	>
1428	>	// scaled positions relative to the box vectors
1429	>	scaled = invBox * rs;
1430	>
1431	>	// wrap the vector back into the unit box by subtracting integer box
1432	>	// numbers
1433	>	for (int j = 0; j < 3; j++) {
1434	>	scaled[j] -= roundMe(scaled[j]);
1435	>	scaled[j] += 0.5;
1436	>	// Handle the special case when an object is exactly on the
1437	>	// boundary (a scaled coordinate of 1.0 is the same as
1438	>	// scaled coordinate of 0.0)
1439	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1440	>	}
1441	>
1442	>	// find xyz-indices of cell that cutoffGroup is in.
1443	>	whichCell.x() = nCells_.x() * scaled.x();
1444	>	whichCell.y() = nCells_.y() * scaled.y();
1445	>	whichCell.z() = nCells_.z() * scaled.z();
1446	>
1447	>	// find single index of this cell:
1448	>	cellIndex = Vlinear(whichCell, nCells_);
1449	>
1450	>	// add this cutoff group to the list of groups in this cell;
1451	>	cellListCol_[cellIndex].push_back(i);
1452	>	}
1453	>
1454	>	#else
1455	>	for (int i = 0; i < nGroups_; i++) {
1456	>	rs = snap_->cgData.position[i];
1457	>
1458	>	// scaled positions relative to the box vectors
1459	>	scaled = invBox * rs;
1460	>
1461	>	// wrap the vector back into the unit box by subtracting integer box
1462	>	// numbers
1463	>	for (int j = 0; j < 3; j++) {
1464	>	scaled[j] -= roundMe(scaled[j]);
1465	>	scaled[j] += 0.5;
1466	>	// Handle the special case when an object is exactly on the
1467	>	// boundary (a scaled coordinate of 1.0 is the same as
1468	>	// scaled coordinate of 0.0)
1469	>	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1470	>	}
1471	>
1472	>	// find xyz-indices of cell that cutoffGroup is in.
1473	>	whichCell.x() = int(nCells_.x() * scaled.x());
1474	>	whichCell.y() = int(nCells_.y() * scaled.y());
1475	>	whichCell.z() = int(nCells_.z() * scaled.z());
1476	>
1477	>	// find single index of this cell:
1478	>	cellIndex = Vlinear(whichCell, nCells_);
1479	>
1480	>	// add this cutoff group to the list of groups in this cell;
1481	>	cellList_[cellIndex].push_back(i);
1482	>	}
1483
525	–	// find xyz-indices of cell that cutoffGroup is in.
526	–	whichCell.x() = nCells.x() * scaled.x();
527	–	whichCell.y() = nCells.y() * scaled.y();
528	–	whichCell.z() = nCells.z() * scaled.z();
529	–
530	–	// find single index of this cell:
531	–	cellIndex = Vlinear(whichCell, nCells);
532	–	// add this cutoff group to the list of groups in this cell;
533	–	CellList[cellIndex].push_back(i);
534	–	}
1484		#endif
1485
1486	+	#ifdef IS_MPI
1487	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1488	+	rs = cgRowData.position[j1];
1489	+	#else
1490
1491	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1492	+	rs = snap_->cgData.position[j1];
1493	+	#endif
1494	+	point[j1] = len;
1495	+
1496	+	// scaled positions relative to the box vectors
1497	+	scaled = invBox * rs;
1498	+
1499	+	// wrap the vector back into the unit box by subtracting integer box
1500	+	// numbers
1501	+	for (int j = 0; j < 3; j++) {
1502	+	scaled[j] -= roundMe(scaled[j]);
1503	+	scaled[j] += 0.5;
1504	+	// Handle the special case when an object is exactly on the
1505	+	// boundary (a scaled coordinate of 1.0 is the same as
1506	+	// scaled coordinate of 0.0)
1507	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1508	+	}
1509	+
1510	+	// find xyz-indices of cell that cutoffGroup is in.
1511	+	whichCell.x() = nCells_.x() * scaled.x();
1512	+	whichCell.y() = nCells_.y() * scaled.y();
1513	+	whichCell.z() = nCells_.z() * scaled.z();
1514	+
1515	+	// find single index of this cell:
1516	+	int m1 = Vlinear(whichCell, nCells_);
1517
1518	<	for (int m1z = 0; m1z < nCells.z(); m1z++) {
1519	<	for (int m1y = 0; m1y < nCells.y(); m1y++) {
1520	<	for (int m1x = 0; m1x < nCells.x(); m1x++) {
1521	<	Vector3i m1v(m1x, m1y, m1z);
543	<	int m1 = Vlinear(m1v, nCells);
544	<	for (int offset = 0; offset < nOffset_; offset++) {
545	<	Vector3i m2v = m1v + cellOffsets_[offset];
1518	>	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1519	>	os != cellOffsets_.end(); ++os) {
1520	>
1521	>	Vector3i m2v = whichCell + (*os);
1522
1523	<	if (m2v.x() >= nCells.x()) {
1524	<	m2v.x() = 0;
1525	<	} else if (m2v.x() < 0) {
1526	<	m2v.x() = nCells.x() - 1;
1527	<	}
1528	<
1529	<	if (m2v.y() >= nCells.y()) {
1530	<	m2v.y() = 0;
1531	<	} else if (m2v.y() < 0) {
1532	<	m2v.y() = nCells.y() - 1;
1533	<	}
1534	<
1535	<	if (m2v.z() >= nCells.z()) {
1536	<	m2v.z() = 0;
1537	<	} else if (m2v.z() < 0) {
1538	<	m2v.z() = nCells.z() - 1;
1539	<	}
1540	<
565	<	int m2 = Vlinear (m2v, nCells);
566	<
1523	>	if (m2v.x() >= nCells_.x()) {
1524	>	m2v.x() = 0;
1525	>	} else if (m2v.x() < 0) {
1526	>	m2v.x() = nCells_.x() - 1;
1527	>	}
1528	>
1529	>	if (m2v.y() >= nCells_.y()) {
1530	>	m2v.y() = 0;
1531	>	} else if (m2v.y() < 0) {
1532	>	m2v.y() = nCells_.y() - 1;
1533	>	}
1534	>
1535	>	if (m2v.z() >= nCells_.z()) {
1536	>	m2v.z() = 0;
1537	>	} else if (m2v.z() < 0) {
1538	>	m2v.z() = nCells_.z() - 1;
1539	>	}
1540	>	int m2 = Vlinear (m2v, nCells_);
1541		#ifdef IS_MPI
1542	<	for (vector<int>::iterator j1 = CellListRow[m1].begin();
1543	<	j1 != CellListRow[m1].end(); ++j1) {
1544	<	for (vector<int>::iterator j2 = CellListCol[m2].begin();
1545	<	j2 != CellListCol[m2].end(); ++j2) {
1546	<
1547	<	// Always do this if we're in different cells or if
1548	<	// we're in the same cell and the global index of the
1549	<	// j2 cutoff group is less than the j1 cutoff group
1550	<
577	<	if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
578	<	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
579	<	snap_->wrapVector(dr);
580	<	if (dr.lengthSquare() < rl2) {
581	<	neighborList.push_back(make_pair((*j1), (*j2)));
582	<	}
583	<	}
584	<	}
1542	>	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1543	>	j2 != cellListCol_[m2].end(); ++j2) {
1544	>
1545	>	// In parallel, we need to visit *all* pairs of row
1546	>	// & column indicies and will divide labor in the
1547	>	// force evaluation later.
1548	>	dr = cgColData.position[(*j2)] - rs;
1549	>	if (usePeriodicBoundaryConditions_) {
1550	>	snap_->wrapVector(dr);
1551		}
1552	+	if (dr.lengthSquare() < rListSq_) {
1553	+	neighborList.push_back( (*j2) );
1554	+	++len;
1555	+	}
1556	+	}
1557		#else
1558	<	for (vector<int>::iterator j1 = CellList[m1].begin();
1559	<	j1 != CellList[m1].end(); ++j1) {
1560	<	for (vector<int>::iterator j2 = CellList[m2].begin();
1561	<	j2 != CellList[m2].end(); ++j2) {
1562	<
1563	<	// Always do this if we're in different cells or if
1564	<	// we're in the same cell and the global index of the
1565	<	// j2 cutoff group is less than the j1 cutoff group
1566	<
1567	<	if (m2 != m1 || (*j2) < (*j1)) {
1568	<	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1569	<	snap_->wrapVector(dr);
1570	<	if (dr.lengthSquare() < rl2) {
1571	<	neighborList.push_back(make_pair((*j1), (*j2)));
1572	<	}
1573	<	}
1558	>	for (vector<int>::iterator j2 = cellList_[m2].begin();
1559	>	j2 != cellList_[m2].end(); ++j2) {
1560	>
1561	>	// Always do this if we're in different cells or if
1562	>	// we're in the same cell and the global index of
1563	>	// the j2 cutoff group is greater than or equal to
1564	>	// the j1 cutoff group.  Note that Rappaport's code
1565	>	// has a "less than" conditional here, but that
1566	>	// deals with atom-by-atom computation.  OpenMD
1567	>	// allows atoms within a single cutoff group to
1568	>	// interact with each other.
1569	>
1570	>	if ( (*j2) >= j1 ) {
1571	>
1572	>	dr = snap_->cgData.position[(*j2)] - rs;
1573	>	if (usePeriodicBoundaryConditions_) {
1574	>	snap_->wrapVector(dr);
1575		}
1576	+	if ( dr.lengthSquare() < rListSq_) {
1577	+	neighborList.push_back( (*j2) );
1578	+	++len;
1579	+	}
1580		}
1581	+	}
1582		#endif
1583	+	}
1584	+	}
1585	+	} else {
1586	+	// branch to do all cutoff group pairs
1587	+	#ifdef IS_MPI
1588	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1589	+	point[j1] = len;
1590	+	rs = cgRowData.position[j1];
1591	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1592	+	dr = cgColData.position[j2] - rs;
1593	+	if (usePeriodicBoundaryConditions_) {
1594	+	snap_->wrapVector(dr);
1595		}
1596	+	if (dr.lengthSquare() < rListSq_) {
1597	+	neighborList.push_back( j2 );
1598	+	++len;
1599	+	}
1600		}
1601	+	}
1602	+	#else
1603	+	// include all groups here.
1604	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1605	+	point[j1] = len;
1606	+	rs = snap_->cgData.position[j1];
1607	+	// include self group interactions j2 == j1
1608	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1609	+	dr = snap_->cgData.position[j2] - rs;
1610	+	if (usePeriodicBoundaryConditions_) {
1611	+	snap_->wrapVector(dr);
1612	+	}
1613	+	if (dr.lengthSquare() < rListSq_) {
1614	+	neighborList.push_back( j2 );
1615	+	++len;
1616	+	}
1617	+	}
1618		}
1619	+	#endif
1620		}
1621	<	return neighborList;
1621	>
1622	>	#ifdef IS_MPI
1623	>	point[nGroupsInRow_] = len;
1624	>	#else
1625	>	point[nGroups_] = len;
1626	>	#endif
1627	>
1628	>	// save the local cutoff group positions for the check that is
1629	>	// done on each loop:
1630	>	saved_CG_positions_.clear();
1631	>	saved_CG_positions_.reserve(nGroups_);
1632	>	for (int i = 0; i < nGroups_; i++)
1633	>	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1634		}
1635		} //end namespace OpenMD

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