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root/OpenMD/branches/devel_omp/src/parallel/ForceMatrixDecomposition.cpp

Comparing:
branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1538 by chuckv, Tue Jan 11 18:58:12 2011 UTC vs.
branches/devel_omp/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1599 by mciznick, Fri Jul 29 19:03:36 2011 UTC

#	Line 1 | Line 1
1	<	/**
2	<	* @file ForceDecomposition.cpp
3	<	* @author Charles Vardeman <cvardema.at.nd.edu>
4	<	* @date 08/18/2010
5	<	* @time 11:56am
6	<	* @version 1.0
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
8	–	* @section LICENSE
9	–	* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
10	–	*
4		* The University of Notre Dame grants you ("Licensee") a
5		* non-exclusive, royalty free, license to use, modify and
6		* redistribute this software in source and binary code form, provided
#	Line 45 | Line 38
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39		* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41	+	#include "parallel/ForceMatrixDecomposition.hpp"
42	+	#include "math/SquareMatrix3.hpp"
43	+	#include "nonbonded/NonBondedInteraction.hpp"
44	+	#include "brains/SnapshotManager.hpp"
45	+	#include "brains/PairList.hpp"
46	+	#include "primitives/Molecule.hpp"
47
48	+	using namespace std;
49	+	namespace OpenMD {
50
51	<
52	<	/*  -*- c++ -*-  */
53	<	#include "config.h"
54	<	#include <stdlib.h>
51	>	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) :
52	>	ForceDecomposition(info, iMan) {
53	>	// In a parallel computation, row and colum scans must visit all
54	>	// surrounding cells (not just the 14 upper triangular blocks that
55	>	// are used when the processor can see all pairs)
56		#ifdef IS_MPI
57	<	#include <mpi.h>
58	<	#endif
57	>	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
58	>	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
59	>	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
60	>	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
61	>	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
62	>	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
63	>	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
64	>	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
65	>	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
66	>	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
67	>	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
68	>	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
69	>	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
70	>	#endif
71	>	}
72
73	<	#include <iostream>
74	<	#include <vector>
75	<	#include <algorithm>
76	<	#include <cmath>
77	<	#include "parallel/ForceDecomposition.hpp"
73	>	/**
74	>	* distributeInitialData is essentially a copy of the older fortran
75	>	* SimulationSetup
76	>	*/
77	>	void ForceMatrixDecomposition::distributeInitialData() {
78	>	snap_ = sman_->getCurrentSnapshot();
79	>	storageLayout_ = sman_->getStorageLayout();
80	>	ff_ = info_->getForceField();
81	>	nLocal_ = snap_->getNumberOfAtoms();
82
83	+	nGroups_ = info_->getNLocalCutoffGroups();
84	+	// gather the information for atomtype IDs (atids):
85	+	idents = info_->getIdentArray();
86	+	AtomLocalToGlobal = info_->getGlobalAtomIndices();
87	+	cgLocalToGlobal = info_->getGlobalGroupIndices();
88	+	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
89
90	<	using namespace std;
66	<	using namespace OpenMD;
90	>	massFactors = info_->getMassFactors();
91
92	<	//__static
92	>	PairList* excludes = info_->getExcludedInteractions();
93	>	PairList* oneTwo = info_->getOneTwoInteractions();
94	>	PairList* oneThree = info_->getOneThreeInteractions();
95	>	PairList* oneFour = info_->getOneFourInteractions();
96	>
97		#ifdef IS_MPI
70	–	static vector<MPI:Comm> communictors;
71	–	#endif
98
99	<	//____ MPITypeTraits
100	<	template<typename T>
75	<	struct MPITypeTraits;
99	>	MPI::Intracomm row = rowComm.getComm();
100	>	MPI::Intracomm col = colComm.getComm();
101
102	<	#ifdef IS_MPI
103	<	template<>
104	<	struct MPITypeTraits<RealType> {
105	<	static const MPI::Datatype datatype;
106	<	};
82	<	const MPI_Datatype MPITypeTraits<RealType>::datatype = MY_MPI_REAL;
102	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
103	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
104	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
105	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
106	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
107
108	<	template<>
109	<	struct MPITypeTraits<int> {
110	<	static const MPI::Datatype datatype;
111	<	};
112	<	const MPI::Datatype MPITypeTraits<int>::datatype = MPI_INT;
89	<	#endif
108	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
109	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
110	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
111	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
112	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
113
114	<	/**
115	<	* Constructor for ForceDecomposition Parallel Decomposition Method
116	<	* Will try to construct a symmetric grid of processors. Ideally, the
117	<	* number of processors will be a square ex: 4, 9, 16, 25.
95	<	*
96	<	*/
114	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
115	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
116	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
117	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
118
119	<	ForceDecomposition::ForceDecomposition() {
119	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
120	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
121	>	nGroupsInRow_ = cgPlanIntRow->getSize();
122	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
123
124	<	#ifdef IS_MPI
125	<	int nProcs = MPI::COMM_WORLD.Get_size();
126	<	int worldRank = MPI::COMM_WORLD.Get_rank();
124	>	// Modify the data storage objects with the correct layouts and sizes:
125	>	atomRowData.resize(nAtomsInRow_);
126	>	atomRowData.setStorageLayout(storageLayout_);
127	>	atomColData.resize(nAtomsInCol_);
128	>	atomColData.setStorageLayout(storageLayout_);
129	>	cgRowData.resize(nGroupsInRow_);
130	>	cgRowData.setStorageLayout(DataStorage::dslPosition);
131	>	cgColData.resize(nGroupsInCol_);
132	>	cgColData.setStorageLayout(DataStorage::dslPosition);
133	>
134	>	identsRow.resize(nAtomsInRow_);
135	>	identsCol.resize(nAtomsInCol_);
136	>
137	>	AtomPlanIntRow->gather(idents, identsRow);
138	>	AtomPlanIntColumn->gather(idents, identsCol);
139	>
140	>	// allocate memory for the parallel objects
141	>	atypesRow.resize(nAtomsInRow_);
142	>	atypesCol.resize(nAtomsInCol_);
143	>
144	>	for (int i = 0; i < nAtomsInRow_; i++)
145	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
146	>	for (int i = 0; i < nAtomsInCol_; i++)
147	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
148	>
149	>	pot_row.resize(nAtomsInRow_);
150	>	pot_col.resize(nAtomsInCol_);
151	>
152	>	AtomRowToGlobal.resize(nAtomsInRow_);
153	>	AtomColToGlobal.resize(nAtomsInCol_);
154	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156	>
157	>	cerr << "Atoms in Local:\n";
158	>	for (int i = 0; i < AtomLocalToGlobal.size(); i++)
159	>	{
160	>	cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
161	>	}
162	>	cerr << "Atoms in Row:\n";
163	>	for (int i = 0; i < AtomRowToGlobal.size(); i++)
164	>	{
165	>	cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
166	>	}
167	>	cerr << "Atoms in Col:\n";
168	>	for (int i = 0; i < AtomColToGlobal.size(); i++)
169	>	{
170	>	cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
171	>	}
172	>
173	>	cgRowToGlobal.resize(nGroupsInRow_);
174	>	cgColToGlobal.resize(nGroupsInCol_);
175	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177	>
178	>	cerr << "Gruops in Local:\n";
179	>	for (int i = 0; i < cgLocalToGlobal.size(); i++)
180	>	{
181	>	cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
182	>	}
183	>	cerr << "Groups in Row:\n";
184	>	for (int i = 0; i < cgRowToGlobal.size(); i++)
185	>	{
186	>	cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
187	>	}
188	>	cerr << "Groups in Col:\n";
189	>	for (int i = 0; i < cgColToGlobal.size(); i++)
190	>	{
191	>	cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
192	>	}
193	>
194	>	massFactorsRow.resize(nAtomsInRow_);
195	>	massFactorsCol.resize(nAtomsInCol_);
196	>	AtomPlanRealRow->gather(massFactors, massFactorsRow);
197	>	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
198	>
199	>	groupListRow_.clear();
200	>	groupListRow_.resize(nGroupsInRow_);
201	>	for (int i = 0; i < nGroupsInRow_; i++)
202	>	{
203	>	int gid = cgRowToGlobal[i];
204	>	for (int j = 0; j < nAtomsInRow_; j++)
205	>	{
206	>	int aid = AtomRowToGlobal[j];
207	>	if (globalGroupMembership[aid] == gid)
208	>	groupListRow_[i].push_back(j);
209	>	}
210	>	}
211	>
212	>	groupListCol_.clear();
213	>	groupListCol_.resize(nGroupsInCol_);
214	>	for (int i = 0; i < nGroupsInCol_; i++)
215	>	{
216	>	int gid = cgColToGlobal[i];
217	>	for (int j = 0; j < nAtomsInCol_; j++)
218	>	{
219	>	int aid = AtomColToGlobal[j];
220	>	if (globalGroupMembership[aid] == gid)
221	>	groupListCol_[i].push_back(j);
222	>	}
223	>	}
224	>
225	>	excludesForAtom.clear();
226	>	excludesForAtom.resize(nAtomsInRow_);
227	>	toposForAtom.clear();
228	>	toposForAtom.resize(nAtomsInRow_);
229	>	topoDist.clear();
230	>	topoDist.resize(nAtomsInRow_);
231	>	for (int i = 0; i < nAtomsInRow_; i++)
232	>	{
233	>	int iglob = AtomRowToGlobal[i];
234	>
235	>	for (int j = 0; j < nAtomsInCol_; j++)
236	>	{
237	>	int jglob = AtomColToGlobal[j];
238	>
239	>	if (excludes->hasPair(iglob, jglob))
240	>	excludesForAtom[i].push_back(j);
241	>
242	>	if (oneTwo->hasPair(iglob, jglob))
243	>	{
244	>	toposForAtom[i].push_back(j);
245	>	topoDist[i].push_back(1);
246	>	} else
247	>	{
248	>	if (oneThree->hasPair(iglob, jglob))
249	>	{
250	>	toposForAtom[i].push_back(j);
251	>	topoDist[i].push_back(2);
252	>	} else
253	>	{
254	>	if (oneFour->hasPair(iglob, jglob))
255	>	{
256	>	toposForAtom[i].push_back(j);
257	>	topoDist[i].push_back(3);
258	>	}
259	>	}
260	>	}
261	>	}
262	>	}
263	>
264		#endif
265
266	<	// First time through, construct column stride.
267	<	if (communicators.size() == 0)
107	<	{
108	<	int nColumnsMax = (int) round(sqrt((float) nProcs));
109	<	for (int i = 0; i < nProcs; ++i)
110	<	{
111	<	if (nProcs%i==0) nColumns=i;
112	<	}
266	>	// allocate memory for the parallel objects
267	>	atypesLocal.resize(nLocal_);
268
269	<	int nRows = nProcs/nColumns;
270	<	myRank_ = (int) worldRank%nColumns;
271	<	}
272	<	else
273	<	{
274	<	myRank_ = myRank/nColumns;
275	<	}
276	<	MPI::Comm newComm = MPI:COMM_WORLD.Split(myRank_,0);
277	<
278	<	isColumn_ = false;
279	<
269	>	for (int i = 0; i < nLocal_; i++)
270	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
271	>
272	>	groupList_.clear();
273	>	groupList_.resize(nGroups_);
274	>	for (int i = 0; i < nGroups_; i++)
275	>	{
276	>	int gid = cgLocalToGlobal[i];
277	>	for (int j = 0; j < nLocal_; j++)
278	>	{
279	>	int aid = AtomLocalToGlobal[j];
280	>	if (globalGroupMembership[aid] == gid)
281	>	{
282	>	groupList_[i].push_back(j);
283	>	}
284	>	}
285	>	}
286	>
287	>	excludesForAtom.clear();
288	>	excludesForAtom.resize(nLocal_);
289	>	toposForAtom.clear();
290	>	toposForAtom.resize(nLocal_);
291	>	topoDist.clear();
292	>	topoDist.resize(nLocal_);
293	>
294	>	for (int i = 0; i < nLocal_; i++)
295	>	{
296	>	int iglob = AtomLocalToGlobal[i];
297	>
298	>	for (int j = 0; j < nLocal_; j++)
299	>	{
300	>	int jglob = AtomLocalToGlobal[j];
301	>
302	>	if (excludes->hasPair(iglob, jglob))
303	>	excludesForAtom[i].push_back(j);
304	>
305	>	if (oneTwo->hasPair(iglob, jglob))
306	>	{
307	>	toposForAtom[i].push_back(j);
308	>	topoDist[i].push_back(1);
309	>	} else
310	>	{
311	>	if (oneThree->hasPair(iglob, jglob))
312	>	{
313	>	toposForAtom[i].push_back(j);
314	>	topoDist[i].push_back(2);
315	>	} else
316	>	{
317	>	if (oneFour->hasPair(iglob, jglob))
318	>	{
319	>	toposForAtom[i].push_back(j);
320	>	topoDist[i].push_back(3);
321	>	}
322	>	}
323	>	}
324	>	}
325	>	}
326	>
327	>	Globals* simParams_ = info_->getSimParams();
328	>	if (simParams_->haveNeighborListReorderFreq())
329	>	{
330	>	neighborListReorderFreq = simParams_->getNeighborListReorderFreq();
331	>	} else
332	>	{
333	>	neighborListReorderFreq = 0;
334	>	}
335	>	reorderFreqCounter = 1;
336	>
337	>	createGtypeCutoffMap();
338	>
339		}
340
341	<	ForceDecomposition::gather(sendbuf, receivebuf){
342	<	communicators(myIndex_).Allgatherv();
341	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
342	>
343	>	RealType tol = 1e-6;
344	>	largestRcut_ = 0.0;
345	>	RealType rc;
346	>	int atid;
347	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
348	>
349	>	map<int, RealType> atypeCutoff;
350	>
351	>	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at)
352	>	{
353	>	atid = (*at)->getIdent();
354	>	if (userChoseCutoff_)
355	>	atypeCutoff[atid] = userCutoff_;
356	>	else
357	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
358	>	}
359	>
360	>	vector<RealType> gTypeCutoffs;
361	>	// first we do a single loop over the cutoff groups to find the
362	>	// largest cutoff for any atypes present in this group.
363	>	#ifdef IS_MPI
364	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
365	>	groupRowToGtype.resize(nGroupsInRow_);
366	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++)
367	>	{
368	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
369	>	for (vector<int>::iterator ia = atomListRow.begin();
370	>	ia != atomListRow.end(); ++ia)
371	>	{
372	>	int atom1 = (*ia);
373	>	atid = identsRow[atom1];
374	>	if (atypeCutoff[atid] > groupCutoffRow[cg1])
375	>	{
376	>	groupCutoffRow[cg1] = atypeCutoff[atid];
377	>	}
378	>	}
379	>
380	>	bool gTypeFound = false;
381	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
382	>	{
383	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol)
384	>	{
385	>	groupRowToGtype[cg1] = gt;
386	>	gTypeFound = true;
387	>	}
388	>	}
389	>	if (!gTypeFound)
390	>	{
391	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
392	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
393	>	}
394	>
395	>	}
396	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
397	>	groupColToGtype.resize(nGroupsInCol_);
398	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++)
399	>	{
400	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
401	>	for (vector<int>::iterator jb = atomListCol.begin();
402	>	jb != atomListCol.end(); ++jb)
403	>	{
404	>	int atom2 = (*jb);
405	>	atid = identsCol[atom2];
406	>	if (atypeCutoff[atid] > groupCutoffCol[cg2])
407	>	{
408	>	groupCutoffCol[cg2] = atypeCutoff[atid];
409	>	}
410	>	}
411	>	bool gTypeFound = false;
412	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
413	>	{
414	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol)
415	>	{
416	>	groupColToGtype[cg2] = gt;
417	>	gTypeFound = true;
418	>	}
419	>	}
420	>	if (!gTypeFound)
421	>	{
422	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
423	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
424	>	}
425	>	}
426	>	#else
427	>
428	>	vector<RealType> groupCutoff(nGroups_, 0.0);
429	>	groupToGtype.resize(nGroups_);
430	>	for (int cg1 = 0; cg1 < nGroups_; cg1++)
431	>	{
432	>	groupCutoff[cg1] = 0.0;
433	>	vector<int> atomList = getAtomsInGroupRow(cg1);
434	>	for (vector<int>::iterator ia = atomList.begin(); ia != atomList.end(); ++ia)
435	>	{
436	>	int atom1 = (*ia);
437	>	atid = idents[atom1];
438	>	if (atypeCutoff[atid] > groupCutoff[cg1])
439	>	groupCutoff[cg1] = atypeCutoff[atid];
440	>	}
441	>
442	>	bool gTypeFound = false;
443	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
444	>	{
445	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol)
446	>	{
447	>	groupToGtype[cg1] = gt;
448	>	gTypeFound = true;
449	>	}
450	>	}
451	>	if (!gTypeFound)
452	>	{
453	>	gTypeCutoffs.push_back(groupCutoff[cg1]);
454	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
455	>	}
456	>	}
457	>	#endif
458	>
459	>	// Now we find the maximum group cutoff value present in the simulation
460	>
461	>	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
462	>
463	>	#ifdef IS_MPI
464	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
465	>	MPI::MAX);
466	>	#endif
467	>
468	>	RealType tradRcut = groupMax;
469	>
470	>	for (int i = 0; i < gTypeCutoffs.size(); i++)
471	>	{
472	>	for (int j = 0; j < gTypeCutoffs.size(); j++)
473	>	{
474	>	RealType thisRcut;
475	>	switch (cutoffPolicy_) {
476	>	case TRADITIONAL:
477	>	thisRcut = tradRcut;
478	>	break;
479	>	case MIX:
480	>	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
481	>	break;
482	>	case MAX:
483	>	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
484	>	break;
485	>	default:
486	>	sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap "
487	>	"hit an unknown cutoff policy!\n");
488	>	painCave.severity = OPENMD_ERROR;
489	>	painCave.isFatal = 1;
490	>	simError();
491	>	break;
492	>	}
493	>
494	>	pair<int, int> key = make_pair(i, j);
495	>	gTypeCutoffMap[key].first = thisRcut;
496	>	if (thisRcut > largestRcut_)
497	>	largestRcut_ = thisRcut;
498	>	gTypeCutoffMap[key].second = thisRcut * thisRcut;
499	>	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
500	>	// sanity check
501	>
502	>	if (userChoseCutoff_)
503	>	{
504	>	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001)
505	>	{
506	>	sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap "
507	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
508	>	painCave.severity = OPENMD_ERROR;
509	>	painCave.isFatal = 1;
510	>	simError();
511	>	}
512	>	}
513	>	}
514	>	}
515		}
516
517	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
518	+	int i, j;
519	+	#ifdef IS_MPI
520	+	i = groupRowToGtype[cg1];
521	+	j = groupColToGtype[cg2];
522	+	#else
523	+	i = groupToGtype[cg1];
524	+	j = groupToGtype[cg2];
525	+	#endif
526	+	return gTypeCutoffMap[make_pair(i, j)];
527	+	}
528
529	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
530	+	for (int j = 0; j < toposForAtom[atom1].size(); j++)
531	+	{
532	+	if (toposForAtom[atom1][j] == atom2)
533	+	return topoDist[atom1][j];
534	+	}
535	+	return 0;
536	+	}
537
538	<	ForceDecomposition::scatter(sbuffer, rbuffer){
539	<	communicators(myIndex_).Reduce_scatter(sbuffer, recevbuf. recvcounts, MPI::DOUBLE, MPI::SUM);
538	>	void ForceMatrixDecomposition::zeroWorkArrays() {
539	>	pairwisePot = 0.0;
540	>	embeddingPot = 0.0;
541	>
542	>	#ifdef IS_MPI
543	>	if (storageLayout_ & DataStorage::dslForce)
544	>	{
545	>	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
546	>	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
547	>	}
548	>
549	>	if (storageLayout_ & DataStorage::dslTorque)
550	>	{
551	>	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
552	>	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
553	>	}
554	>
555	>	fill(pot_row.begin(), pot_row.end(),
556	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
557	>
558	>	fill(pot_col.begin(), pot_col.end(),
559	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
560	>
561	>	if (storageLayout_ & DataStorage::dslParticlePot)
562	>	{
563	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
564	>	0.0);
565	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
566	>	0.0);
567	>	}
568	>
569	>	if (storageLayout_ & DataStorage::dslDensity)
570	>	{
571	>	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
572	>	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
573	>	}
574	>
575	>	if (storageLayout_ & DataStorage::dslFunctional)
576	>	{
577	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
578	>	0.0);
579	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
580	>	0.0);
581	>	}
582	>
583	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
584	>	{
585	>	fill(atomRowData.functionalDerivative.begin(),
586	>	atomRowData.functionalDerivative.end(), 0.0);
587	>	fill(atomColData.functionalDerivative.begin(),
588	>	atomColData.functionalDerivative.end(), 0.0);
589	>	}
590	>
591	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
592	>	{
593	>	fill(atomRowData.skippedCharge.begin(),
594	>	atomRowData.skippedCharge.end(), 0.0);
595	>	fill(atomColData.skippedCharge.begin(),
596	>	atomColData.skippedCharge.end(), 0.0);
597	>	}
598	>
599	>	#endif
600	>	// even in parallel, we need to zero out the local arrays:
601	>
602	>	if (storageLayout_ & DataStorage::dslParticlePot)
603	>	{
604	>	fill(snap_->atomData.particlePot.begin(), snap_->atomData.particlePot.end(), 0.0);
605	>	}
606	>
607	>	if (storageLayout_ & DataStorage::dslDensity)
608	>	{
609	>	fill(snap_->atomData.density.begin(), snap_->atomData.density.end(), 0.0);
610	>	}
611	>	if (storageLayout_ & DataStorage::dslFunctional)
612	>	{
613	>	fill(snap_->atomData.functional.begin(), snap_->atomData.functional.end(), 0.0);
614	>	}
615	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
616	>	{
617	>	fill(snap_->atomData.functionalDerivative.begin(), snap_->atomData.functionalDerivative.end(), 0.0);
618	>	}
619	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
620	>	{
621	>	fill(snap_->atomData.skippedCharge.begin(), snap_->atomData.skippedCharge.end(), 0.0);
622	>	}
623	>
624		}
625
626	+	void ForceMatrixDecomposition::distributeData() {
627	+	snap_ = sman_->getCurrentSnapshot();
628	+	storageLayout_ = sman_->getStorageLayout();
629	+	#ifdef IS_MPI
630
631	+	// gather up the atomic positions
632	+	AtomPlanVectorRow->gather(snap_->atomData.position,
633	+	atomRowData.position);
634	+	AtomPlanVectorColumn->gather(snap_->atomData.position,
635	+	atomColData.position);
636	+
637	+	// gather up the cutoff group positions
638	+
639	+	cerr << "before gather\n";
640	+	for (int i = 0; i < snap_->cgData.position.size(); i++)
641	+	{
642	+	cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
643	+	}
644	+
645	+	cgPlanVectorRow->gather(snap_->cgData.position,
646	+	cgRowData.position);
647	+
648	+	cerr << "after gather\n";
649	+	for (int i = 0; i < cgRowData.position.size(); i++)
650	+	{
651	+	cerr << "cgRpos = " << cgRowData.position[i] << "\n";
652	+	}
653	+
654	+	cgPlanVectorColumn->gather(snap_->cgData.position,
655	+	cgColData.position);
656	+	for (int i = 0; i < cgColData.position.size(); i++)
657	+	{
658	+	cerr << "cgCpos = " << cgColData.position[i] << "\n";
659	+	}
660	+
661	+	// if needed, gather the atomic rotation matrices
662	+	if (storageLayout_ & DataStorage::dslAmat)
663	+	{
664	+	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
665	+	atomRowData.aMat);
666	+	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
667	+	atomColData.aMat);
668	+	}
669	+
670	+	// if needed, gather the atomic eletrostatic frames
671	+	if (storageLayout_ & DataStorage::dslElectroFrame)
672	+	{
673	+	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
674	+	atomRowData.electroFrame);
675	+	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
676	+	atomColData.electroFrame);
677	+	}
678	+
679	+	#endif
680	+	}
681	+
682	+	/* collects information obtained during the pre-pair loop onto local
683	+	* data structures.
684	+	*/
685	+	void ForceMatrixDecomposition::collectIntermediateData() {
686	+	snap_ = sman_->getCurrentSnapshot();
687	+	storageLayout_ = sman_->getStorageLayout();
688	+	#ifdef IS_MPI
689	+
690	+	if (storageLayout_ & DataStorage::dslDensity)
691	+	{
692	+
693	+	AtomPlanRealRow->scatter(atomRowData.density,
694	+	snap_->atomData.density);
695	+
696	+	int n = snap_->atomData.density.size();
697	+	vector<RealType> rho_tmp(n, 0.0);
698	+	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
699	+	for (int i = 0; i < n; i++)
700	+	snap_->atomData.density[i] += rho_tmp[i];
701	+	}
702	+	#endif
703	+	}
704	+
705	+	/*
706	+	* redistributes information obtained during the pre-pair loop out to
707	+	* row and column-indexed data structures
708	+	*/
709	+	void ForceMatrixDecomposition::distributeIntermediateData() {
710	+	snap_ = sman_->getCurrentSnapshot();
711	+	storageLayout_ = sman_->getStorageLayout();
712	+	#ifdef IS_MPI
713	+	if (storageLayout_ & DataStorage::dslFunctional)
714	+	{
715	+	AtomPlanRealRow->gather(snap_->atomData.functional,
716	+	atomRowData.functional);
717	+	AtomPlanRealColumn->gather(snap_->atomData.functional,
718	+	atomColData.functional);
719	+	}
720	+
721	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
722	+	{
723	+	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
724	+	atomRowData.functionalDerivative);
725	+	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
726	+	atomColData.functionalDerivative);
727	+	}
728	+	#endif
729	+	}
730	+
731	+	void ForceMatrixDecomposition::collectData() {
732	+	snap_ = sman_->getCurrentSnapshot();
733	+	storageLayout_ = sman_->getStorageLayout();
734	+	#ifdef IS_MPI
735	+	int n = snap_->atomData.force.size();
736	+	vector<Vector3d> frc_tmp(n, V3Zero);
737	+
738	+	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
739	+	for (int i = 0; i < n; i++)
740	+	{
741	+	snap_->atomData.force[i] += frc_tmp[i];
742	+	frc_tmp[i] = 0.0;
743	+	}
744	+
745	+	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
746	+	for (int i = 0; i < n; i++)
747	+	{
748	+	snap_->atomData.force[i] += frc_tmp[i];
749	+	}
750	+
751	+	if (storageLayout_ & DataStorage::dslTorque)
752	+	{
753	+
754	+	int nt = snap_->atomData.torque.size();
755	+	vector<Vector3d> trq_tmp(nt, V3Zero);
756	+
757	+	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
758	+	for (int i = 0; i < nt; i++)
759	+	{
760	+	snap_->atomData.torque[i] += trq_tmp[i];
761	+	trq_tmp[i] = 0.0;
762	+	}
763	+
764	+	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
765	+	for (int i = 0; i < nt; i++)
766	+	snap_->atomData.torque[i] += trq_tmp[i];
767	+	}
768	+
769	+	if (storageLayout_ & DataStorage::dslSkippedCharge)
770	+	{
771	+
772	+	int ns = snap_->atomData.skippedCharge.size();
773	+	vector<RealType> skch_tmp(ns, 0.0);
774	+
775	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
776	+	for (int i = 0; i < ns; i++)
777	+	{
778	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
779	+	skch_tmp[i] = 0.0;
780	+	}
781	+
782	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
783	+	for (int i = 0; i < ns; i++)
784	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
785	+	}
786	+
787	+	nLocal_ = snap_->getNumberOfAtoms();
788	+
789	+	vector<potVec> pot_temp(nLocal_,
790	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
791	+
792	+	// scatter/gather pot_row into the members of my column
793	+
794	+	AtomPlanPotRow->scatter(pot_row, pot_temp);
795	+
796	+	for (int ii = 0; ii < pot_temp.size(); ii++ )
797	+	pairwisePot += pot_temp[ii];
798	+
799	+	fill(pot_temp.begin(), pot_temp.end(),
800	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
801	+
802	+	AtomPlanPotColumn->scatter(pot_col, pot_temp);
803	+
804	+	for (int ii = 0; ii < pot_temp.size(); ii++ )
805	+	pairwisePot += pot_temp[ii];
806	+	#endif
807	+
808	+	//      cerr << "pairwisePot = " << pairwisePot << "\n";
809	+	}
810	+
811	+	int ForceMatrixDecomposition::getNAtomsInRow() {
812	+	#ifdef IS_MPI
813	+	return nAtomsInRow_;
814	+	#else
815	+	return nLocal_;
816	+	#endif
817	+	}
818	+
819	+	/**
820	+	* returns the list of atoms belonging to this group.
821	+	*/
822	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1) {
823	+	#ifdef IS_MPI
824	+	return groupListRow_[cg1];
825	+	#else
826	+	return groupList_[cg1];
827	+	#endif
828	+	}
829	+
830	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2) {
831	+	#ifdef IS_MPI
832	+	return groupListCol_[cg2];
833	+	#else
834	+	return groupList_[cg2];
835	+	#endif
836	+	}
837	+
838	+	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2) {
839	+	Vector3d d;
840	+
841	+	#ifdef IS_MPI
842	+	d = cgColData.position[cg2] - cgRowData.position[cg1];
843	+	cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
844	+	cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
845	+	#else
846	+	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
847	+	cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
848	+	cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
849	+	#endif
850	+
851	+	snap_->wrapVector(d);
852	+	return d;
853	+	}
854	+
855	+	Vector3d ForceMatrixDecomposition::getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2) {
856	+	Vector3d d;
857	+
858	+	d = snap_->cgData.position[cg2->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
859	+	/*      cerr << "cg1_gid = " << cg1->getGlobalIndex() << "\tcg1_lid = " << cg1->getLocalIndex() << "\tcg1p = "
860	+	<< snap_->cgData.position[cg1->getLocalIndex()] << "\n";
861	+	cerr << "cg2_gid = " << cg2->getGlobalIndex() << "\tcg2_lid = " << cg2->getLocalIndex() << "\tcg2p = "
862	+	<< snap_->cgData.position[cg2->getLocalIndex()] << "\n";*/
863	+
864	+	snap_->wrapVector(d);
865	+	return d;
866	+	}
867	+
868	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1) {
869	+
870	+	Vector3d d;
871	+
872	+	#ifdef IS_MPI
873	+	d = cgRowData.position[cg1] - atomRowData.position[atom1];
874	+	#else
875	+	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
876	+	#endif
877	+
878	+	snap_->wrapVector(d);
879	+	return d;
880	+	}
881	+
882	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2) {
883	+	Vector3d d;
884	+
885	+	#ifdef IS_MPI
886	+	d = cgColData.position[cg2] - atomColData.position[atom2];
887	+	#else
888	+	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
889	+	#endif
890	+
891	+	snap_->wrapVector(d);
892	+	return d;
893	+	}
894	+
895	+	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
896	+	#ifdef IS_MPI
897	+	return massFactorsRow[atom1];
898	+	#else
899	+	return massFactors[atom1];
900	+	#endif
901	+	}
902	+
903	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
904	+	#ifdef IS_MPI
905	+	return massFactorsCol[atom2];
906	+	#else
907	+	return massFactors[atom2];
908	+	#endif
909	+
910	+	}
911	+
912	+	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2) {
913	+	Vector3d d;
914	+
915	+	#ifdef IS_MPI
916	+	d = atomColData.position[atom2] - atomRowData.position[atom1];
917	+	#else
918	+	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
919	+	#endif
920	+
921	+	snap_->wrapVector(d);
922	+	return d;
923	+	}
924	+
925	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
926	+	return excludesForAtom[atom1];
927	+	}
928	+
929	+	/**
930	+	* We need to exclude some overcounted interactions that result from
931	+	* the parallel decomposition.
932	+	*/
933	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
934	+	int unique_id_1, unique_id_2;
935	+
936	+	//      cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
937	+	#ifdef IS_MPI
938	+	// in MPI, we have to look up the unique IDs for each atom
939	+	unique_id_1 = AtomRowToGlobal[atom1];
940	+	unique_id_2 = AtomColToGlobal[atom2];
941	+
942	+	cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
943	+	// this situation should only arise in MPI simulations
944	+	if (unique_id_1 == unique_id_2) return true;
945	+
946	+	// this prevents us from doing the pair on multiple processors
947	+	if (unique_id_1 < unique_id_2)
948	+	{
949	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
950	+	} else
951	+	{
952	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
953	+	}
954	+	#endif
955	+	return false;
956	+	}
957	+
958	+	/**
959	+	* We need to handle the interactions for atoms who are involved in
960	+	* the same rigid body as well as some short range interactions
961	+	* (bonds, bends, torsions) differently from other interactions.
962	+	* We'll still visit the pairwise routines, but with a flag that
963	+	* tells those routines to exclude the pair from direct long range
964	+	* interactions.  Some indirect interactions (notably reaction
965	+	* field) must still be handled for these pairs.
966	+	*/
967	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
968	+	int unique_id_2;
969	+	#ifdef IS_MPI
970	+	// in MPI, we have to look up the unique IDs for the row atom.
971	+	unique_id_2 = AtomColToGlobal[atom2];
972	+	#else
973	+	// in the normal loop, the atom numbers are unique
974	+	unique_id_2 = atom2;
975	+	#endif
976	+
977	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin(); i != excludesForAtom[atom1].end(); ++i)
978	+	{
979	+	if ((*i) == unique_id_2)
980	+	return true;
981	+	}
982	+
983	+	return false;
984	+	}
985	+
986	+	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg) {
987	+	#ifdef IS_MPI
988	+	atomRowData.force[atom1] += fg;
989	+	#else
990	+	snap_->atomData.force[atom1] += fg;
991	+	#endif
992	+	}
993	+
994	+	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg) {
995	+	#ifdef IS_MPI
996	+	atomColData.force[atom2] += fg;
997	+	#else
998	+	snap_->atomData.force[atom2] += fg;
999	+	#endif
1000	+	}
1001	+
1002	+	// filling interaction blocks with pointers
1003	+	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, int atom1, int atom2) {
1004	+
1005	+	idat.excluded = excludeAtomPair(atom1, atom2);
1006	+
1007	+	#ifdef IS_MPI
1008	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1009	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1010	+	//                         ff_->getAtomType(identsCol[atom2]) );
1011	+
1012	+	if (storageLayout_ & DataStorage::dslAmat)
1013	+	{
1014	+	idat.A1 = &(atomRowData.aMat[atom1]);
1015	+	idat.A2 = &(atomColData.aMat[atom2]);
1016	+	}
1017	+
1018	+	if (storageLayout_ & DataStorage::dslElectroFrame)
1019	+	{
1020	+	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1021	+	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1022	+	}
1023	+
1024	+	if (storageLayout_ & DataStorage::dslTorque)
1025	+	{
1026	+	idat.t1 = &(atomRowData.torque[atom1]);
1027	+	idat.t2 = &(atomColData.torque[atom2]);
1028	+	}
1029	+
1030	+	if (storageLayout_ & DataStorage::dslDensity)
1031	+	{
1032	+	idat.rho1 = &(atomRowData.density[atom1]);
1033	+	idat.rho2 = &(atomColData.density[atom2]);
1034	+	}
1035	+
1036	+	if (storageLayout_ & DataStorage::dslFunctional)
1037	+	{
1038	+	idat.frho1 = &(atomRowData.functional[atom1]);
1039	+	idat.frho2 = &(atomColData.functional[atom2]);
1040	+	}
1041	+
1042	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
1043	+	{
1044	+	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1045	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1046	+	}
1047	+
1048	+	if (storageLayout_ & DataStorage::dslParticlePot)
1049	+	{
1050	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1051	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1052	+	}
1053	+
1054	+	if (storageLayout_ & DataStorage::dslSkippedCharge)
1055	+	{
1056	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1057	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1058	+	}
1059	+
1060	+	#else
1061	+
1062	+	idat.atypes = make_pair(atypesLocal[atom1], atypesLocal[atom2]);
1063	+	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1064	+	//                         ff_->getAtomType(idents[atom2]) );
1065	+
1066	+	if (storageLayout_ & DataStorage::dslAmat)
1067	+	{
1068	+	idat.A1 = &(snap_->atomData.aMat[atom1]);
1069	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1070	+	}
1071	+
1072	+	if (storageLayout_ & DataStorage::dslElectroFrame)
1073	+	{
1074	+	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1075	+	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1076	+	}
1077	+
1078	+	if (storageLayout_ & DataStorage::dslTorque)
1079	+	{
1080	+	idat.t1 = &(snap_->atomData.torque[atom1]);
1081	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1082	+	}
1083	+
1084	+	if (storageLayout_ & DataStorage::dslDensity)
1085	+	{
1086	+	idat.rho1 = &(snap_->atomData.density[atom1]);
1087	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1088	+	}
1089	+
1090	+	if (storageLayout_ & DataStorage::dslFunctional)
1091	+	{
1092	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1093	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1094	+	}
1095	+
1096	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
1097	+	{
1098	+	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1099	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1100	+	}
1101	+
1102	+	if (storageLayout_ & DataStorage::dslParticlePot)
1103	+	{
1104	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1105	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1106	+	}
1107	+
1108	+	if (storageLayout_ & DataStorage::dslSkippedCharge)
1109	+	{
1110	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1111	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1112	+	}
1113	+	#endif
1114	+	}
1115	+
1116	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1117	+	#ifdef IS_MPI
1118	+	pot_row[atom1] += 0.5 * *(idat.pot);
1119	+	pot_col[atom2] += 0.5 * *(idat.pot);
1120	+
1121	+	atomRowData.force[atom1] += *(idat.f1);
1122	+	atomColData.force[atom2] -= *(idat.f1);
1123	+	#else
1124	+	pairwisePot += *(idat.pot);
1125	+
1126	+	snap_->atomData.force[atom1] += *(idat.f1);
1127	+	snap_->atomData.force[atom2] -= *(idat.f1);
1128	+	#endif
1129	+
1130	+	}
1131	+
1132	+	void ForceMatrixDecomposition::reorderGroupCutoffs(vector<int> &order) {
1133	+	vector<int> tmp = vector<int> (groupToGtype.size());
1134	+
1135	+	for (int i = 0; i < groupToGtype.size(); ++i)
1136	+	{
1137	+	tmp[i] = groupToGtype[i];
1138	+	}
1139	+
1140	+	for (int i = 0; i < groupToGtype.size(); ++i)
1141	+	{
1142	+	groupToGtype[i] = tmp[order[i]];
1143	+	}
1144	+	}
1145	+
1146	+	void ForceMatrixDecomposition::reorderPosition(vector<int> &order) {
1147	+	Snapshot* snap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1148	+	DataStorage* cgConfig = &(snap_->cgData);
1149	+	vector<Vector3d> tmp = vector<Vector3d> (nGroups_);
1150	+
1151	+	for (int i = 0; i < nGroups_; ++i)
1152	+	{
1153	+	tmp[i] = snap_->cgData.position[i];
1154	+	}
1155	+
1156	+	vector<int> mapPos = vector<int> (nGroups_);
1157	+	for (int i = 0; i < nGroups_; ++i)
1158	+	{
1159	+	snap_->cgData.position[i] = tmp[order[i]];
1160	+	mapPos[order[i]] = i;
1161	+	}
1162	+
1163	+	SimInfo::MoleculeIterator mi;
1164	+	Molecule* mol;
1165	+	Molecule::CutoffGroupIterator ci;
1166	+	CutoffGroup* cg;
1167	+
1168	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1169	+	{
1170	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1171	+	{
1172	+	cg->setLocalIndex(mapPos[cg->getLocalIndex()]);
1173	+	}
1174	+	}
1175	+
1176	+	/*      if (info_->getNCutoffGroups() > 0)
1177	+	{
1178	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1179	+	{
1180	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1181	+	{
1182	+	printf("gbI:%d locI:%d x:%f y:%f z:%f\n", cg->getGlobalIndex(), cg->getLocalIndex(),
1183	+	cgConfig->position[cg->getLocalIndex()].x(), cgConfig->position[cg->getLocalIndex()].y(),
1184	+	cgConfig->position[cg->getLocalIndex()].z());
1185	+	}
1186	+	}
1187	+	} else
1188	+	{
1189	+	// center of mass of the group is the same as position of the atom
1190	+	// if cutoff group does not exist
1191	+	printf("ERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
1192	+	//                     cgConfig->position = config->position;
1193	+	}*/
1194	+	}
1195	+
1196	+	void ForceMatrixDecomposition::reorderGroupList(vector<int> &order) {
1197	+	vector<vector<int> > tmp = vector<vector<int> > (groupList_.size());
1198	+
1199	+	for (int i = 0; i < groupList_.size(); ++i)
1200	+	{
1201	+	tmp[i] = groupList_[i];
1202	+	}
1203	+
1204	+	for (int i = 0; i < groupList_.size(); ++i)
1205	+	{
1206	+	groupList_[i] = tmp[order[i]];
1207	+	}
1208	+	}
1209	+
1210	+	void ForceMatrixDecomposition::reorderMemory(vector<vector<CutoffGroup *> > &H_c_l) {
1211	+	int n = 0;
1212	+	//      printf("Reorder memory time:%f!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
1213	+	//                      info_->getSnapshotManager()->getCurrentSnapshot()->getTime());
1214	+
1215	+	/* record the reordered atom indices */
1216	+	vector<int> k = vector<int> (nGroups_);
1217	+
1218	+	for (int c = 0; c < H_c_l.size(); ++c)
1219	+	{
1220	+	for (vector<CutoffGroup *>::iterator cg = H_c_l[c].begin(); cg != H_c_l[c].end(); ++cg)
1221	+	{
1222	+	int i = (*cg)->getGlobalIndex();
1223	+	k[n] = i;
1224	+	++n;
1225	+	}
1226	+	}
1227	+
1228	+	//      reorderGroupCutoffs(k);
1229	+	//      reorderGroupList(k);
1230	+	reorderPosition(k);
1231	+	}
1232	+
1233	+	vector<vector<CutoffGroup *> > ForceMatrixDecomposition::buildLayerBasedNeighborList() {
1234	+	//      printf("buildLayerBasedNeighborList; nGroups:%d\n", nGroups_);
1235	+	// Na = nGroups_
1236	+	/* cell occupancy counter */
1237	+	//      vector<int> k_c;
1238	+	/* c_i - has cell containing atom i (size Na) */
1239	+	vector<int> c = vector<int> (nGroups_);
1240	+	/* l_i - layer containing atom i (size Na) */
1241	+	//      vector<int> l;
1242	+
1243	+	RealType rList_ = (largestRcut_ + skinThickness_);
1244	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1245	+	Mat3x3d Hmat = snap_->getHmat();
1246	+	Vector3d Hx = Hmat.getColumn(0);
1247	+	Vector3d Hy = Hmat.getColumn(1);
1248	+	Vector3d Hz = Hmat.getColumn(2);
1249	+
1250	+	nCells_.x() = (int) (Hx.length()) / rList_;
1251	+	nCells_.y() = (int) (Hy.length()) / rList_;
1252	+	nCells_.z() = (int) (Hz.length()) / rList_;
1253	+
1254	+	Mat3x3d invHmat = snap_->getInvHmat();
1255	+	Vector3d rs, scaled, dr;
1256	+	Vector3i whichCell;
1257	+	int cellIndex;
1258	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1259	+
1260	+	//      k_c = vector<int> (nCtot, 0);
1261	+
1262	+	SimInfo::MoleculeIterator mi;
1263	+	Molecule* mol;
1264	+	Molecule::CutoffGroupIterator ci;
1265	+	CutoffGroup* cg;
1266	+
1267	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1268	+	{
1269	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1270	+	{
1271	+	rs = snap_->cgData.position[cg->getLocalIndex()];
1272	+
1273	+	// scaled positions relative to the box vectors
1274	+	scaled = invHmat * rs;
1275	+
1276	+	// wrap the vector back into the unit box by subtracting integer box
1277	+	// numbers
1278	+	for (int j = 0; j < 3; j++)
1279	+	{
1280	+	scaled[j] -= roundMe(scaled[j]);
1281	+	scaled[j] += 0.5;
1282	+	}
1283	+
1284	+	// find xyz-indices of cell that cutoffGroup is in.
1285	+	whichCell.x() = nCells_.x() * scaled.x();
1286	+	whichCell.y() = nCells_.y() * scaled.y();
1287	+	whichCell.z() = nCells_.z() * scaled.z();
1288	+
1289	+	//                      printf("pos x:%f y:%f z:%f cell x:%d y:%d z:%d\n", rs.x(), rs.y(), rs.z(), whichCell.x(), whichCell.y(),
1290	+	//                                      whichCell.z());
1291	+
1292	+	// find single index of this cell:
1293	+	cellIndex = Vlinear(whichCell, nCells_);
1294	+
1295	+	c[cg->getGlobalIndex()] = cellIndex;
1296	+	}
1297	+	}
1298	+
1299	+	//      int k_c_curr;
1300	+	//      int k_c_max = 0;
1301	+	/* the cell-layer occupancy matrix */
1302	+	vector<vector<CutoffGroup *> > H_c_l = vector<vector<CutoffGroup *> > (nCtot);
1303	+
1304	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1305	+	{
1306	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1307	+
1308	+	{
1309	+	//                      k_c_curr = ++k_c[c[cg1->getGlobalIndex()]];
1310	+	//                      l.push_back(k_c_curr);
1311	+	//
1312	+	//                      /* determines the number of layers in use */
1313	+	//                      if (k_c_max < k_c_curr)
1314	+	//                      {
1315	+	//                              k_c_max = k_c_curr;
1316	+	//                      }
1317	+	H_c_l[c[cg->getGlobalIndex()]].push_back(/*l[*/cg/*]*/);
1318	+	}
1319	+	}
1320	+
1321	+	/* Frequency of reordering the memory */
1322	+	if (neighborListReorderFreq != 0)
1323	+	{
1324	+	if (reorderFreqCounter == neighborListReorderFreq)
1325	+	{
1326	+	//printf("neighborListReorderFreq:%d\n", neighborListReorderFreq);
1327	+	reorderMemory(H_c_l);
1328	+	reorderFreqCounter = 1;
1329	+	} else
1330	+	{
1331	+	reorderFreqCounter++;
1332	+	}
1333	+	}
1334	+
1335	+	int m;
1336	+	/* the neighbor matrix */
1337	+	vector<vector<CutoffGroup *> > neighborMatW = vector<vector<CutoffGroup *> > (nGroups_);
1338	+
1339	+	groupCutoffs cuts;
1340	+	CutoffGroup *cg1;
1341	+
1342	+	/* loops over objects(atoms, rigidBodies, cutoffGroups, etc.) */
1343	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1344	+	{
1345	+	for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
1346	+	{
1347	+	/* c' */
1348	+	int c1 = c[cg1->getGlobalIndex()];
1349	+	Vector3i c1v = idxToV(c1, nCells_);
1350	+
1351	+	/* loops over the neighboring cells c'' */
1352	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1353	+	{
1354	+	Vector3i c2v = c1v + (*os);
1355	+
1356	+	if (c2v.x() >= nCells_.x())
1357	+	{
1358	+	c2v.x() = 0;
1359	+	} else if (c2v.x() < 0)
1360	+	{
1361	+	c2v.x() = nCells_.x() - 1;
1362	+	}
1363	+
1364	+	if (c2v.y() >= nCells_.y())
1365	+	{
1366	+	c2v.y() = 0;
1367	+	} else if (c2v.y() < 0)
1368	+	{
1369	+	c2v.y() = nCells_.y() - 1;
1370	+	}
1371	+
1372	+	if (c2v.z() >= nCells_.z())
1373	+	{
1374	+	c2v.z() = 0;
1375	+	} else if (c2v.z() < 0)
1376	+	{
1377	+	c2v.z() = nCells_.z() - 1;
1378	+	}
1379	+
1380	+	int c2 = Vlinear(c2v, nCells_);
1381	+	/* loops over layers l to access the neighbor atoms */
1382	+	for (vector<CutoffGroup *>::iterator cg2 = H_c_l[c2].begin(); cg2 != H_c_l[c2].end(); ++cg2)
1383	+	{
1384	+	//                              if i'' = 0 then break // doesn't apply to vector implementation of matrix
1385	+	//                              if(i != *j)
1386	+	if (c2 != c1 || (*cg2)->getGlobalIndex() < cg1->getGlobalIndex())
1387	+	{
1388	+	dr = snap_->cgData.position[(*cg2)->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
1389	+	snap_->wrapVector(dr);
1390	+	cuts = getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex());
1391	+	if (dr.lengthSquare() < cuts.third)
1392	+	{
1393	+	/* transposed version of Rapaport W mat, to occupy successive memory locations on CPU */
1394	+	neighborMatW[cg1->getGlobalIndex()].push_back((*cg2));
1395	+	}
1396	+	}
1397	+	}
1398	+	}
1399	+	}
1400	+	}
1401	+
1402	+	// save the local cutoff group positions for the check that is
1403	+	// done on each loop:
1404	+	saved_CG_positions_.clear();
1405	+	for (int i = 0; i < nGroups_; i++)
1406	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1407	+
1408	+	return neighborMatW;
1409	+	}
1410	+
1411	+	/*
1412	+	* buildNeighborList
1413	+	*
1414	+	* first element of pair is row-indexed CutoffGroup
1415	+	* second element of pair is column-indexed CutoffGroup
1416	+	*/
1417	+	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1418	+
1419	+	vector<pair<int, int> > neighborList;
1420	+	groupCutoffs cuts;
1421	+	bool doAllPairs = false;
1422	+
1423	+	#ifdef IS_MPI
1424	+	cellListRow_.clear();
1425	+	cellListCol_.clear();
1426	+	#else
1427	+	cellList_.clear();
1428	+	#endif
1429	+
1430	+	RealType rList_ = (largestRcut_ + skinThickness_);
1431	+	RealType rl2 = rList_ * rList_;
1432	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1433	+	Mat3x3d Hmat = snap_->getHmat();
1434	+	Vector3d Hx = Hmat.getColumn(0);
1435	+	Vector3d Hy = Hmat.getColumn(1);
1436	+	Vector3d Hz = Hmat.getColumn(2);
1437	+
1438	+	nCells_.x() = (int) (Hx.length()) / rList_;
1439	+	nCells_.y() = (int) (Hy.length()) / rList_;
1440	+	nCells_.z() = (int) (Hz.length()) / rList_;
1441	+
1442	+	// handle small boxes where the cell offsets can end up repeating cells
1443	+
1444	+	if (nCells_.x() < 3)
1445	+	doAllPairs = true;
1446	+	if (nCells_.y() < 3)
1447	+	doAllPairs = true;
1448	+	if (nCells_.z() < 3)
1449	+	doAllPairs = true;
1450	+
1451	+	Mat3x3d invHmat = snap_->getInvHmat();
1452	+	Vector3d rs, scaled, dr;
1453	+	Vector3i whichCell;
1454	+	int cellIndex;
1455	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1456	+
1457	+	#ifdef IS_MPI
1458	+	cellListRow_.resize(nCtot);
1459	+	cellListCol_.resize(nCtot);
1460	+	#else
1461	+	cellList_.resize(nCtot);
1462	+	#endif
1463	+
1464	+	if (!doAllPairs)
1465	+	{
1466	+	#ifdef IS_MPI
1467	+
1468	+	for (int i = 0; i < nGroupsInRow_; i++)
1469	+	{
1470	+	rs = cgRowData.position[i];
1471	+
1472	+	// scaled positions relative to the box vectors
1473	+	scaled = invHmat * rs;
1474	+
1475	+	// wrap the vector back into the unit box by subtracting integer box
1476	+	// numbers
1477	+	for (int j = 0; j < 3; j++)
1478	+	{
1479	+	scaled[j] -= roundMe(scaled[j]);
1480	+	scaled[j] += 0.5;
1481	+	}
1482	+
1483	+	// find xyz-indices of cell that cutoffGroup is in.
1484	+	whichCell.x() = nCells_.x() * scaled.x();
1485	+	whichCell.y() = nCells_.y() * scaled.y();
1486	+	whichCell.z() = nCells_.z() * scaled.z();
1487	+
1488	+	// find single index of this cell:
1489	+	cellIndex = Vlinear(whichCell, nCells_);
1490	+
1491	+	// add this cutoff group to the list of groups in this cell;
1492	+	cellListRow_[cellIndex].push_back(i);
1493	+	}
1494	+	for (int i = 0; i < nGroupsInCol_; i++)
1495	+	{
1496	+	rs = cgColData.position[i];
1497	+
1498	+	// scaled positions relative to the box vectors
1499	+	scaled = invHmat * rs;
1500	+
1501	+	// wrap the vector back into the unit box by subtracting integer box
1502	+	// numbers
1503	+	for (int j = 0; j < 3; j++)
1504	+	{
1505	+	scaled[j] -= roundMe(scaled[j]);
1506	+	scaled[j] += 0.5;
1507	+	}
1508	+
1509	+	// find xyz-indices of cell that cutoffGroup is in.
1510	+	whichCell.x() = nCells_.x() * scaled.x();
1511	+	whichCell.y() = nCells_.y() * scaled.y();
1512	+	whichCell.z() = nCells_.z() * scaled.z();
1513	+
1514	+	// find single index of this cell:
1515	+	cellIndex = Vlinear(whichCell, nCells_);
1516	+
1517	+	// add this cutoff group to the list of groups in this cell;
1518	+	cellListCol_[cellIndex].push_back(i);
1519	+	}
1520	+	#else
1521	+	for (int i = 0; i < nGroups_; i++)
1522	+	{
1523	+	rs = snap_->cgData.position[i];
1524	+
1525	+	// scaled positions relative to the box vectors
1526	+	scaled = invHmat * rs;
1527	+
1528	+	// wrap the vector back into the unit box by subtracting integer box
1529	+	// numbers
1530	+	for (int j = 0; j < 3; j++)
1531	+	{
1532	+	scaled[j] -= roundMe(scaled[j]);
1533	+	scaled[j] += 0.5;
1534	+	}
1535	+
1536	+	// find xyz-indices of cell that cutoffGroup is in.
1537	+	whichCell.x() = nCells_.x() * scaled.x();
1538	+	whichCell.y() = nCells_.y() * scaled.y();
1539	+	whichCell.z() = nCells_.z() * scaled.z();
1540	+
1541	+	// find single index of this cell:
1542	+	cellIndex = Vlinear(whichCell, nCells_);
1543	+
1544	+	// add this cutoff group to the list of groups in this cell;
1545	+	cellList_[cellIndex].push_back(i);
1546	+	}
1547	+	#endif
1548	+
1549	+	for (int m1z = 0; m1z < nCells_.z(); m1z++)
1550	+	{
1551	+	for (int m1y = 0; m1y < nCells_.y(); m1y++)
1552	+	{
1553	+	for (int m1x = 0; m1x < nCells_.x(); m1x++)
1554	+	{
1555	+	Vector3i m1v(m1x, m1y, m1z);
1556	+	int m1 = Vlinear(m1v, nCells_);
1557	+
1558	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1559	+	{
1560	+
1561	+	Vector3i m2v = m1v + (*os);
1562	+
1563	+	if (m2v.x() >= nCells_.x())
1564	+	{
1565	+	m2v.x() = 0;
1566	+	} else if (m2v.x() < 0)
1567	+	{
1568	+	m2v.x() = nCells_.x() - 1;
1569	+	}
1570	+
1571	+	if (m2v.y() >= nCells_.y())
1572	+	{
1573	+	m2v.y() = 0;
1574	+	} else if (m2v.y() < 0)
1575	+	{
1576	+	m2v.y() = nCells_.y() - 1;
1577	+	}
1578	+
1579	+	if (m2v.z() >= nCells_.z())
1580	+	{
1581	+	m2v.z() = 0;
1582	+	} else if (m2v.z() < 0)
1583	+	{
1584	+	m2v.z() = nCells_.z() - 1;
1585	+	}
1586	+
1587	+	int m2 = Vlinear(m2v, nCells_);
1588	+
1589	+	#ifdef IS_MPI
1590	+	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1591	+	j1 != cellListRow_[m1].end(); ++j1)
1592	+	{
1593	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1594	+	j2 != cellListCol_[m2].end(); ++j2)
1595	+	{
1596	+
1597	+	// In parallel, we need to visit *all* pairs of row &
1598	+	// column indicies and will truncate later on.
1599	+	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1600	+	snap_->wrapVector(dr);
1601	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1602	+	if (dr.lengthSquare() < cuts.third)
1603	+	{
1604	+	neighborList.push_back(make_pair((*j1), (*j2)));
1605	+	}
1606	+	}
1607	+	}
1608	+	#else
1609	+
1610	+	for (vector<int>::iterator j1 = cellList_[m1].begin(); j1 != cellList_[m1].end(); ++j1)
1611	+	{
1612	+	for (vector<int>::iterator j2 = cellList_[m2].begin(); j2 != cellList_[m2].end(); ++j2)
1613	+	{
1614	+
1615	+	// Always do this if we're in different cells or if
1616	+	// we're in the same cell and the global index of the
1617	+	// j2 cutoff group is less than the j1 cutoff group
1618	+
1619	+	if (m2 != m1 || (*j2) < (*j1))
1620	+	{
1621	+	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1622	+	snap_->wrapVector(dr);
1623	+	cuts = getGroupCutoffs((*j1), (*j2));
1624	+	if (dr.lengthSquare() < cuts.third)
1625	+	{
1626	+	neighborList.push_back(make_pair((*j1), (*j2)));
1627	+	}
1628	+	}
1629	+	}
1630	+	}
1631	+	#endif
1632	+	}
1633	+	}
1634	+	}
1635	+	}
1636	+	} else
1637	+	{
1638	+	// branch to do all cutoff group pairs
1639	+	#ifdef IS_MPI
1640	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++)
1641	+	{
1642	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++)
1643	+	{
1644	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1645	+	snap_->wrapVector(dr);
1646	+	cuts = getGroupCutoffs( j1, j2 );
1647	+	if (dr.lengthSquare() < cuts.third)
1648	+	{
1649	+	neighborList.push_back(make_pair(j1, j2));
1650	+	}
1651	+	}
1652	+	}
1653	+	#else
1654	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++)
1655	+	{
1656	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++)
1657	+	{
1658	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1659	+	snap_->wrapVector(dr);
1660	+	cuts = getGroupCutoffs(j1, j2);
1661	+	if (dr.lengthSquare() < cuts.third)
1662	+	{
1663	+	neighborList.push_back(make_pair(j1, j2));
1664	+	}
1665	+	}
1666	+	}
1667	+	#endif
1668	+	}
1669	+
1670	+	// save the local cutoff group positions for the check that is
1671	+	// done on each loop:
1672	+	saved_CG_positions_.clear();
1673	+	for (int i = 0; i < nGroups_; i++)
1674	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1675	+
1676	+	return neighborList;
1677	+	}
1678	+	} //end namespace OpenMD

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