ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1598 by mciznick, Wed Jul 27 14:26:53 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	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) :
52	+	ForceDecomposition(info, iMan) {
53
54	<	/*  -*- c++ -*-  */
55	<	#include "config.h"
56	<	#include <stdlib.h>
54	>	// In a parallel computation, row and colum scans must visit all
55	>	// surrounding cells (not just the 14 upper triangular blocks that
56	>	// are used when the processor can see all pairs)
57		#ifdef IS_MPI
58	<	#include <mpi.h>
59	<	#endif
58	>	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
59	>	cellOffsets_.push_back( Vector3i(-1,-1, 0) );
60	>	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
61	>	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
62	>	cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63	>	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
64	>	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
65	>	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
66	>	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
67	>	cellOffsets_.push_back( Vector3i( 1, 0,-1) );
68	>	cellOffsets_.push_back( Vector3i( 1, 1,-1) );
69	>	cellOffsets_.push_back( Vector3i( 0, 1,-1) );
70	>	cellOffsets_.push_back( Vector3i(-1, 1,-1) );
71	>	#endif
72	>	}
73
74	<	#include <iostream>
75	<	#include <vector>
76	<	#include <algorithm>
77	<	#include <cmath>
78	<	#include "parallel/ForceDecomposition.hpp"
74	>	/**
75	>	* distributeInitialData is essentially a copy of the older fortran
76	>	* SimulationSetup
77	>	*/
78	>	void ForceMatrixDecomposition::distributeInitialData() {
79	>	snap_ = sman_->getCurrentSnapshot();
80	>	storageLayout_ = sman_->getStorageLayout();
81	>	ff_ = info_->getForceField();
82	>	nLocal_ = snap_->getNumberOfAtoms();
83
84	+	nGroups_ = info_->getNLocalCutoffGroups();
85	+	// gather the information for atomtype IDs (atids):
86	+	idents = info_->getIdentArray();
87	+	AtomLocalToGlobal = info_->getGlobalAtomIndices();
88	+	cgLocalToGlobal = info_->getGlobalGroupIndices();
89	+	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
90
91	<	using namespace std;
66	<	using namespace OpenMD;
91	>	massFactors = info_->getMassFactors();
92
93	<	//__static
93	>	PairList* excludes = info_->getExcludedInteractions();
94	>	PairList* oneTwo = info_->getOneTwoInteractions();
95	>	PairList* oneThree = info_->getOneThreeInteractions();
96	>	PairList* oneFour = info_->getOneFourInteractions();
97	>
98		#ifdef IS_MPI
70	–	static vector<MPI:Comm> communictors;
71	–	#endif
99
100	<	//____ MPITypeTraits
101	<	template<typename T>
75	<	struct MPITypeTraits;
100	>	MPI::Intracomm row = rowComm.getComm();
101	>	MPI::Intracomm col = colComm.getComm();
102
103	<	#ifdef IS_MPI
104	<	template<>
105	<	struct MPITypeTraits<RealType> {
106	<	static const MPI::Datatype datatype;
107	<	};
82	<	const MPI_Datatype MPITypeTraits<RealType>::datatype = MY_MPI_REAL;
103	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
104	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
105	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
106	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
107	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
108
109	<	template<>
110	<	struct MPITypeTraits<int> {
111	<	static const MPI::Datatype datatype;
112	<	};
113	<	const MPI::Datatype MPITypeTraits<int>::datatype = MPI_INT;
89	<	#endif
109	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
110	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
111	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
112	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
113	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
114
115	<	/**
116	<	* Constructor for ForceDecomposition Parallel Decomposition Method
117	<	* Will try to construct a symmetric grid of processors. Ideally, the
118	<	* number of processors will be a square ex: 4, 9, 16, 25.
95	<	*
96	<	*/
115	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
116	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
117	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
118	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
119
120	<	ForceDecomposition::ForceDecomposition() {
120	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
121	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
122	>	nGroupsInRow_ = cgPlanIntRow->getSize();
123	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
124
125	<	#ifdef IS_MPI
126	<	int nProcs = MPI::COMM_WORLD.Get_size();
127	<	int worldRank = MPI::COMM_WORLD.Get_rank();
125	>	// Modify the data storage objects with the correct layouts and sizes:
126	>	atomRowData.resize(nAtomsInRow_);
127	>	atomRowData.setStorageLayout(storageLayout_);
128	>	atomColData.resize(nAtomsInCol_);
129	>	atomColData.setStorageLayout(storageLayout_);
130	>	cgRowData.resize(nGroupsInRow_);
131	>	cgRowData.setStorageLayout(DataStorage::dslPosition);
132	>	cgColData.resize(nGroupsInCol_);
133	>	cgColData.setStorageLayout(DataStorage::dslPosition);
134	>
135	>	identsRow.resize(nAtomsInRow_);
136	>	identsCol.resize(nAtomsInCol_);
137	>
138	>	AtomPlanIntRow->gather(idents, identsRow);
139	>	AtomPlanIntColumn->gather(idents, identsCol);
140	>
141	>	// allocate memory for the parallel objects
142	>	atypesRow.resize(nAtomsInRow_);
143	>	atypesCol.resize(nAtomsInCol_);
144	>
145	>	for (int i = 0; i < nAtomsInRow_; i++)
146	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
147	>	for (int i = 0; i < nAtomsInCol_; i++)
148	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
149	>
150	>	pot_row.resize(nAtomsInRow_);
151	>	pot_col.resize(nAtomsInCol_);
152	>
153	>	AtomRowToGlobal.resize(nAtomsInRow_);
154	>	AtomColToGlobal.resize(nAtomsInCol_);
155	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
156	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
157	>
158	>	cerr << "Atoms in Local:\n";
159	>	for (int i = 0; i < AtomLocalToGlobal.size(); i++)
160	>	{
161	>	cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
162	>	}
163	>	cerr << "Atoms in Row:\n";
164	>	for (int i = 0; i < AtomRowToGlobal.size(); i++)
165	>	{
166	>	cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
167	>	}
168	>	cerr << "Atoms in Col:\n";
169	>	for (int i = 0; i < AtomColToGlobal.size(); i++)
170	>	{
171	>	cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
172	>	}
173	>
174	>	cgRowToGlobal.resize(nGroupsInRow_);
175	>	cgColToGlobal.resize(nGroupsInCol_);
176	>	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
177	>	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
178	>
179	>	cerr << "Gruops in Local:\n";
180	>	for (int i = 0; i < cgLocalToGlobal.size(); i++)
181	>	{
182	>	cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
183	>	}
184	>	cerr << "Groups in Row:\n";
185	>	for (int i = 0; i < cgRowToGlobal.size(); i++)
186	>	{
187	>	cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
188	>	}
189	>	cerr << "Groups in Col:\n";
190	>	for (int i = 0; i < cgColToGlobal.size(); i++)
191	>	{
192	>	cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
193	>	}
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	>	{
204	>	int gid = cgRowToGlobal[i];
205	>	for (int j = 0; j < nAtomsInRow_; j++)
206	>	{
207	>	int aid = AtomRowToGlobal[j];
208	>	if (globalGroupMembership[aid] == gid)
209	>	groupListRow_[i].push_back(j);
210	>	}
211	>	}
212	>
213	>	groupListCol_.clear();
214	>	groupListCol_.resize(nGroupsInCol_);
215	>	for (int i = 0; i < nGroupsInCol_; i++)
216	>	{
217	>	int gid = cgColToGlobal[i];
218	>	for (int j = 0; j < nAtomsInCol_; j++)
219	>	{
220	>	int aid = AtomColToGlobal[j];
221	>	if (globalGroupMembership[aid] == gid)
222	>	groupListCol_[i].push_back(j);
223	>	}
224	>	}
225	>
226	>	excludesForAtom.clear();
227	>	excludesForAtom.resize(nAtomsInRow_);
228	>	toposForAtom.clear();
229	>	toposForAtom.resize(nAtomsInRow_);
230	>	topoDist.clear();
231	>	topoDist.resize(nAtomsInRow_);
232	>	for (int i = 0; i < nAtomsInRow_; i++)
233	>	{
234	>	int iglob = AtomRowToGlobal[i];
235	>
236	>	for (int j = 0; j < nAtomsInCol_; j++)
237	>	{
238	>	int jglob = AtomColToGlobal[j];
239	>
240	>	if (excludes->hasPair(iglob, jglob))
241	>	excludesForAtom[i].push_back(j);
242	>
243	>	if (oneTwo->hasPair(iglob, jglob))
244	>	{
245	>	toposForAtom[i].push_back(j);
246	>	topoDist[i].push_back(1);
247	>	} else
248	>	{
249	>	if (oneThree->hasPair(iglob, jglob))
250	>	{
251	>	toposForAtom[i].push_back(j);
252	>	topoDist[i].push_back(2);
253	>	} else
254	>	{
255	>	if (oneFour->hasPair(iglob, jglob))
256	>	{
257	>	toposForAtom[i].push_back(j);
258	>	topoDist[i].push_back(3);
259	>	}
260	>	}
261	>	}
262	>	}
263	>	}
264	>
265		#endif
266
267	<	// First time through, construct column stride.
268	<	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	<	}
267	>	// allocate memory for the parallel objects
268	>	atypesLocal.resize(nLocal_);
269
270	<	int nRows = nProcs/nColumns;
271	<	myRank_ = (int) worldRank%nColumns;
272	<	}
273	<	else
274	<	{
275	<	myRank_ = myRank/nColumns;
276	<	}
277	<	MPI::Comm newComm = MPI:COMM_WORLD.Split(myRank_,0);
278	<
279	<	isColumn_ = false;
280	<
270	>	for (int i = 0; i < nLocal_; i++)
271	>	atypesLocal[i] = ff_->getAtomType(idents[i]);
272	>
273	>	groupList_.clear();
274	>	groupList_.resize(nGroups_);
275	>	for (int i = 0; i < nGroups_; i++)
276	>	{
277	>	int gid = cgLocalToGlobal[i];
278	>	for (int j = 0; j < nLocal_; j++)
279	>	{
280	>	int aid = AtomLocalToGlobal[j];
281	>	if (globalGroupMembership[aid] == gid)
282	>	{
283	>	groupList_[i].push_back(j);
284	>	}
285	>	}
286	>	}
287	>
288	>	excludesForAtom.clear();
289	>	excludesForAtom.resize(nLocal_);
290	>	toposForAtom.clear();
291	>	toposForAtom.resize(nLocal_);
292	>	topoDist.clear();
293	>	topoDist.resize(nLocal_);
294	>
295	>	for (int i = 0; i < nLocal_; i++)
296	>	{
297	>	int iglob = AtomLocalToGlobal[i];
298	>
299	>	for (int j = 0; j < nLocal_; j++)
300	>	{
301	>	int jglob = AtomLocalToGlobal[j];
302	>
303	>	if (excludes->hasPair(iglob, jglob))
304	>	excludesForAtom[i].push_back(j);
305	>
306	>	if (oneTwo->hasPair(iglob, jglob))
307	>	{
308	>	toposForAtom[i].push_back(j);
309	>	topoDist[i].push_back(1);
310	>	} else
311	>	{
312	>	if (oneThree->hasPair(iglob, jglob))
313	>	{
314	>	toposForAtom[i].push_back(j);
315	>	topoDist[i].push_back(2);
316	>	} else
317	>	{
318	>	if (oneFour->hasPair(iglob, jglob))
319	>	{
320	>	toposForAtom[i].push_back(j);
321	>	topoDist[i].push_back(3);
322	>	}
323	>	}
324	>	}
325	>	}
326	>	}
327	>
328	>	createGtypeCutoffMap();
329	>
330		}
331
332	<	ForceDecomposition::gather(sendbuf, receivebuf){
333	<	communicators(myIndex_).Allgatherv();
332	>	void ForceMatrixDecomposition::createGtypeCutoffMap() {
333	>
334	>	RealType tol = 1e-6;
335	>	largestRcut_ = 0.0;
336	>	RealType rc;
337	>	int atid;
338	>	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
339	>
340	>	map<int, RealType> atypeCutoff;
341	>
342	>	for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at)
343	>	{
344	>	atid = (*at)->getIdent();
345	>	if (userChoseCutoff_)
346	>	atypeCutoff[atid] = userCutoff_;
347	>	else
348	>	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
349	>	}
350	>
351	>	vector<RealType> gTypeCutoffs;
352	>	// first we do a single loop over the cutoff groups to find the
353	>	// largest cutoff for any atypes present in this group.
354	>	#ifdef IS_MPI
355	>	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
356	>	groupRowToGtype.resize(nGroupsInRow_);
357	>	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++)
358	>	{
359	>	vector<int> atomListRow = getAtomsInGroupRow(cg1);
360	>	for (vector<int>::iterator ia = atomListRow.begin();
361	>	ia != atomListRow.end(); ++ia)
362	>	{
363	>	int atom1 = (*ia);
364	>	atid = identsRow[atom1];
365	>	if (atypeCutoff[atid] > groupCutoffRow[cg1])
366	>	{
367	>	groupCutoffRow[cg1] = atypeCutoff[atid];
368	>	}
369	>	}
370	>
371	>	bool gTypeFound = false;
372	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
373	>	{
374	>	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol)
375	>	{
376	>	groupRowToGtype[cg1] = gt;
377	>	gTypeFound = true;
378	>	}
379	>	}
380	>	if (!gTypeFound)
381	>	{
382	>	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
383	>	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
384	>	}
385	>
386	>	}
387	>	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
388	>	groupColToGtype.resize(nGroupsInCol_);
389	>	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++)
390	>	{
391	>	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
392	>	for (vector<int>::iterator jb = atomListCol.begin();
393	>	jb != atomListCol.end(); ++jb)
394	>	{
395	>	int atom2 = (*jb);
396	>	atid = identsCol[atom2];
397	>	if (atypeCutoff[atid] > groupCutoffCol[cg2])
398	>	{
399	>	groupCutoffCol[cg2] = atypeCutoff[atid];
400	>	}
401	>	}
402	>	bool gTypeFound = false;
403	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
404	>	{
405	>	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol)
406	>	{
407	>	groupColToGtype[cg2] = gt;
408	>	gTypeFound = true;
409	>	}
410	>	}
411	>	if (!gTypeFound)
412	>	{
413	>	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
414	>	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
415	>	}
416	>	}
417	>	#else
418	>
419	>	vector<RealType> groupCutoff(nGroups_, 0.0);
420	>	groupToGtype.resize(nGroups_);
421	>	for (int cg1 = 0; cg1 < nGroups_; cg1++)
422	>	{
423	>	groupCutoff[cg1] = 0.0;
424	>	vector<int> atomList = getAtomsInGroupRow(cg1);
425	>	for (vector<int>::iterator ia = atomList.begin(); ia != atomList.end(); ++ia)
426	>	{
427	>	int atom1 = (*ia);
428	>	atid = idents[atom1];
429	>	if (atypeCutoff[atid] > groupCutoff[cg1])
430	>	groupCutoff[cg1] = atypeCutoff[atid];
431	>	}
432	>
433	>	bool gTypeFound = false;
434	>	for (int gt = 0; gt < gTypeCutoffs.size(); gt++)
435	>	{
436	>	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol)
437	>	{
438	>	groupToGtype[cg1] = gt;
439	>	gTypeFound = true;
440	>	}
441	>	}
442	>	if (!gTypeFound)
443	>	{
444	>	gTypeCutoffs.push_back(groupCutoff[cg1]);
445	>	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
446	>	}
447	>	}
448	>	#endif
449	>
450	>	// Now we find the maximum group cutoff value present in the simulation
451	>
452	>	RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
453	>
454	>	#ifdef IS_MPI
455	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
456	>	MPI::MAX);
457	>	#endif
458	>
459	>	RealType tradRcut = groupMax;
460	>
461	>	for (int i = 0; i < gTypeCutoffs.size(); i++)
462	>	{
463	>	for (int j = 0; j < gTypeCutoffs.size(); j++)
464	>	{
465	>	RealType thisRcut;
466	>	switch (cutoffPolicy_) {
467	>	case TRADITIONAL:
468	>	thisRcut = tradRcut;
469	>	break;
470	>	case MIX:
471	>	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
472	>	break;
473	>	case MAX:
474	>	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
475	>	break;
476	>	default:
477	>	sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap "
478	>	"hit an unknown cutoff policy!\n");
479	>	painCave.severity = OPENMD_ERROR;
480	>	painCave.isFatal = 1;
481	>	simError();
482	>	break;
483	>	}
484	>
485	>	pair<int, int> key = make_pair(i, j);
486	>	gTypeCutoffMap[key].first = thisRcut;
487	>	if (thisRcut > largestRcut_)
488	>	largestRcut_ = thisRcut;
489	>	gTypeCutoffMap[key].second = thisRcut * thisRcut;
490	>	gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
491	>	// sanity check
492	>
493	>	if (userChoseCutoff_)
494	>	{
495	>	if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001)
496	>	{
497	>	sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap "
498	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
499	>	painCave.severity = OPENMD_ERROR;
500	>	painCave.isFatal = 1;
501	>	simError();
502	>	}
503	>	}
504	>	}
505	>	}
506		}
507
508	+	groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
509	+	int i, j;
510	+	#ifdef IS_MPI
511	+	i = groupRowToGtype[cg1];
512	+	j = groupColToGtype[cg2];
513	+	#else
514	+	i = groupToGtype[cg1];
515	+	j = groupToGtype[cg2];
516	+	#endif
517	+	return gTypeCutoffMap[make_pair(i, j)];
518	+	}
519
520	+	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
521	+	for (int j = 0; j < toposForAtom[atom1].size(); j++)
522	+	{
523	+	if (toposForAtom[atom1][j] == atom2)
524	+	return topoDist[atom1][j];
525	+	}
526	+	return 0;
527	+	}
528
529	<	ForceDecomposition::scatter(sbuffer, rbuffer){
530	<	communicators(myIndex_).Reduce_scatter(sbuffer, recevbuf. recvcounts, MPI::DOUBLE, MPI::SUM);
529	>	void ForceMatrixDecomposition::zeroWorkArrays() {
530	>	pairwisePot = 0.0;
531	>	embeddingPot = 0.0;
532	>
533	>	#ifdef IS_MPI
534	>	if (storageLayout_ & DataStorage::dslForce)
535	>	{
536	>	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
537	>	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
538	>	}
539	>
540	>	if (storageLayout_ & DataStorage::dslTorque)
541	>	{
542	>	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
543	>	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
544	>	}
545	>
546	>	fill(pot_row.begin(), pot_row.end(),
547	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
548	>
549	>	fill(pot_col.begin(), pot_col.end(),
550	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
551	>
552	>	if (storageLayout_ & DataStorage::dslParticlePot)
553	>	{
554	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
555	>	0.0);
556	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
557	>	0.0);
558	>	}
559	>
560	>	if (storageLayout_ & DataStorage::dslDensity)
561	>	{
562	>	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
563	>	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
564	>	}
565	>
566	>	if (storageLayout_ & DataStorage::dslFunctional)
567	>	{
568	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
569	>	0.0);
570	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
571	>	0.0);
572	>	}
573	>
574	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
575	>	{
576	>	fill(atomRowData.functionalDerivative.begin(),
577	>	atomRowData.functionalDerivative.end(), 0.0);
578	>	fill(atomColData.functionalDerivative.begin(),
579	>	atomColData.functionalDerivative.end(), 0.0);
580	>	}
581	>
582	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
583	>	{
584	>	fill(atomRowData.skippedCharge.begin(),
585	>	atomRowData.skippedCharge.end(), 0.0);
586	>	fill(atomColData.skippedCharge.begin(),
587	>	atomColData.skippedCharge.end(), 0.0);
588	>	}
589	>
590	>	#endif
591	>	// even in parallel, we need to zero out the local arrays:
592	>
593	>	if (storageLayout_ & DataStorage::dslParticlePot)
594	>	{
595	>	fill(snap_->atomData.particlePot.begin(), snap_->atomData.particlePot.end(), 0.0);
596	>	}
597	>
598	>	if (storageLayout_ & DataStorage::dslDensity)
599	>	{
600	>	fill(snap_->atomData.density.begin(), snap_->atomData.density.end(), 0.0);
601	>	}
602	>	if (storageLayout_ & DataStorage::dslFunctional)
603	>	{
604	>	fill(snap_->atomData.functional.begin(), snap_->atomData.functional.end(), 0.0);
605	>	}
606	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
607	>	{
608	>	fill(snap_->atomData.functionalDerivative.begin(), snap_->atomData.functionalDerivative.end(), 0.0);
609	>	}
610	>	if (storageLayout_ & DataStorage::dslSkippedCharge)
611	>	{
612	>	fill(snap_->atomData.skippedCharge.begin(), snap_->atomData.skippedCharge.end(), 0.0);
613	>	}
614	>
615		}
616
617	+	void ForceMatrixDecomposition::distributeData() {
618	+	snap_ = sman_->getCurrentSnapshot();
619	+	storageLayout_ = sman_->getStorageLayout();
620	+	#ifdef IS_MPI
621	+
622	+	// gather up the atomic positions
623	+	AtomPlanVectorRow->gather(snap_->atomData.position,
624	+	atomRowData.position);
625	+	AtomPlanVectorColumn->gather(snap_->atomData.position,
626	+	atomColData.position);
627	+
628	+	// gather up the cutoff group positions
629	+
630	+	cerr << "before gather\n";
631	+	for (int i = 0; i < snap_->cgData.position.size(); i++)
632	+	{
633	+	cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
634	+	}
635	+
636	+	cgPlanVectorRow->gather(snap_->cgData.position,
637	+	cgRowData.position);
638	+
639	+	cerr << "after gather\n";
640	+	for (int i = 0; i < cgRowData.position.size(); i++)
641	+	{
642	+	cerr << "cgRpos = " << cgRowData.position[i] << "\n";
643	+	}
644	+
645	+	cgPlanVectorColumn->gather(snap_->cgData.position,
646	+	cgColData.position);
647	+	for (int i = 0; i < cgColData.position.size(); i++)
648	+	{
649	+	cerr << "cgCpos = " << cgColData.position[i] << "\n";
650	+	}
651	+
652	+	// if needed, gather the atomic rotation matrices
653	+	if (storageLayout_ & DataStorage::dslAmat)
654	+	{
655	+	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
656	+	atomRowData.aMat);
657	+	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
658	+	atomColData.aMat);
659	+	}
660	+
661	+	// if needed, gather the atomic eletrostatic frames
662	+	if (storageLayout_ & DataStorage::dslElectroFrame)
663	+	{
664	+	AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
665	+	atomRowData.electroFrame);
666	+	AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
667	+	atomColData.electroFrame);
668	+	}
669	+
670	+	#endif
671	+	}
672	+
673	+	/* collects information obtained during the pre-pair loop onto local
674	+	* data structures.
675	+	*/
676	+	void ForceMatrixDecomposition::collectIntermediateData() {
677	+	snap_ = sman_->getCurrentSnapshot();
678	+	storageLayout_ = sman_->getStorageLayout();
679	+	#ifdef IS_MPI
680	+
681	+	if (storageLayout_ & DataStorage::dslDensity)
682	+	{
683	+
684	+	AtomPlanRealRow->scatter(atomRowData.density,
685	+	snap_->atomData.density);
686	+
687	+	int n = snap_->atomData.density.size();
688	+	vector<RealType> rho_tmp(n, 0.0);
689	+	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
690	+	for (int i = 0; i < n; i++)
691	+	snap_->atomData.density[i] += rho_tmp[i];
692	+	}
693	+	#endif
694	+	}
695	+
696	+	/*
697	+	* redistributes information obtained during the pre-pair loop out to
698	+	* row and column-indexed data structures
699	+	*/
700	+	void ForceMatrixDecomposition::distributeIntermediateData() {
701	+	snap_ = sman_->getCurrentSnapshot();
702	+	storageLayout_ = sman_->getStorageLayout();
703	+	#ifdef IS_MPI
704	+	if (storageLayout_ & DataStorage::dslFunctional)
705	+	{
706	+	AtomPlanRealRow->gather(snap_->atomData.functional,
707	+	atomRowData.functional);
708	+	AtomPlanRealColumn->gather(snap_->atomData.functional,
709	+	atomColData.functional);
710	+	}
711	+
712	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
713	+	{
714	+	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
715	+	atomRowData.functionalDerivative);
716	+	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
717	+	atomColData.functionalDerivative);
718	+	}
719	+	#endif
720	+	}
721	+
722	+	void ForceMatrixDecomposition::collectData() {
723	+	snap_ = sman_->getCurrentSnapshot();
724	+	storageLayout_ = sman_->getStorageLayout();
725	+	#ifdef IS_MPI
726	+	int n = snap_->atomData.force.size();
727	+	vector<Vector3d> frc_tmp(n, V3Zero);
728	+
729	+	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
730	+	for (int i = 0; i < n; i++)
731	+	{
732	+	snap_->atomData.force[i] += frc_tmp[i];
733	+	frc_tmp[i] = 0.0;
734	+	}
735	+
736	+	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
737	+	for (int i = 0; i < n; i++)
738	+	{
739	+	snap_->atomData.force[i] += frc_tmp[i];
740	+	}
741	+
742	+	if (storageLayout_ & DataStorage::dslTorque)
743	+	{
744	+
745	+	int nt = snap_->atomData.torque.size();
746	+	vector<Vector3d> trq_tmp(nt, V3Zero);
747	+
748	+	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
749	+	for (int i = 0; i < nt; i++)
750	+	{
751	+	snap_->atomData.torque[i] += trq_tmp[i];
752	+	trq_tmp[i] = 0.0;
753	+	}
754	+
755	+	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
756	+	for (int i = 0; i < nt; i++)
757	+	snap_->atomData.torque[i] += trq_tmp[i];
758	+	}
759	+
760	+	if (storageLayout_ & DataStorage::dslSkippedCharge)
761	+	{
762	+
763	+	int ns = snap_->atomData.skippedCharge.size();
764	+	vector<RealType> skch_tmp(ns, 0.0);
765	+
766	+	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
767	+	for (int i = 0; i < ns; i++)
768	+	{
769	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
770	+	skch_tmp[i] = 0.0;
771	+	}
772	+
773	+	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
774	+	for (int i = 0; i < ns; i++)
775	+	snap_->atomData.skippedCharge[i] += skch_tmp[i];
776	+	}
777	+
778	+	nLocal_ = snap_->getNumberOfAtoms();
779	+
780	+	vector<potVec> pot_temp(nLocal_,
781	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
782	+
783	+	// scatter/gather pot_row into the members of my column
784	+
785	+	AtomPlanPotRow->scatter(pot_row, pot_temp);
786	+
787	+	for (int ii = 0; ii < pot_temp.size(); ii++ )
788	+	pairwisePot += pot_temp[ii];
789	+
790	+	fill(pot_temp.begin(), pot_temp.end(),
791	+	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
792	+
793	+	AtomPlanPotColumn->scatter(pot_col, pot_temp);
794	+
795	+	for (int ii = 0; ii < pot_temp.size(); ii++ )
796	+	pairwisePot += pot_temp[ii];
797	+	#endif
798	+
799	+	cerr << "pairwisePot = " << pairwisePot << "\n";
800	+	}
801	+
802	+	int ForceMatrixDecomposition::getNAtomsInRow() {
803	+	#ifdef IS_MPI
804	+	return nAtomsInRow_;
805	+	#else
806	+	return nLocal_;
807	+	#endif
808	+	}
809	+
810	+	/**
811	+	* returns the list of atoms belonging to this group.
812	+	*/
813	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1) {
814	+	#ifdef IS_MPI
815	+	return groupListRow_[cg1];
816	+	#else
817	+	return groupList_[cg1];
818	+	#endif
819	+	}
820	+
821	+	vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2) {
822	+	#ifdef IS_MPI
823	+	return groupListCol_[cg2];
824	+	#else
825	+	return groupList_[cg2];
826	+	#endif
827	+	}
828	+
829	+	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2) {
830	+	Vector3d d;
831
832	+	#ifdef IS_MPI
833	+	d = cgColData.position[cg2] - cgRowData.position[cg1];
834	+	cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
835	+	cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
836	+	#else
837	+	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
838	+	cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
839	+	cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
840	+	#endif
841	+
842	+	snap_->wrapVector(d);
843	+	return d;
844	+	}
845	+
846	+	Vector3d ForceMatrixDecomposition::getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2) {
847	+	Vector3d d;
848	+
849	+	d = snap_->cgData.position[cg2->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
850	+	/*      cerr << "cg1_gid = " << cg1->getGlobalIndex() << "\tcg1_lid = " << cg1->getLocalIndex() << "\tcg1p = "
851	+	<< snap_->cgData.position[cg1->getLocalIndex()] << "\n";
852	+	cerr << "cg2_gid = " << cg2->getGlobalIndex() << "\tcg2_lid = " << cg2->getLocalIndex() << "\tcg2p = "
853	+	<< snap_->cgData.position[cg2->getLocalIndex()] << "\n";*/
854	+
855	+	snap_->wrapVector(d);
856	+	return d;
857	+	}
858	+
859	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1) {
860	+
861	+	Vector3d d;
862	+
863	+	#ifdef IS_MPI
864	+	d = cgRowData.position[cg1] - atomRowData.position[atom1];
865	+	#else
866	+	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
867	+	#endif
868	+
869	+	snap_->wrapVector(d);
870	+	return d;
871	+	}
872	+
873	+	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2) {
874	+	Vector3d d;
875	+
876	+	#ifdef IS_MPI
877	+	d = cgColData.position[cg2] - atomColData.position[atom2];
878	+	#else
879	+	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
880	+	#endif
881	+
882	+	snap_->wrapVector(d);
883	+	return d;
884	+	}
885	+
886	+	RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
887	+	#ifdef IS_MPI
888	+	return massFactorsRow[atom1];
889	+	#else
890	+	return massFactors[atom1];
891	+	#endif
892	+	}
893	+
894	+	RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
895	+	#ifdef IS_MPI
896	+	return massFactorsCol[atom2];
897	+	#else
898	+	return massFactors[atom2];
899	+	#endif
900	+
901	+	}
902	+
903	+	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2) {
904	+	Vector3d d;
905	+
906	+	#ifdef IS_MPI
907	+	d = atomColData.position[atom2] - atomRowData.position[atom1];
908	+	#else
909	+	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
910	+	#endif
911	+
912	+	snap_->wrapVector(d);
913	+	return d;
914	+	}
915	+
916	+	vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
917	+	return excludesForAtom[atom1];
918	+	}
919	+
920	+	/**
921	+	* We need to exclude some overcounted interactions that result from
922	+	* the parallel decomposition.
923	+	*/
924	+	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
925	+	int unique_id_1, unique_id_2;
926	+
927	+	//      cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
928	+	#ifdef IS_MPI
929	+	// in MPI, we have to look up the unique IDs for each atom
930	+	unique_id_1 = AtomRowToGlobal[atom1];
931	+	unique_id_2 = AtomColToGlobal[atom2];
932	+
933	+	cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
934	+	// this situation should only arise in MPI simulations
935	+	if (unique_id_1 == unique_id_2) return true;
936	+
937	+	// this prevents us from doing the pair on multiple processors
938	+	if (unique_id_1 < unique_id_2)
939	+	{
940	+	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
941	+	} else
942	+	{
943	+	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
944	+	}
945	+	#endif
946	+	return false;
947	+	}
948	+
949	+	/**
950	+	* We need to handle the interactions for atoms who are involved in
951	+	* the same rigid body as well as some short range interactions
952	+	* (bonds, bends, torsions) differently from other interactions.
953	+	* We'll still visit the pairwise routines, but with a flag that
954	+	* tells those routines to exclude the pair from direct long range
955	+	* interactions.  Some indirect interactions (notably reaction
956	+	* field) must still be handled for these pairs.
957	+	*/
958	+	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
959	+	int unique_id_2;
960	+	#ifdef IS_MPI
961	+	// in MPI, we have to look up the unique IDs for the row atom.
962	+	unique_id_2 = AtomColToGlobal[atom2];
963	+	#else
964	+	// in the normal loop, the atom numbers are unique
965	+	unique_id_2 = atom2;
966	+	#endif
967	+
968	+	for (vector<int>::iterator i = excludesForAtom[atom1].begin(); i != excludesForAtom[atom1].end(); ++i)
969	+	{
970	+	if ((*i) == unique_id_2)
971	+	return true;
972	+	}
973	+
974	+	return false;
975	+	}
976	+
977	+	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg) {
978	+	#ifdef IS_MPI
979	+	atomRowData.force[atom1] += fg;
980	+	#else
981	+	snap_->atomData.force[atom1] += fg;
982	+	#endif
983	+	}
984	+
985	+	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg) {
986	+	#ifdef IS_MPI
987	+	atomColData.force[atom2] += fg;
988	+	#else
989	+	snap_->atomData.force[atom2] += fg;
990	+	#endif
991	+	}
992	+
993	+	// filling interaction blocks with pointers
994	+	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, int atom1, int atom2) {
995	+
996	+	idat.excluded = excludeAtomPair(atom1, atom2);
997	+
998	+	#ifdef IS_MPI
999	+	idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1000	+	//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1001	+	//                         ff_->getAtomType(identsCol[atom2]) );
1002	+
1003	+	if (storageLayout_ & DataStorage::dslAmat)
1004	+	{
1005	+	idat.A1 = &(atomRowData.aMat[atom1]);
1006	+	idat.A2 = &(atomColData.aMat[atom2]);
1007	+	}
1008	+
1009	+	if (storageLayout_ & DataStorage::dslElectroFrame)
1010	+	{
1011	+	idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1012	+	idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1013	+	}
1014	+
1015	+	if (storageLayout_ & DataStorage::dslTorque)
1016	+	{
1017	+	idat.t1 = &(atomRowData.torque[atom1]);
1018	+	idat.t2 = &(atomColData.torque[atom2]);
1019	+	}
1020	+
1021	+	if (storageLayout_ & DataStorage::dslDensity)
1022	+	{
1023	+	idat.rho1 = &(atomRowData.density[atom1]);
1024	+	idat.rho2 = &(atomColData.density[atom2]);
1025	+	}
1026	+
1027	+	if (storageLayout_ & DataStorage::dslFunctional)
1028	+	{
1029	+	idat.frho1 = &(atomRowData.functional[atom1]);
1030	+	idat.frho2 = &(atomColData.functional[atom2]);
1031	+	}
1032	+
1033	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
1034	+	{
1035	+	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1036	+	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1037	+	}
1038	+
1039	+	if (storageLayout_ & DataStorage::dslParticlePot)
1040	+	{
1041	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1042	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1043	+	}
1044	+
1045	+	if (storageLayout_ & DataStorage::dslSkippedCharge)
1046	+	{
1047	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1048	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1049	+	}
1050	+
1051	+	#else
1052	+
1053	+	idat.atypes = make_pair(atypesLocal[atom1], atypesLocal[atom2]);
1054	+	//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1055	+	//                         ff_->getAtomType(idents[atom2]) );
1056	+
1057	+	if (storageLayout_ & DataStorage::dslAmat)
1058	+	{
1059	+	idat.A1 = &(snap_->atomData.aMat[atom1]);
1060	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1061	+	}
1062	+
1063	+	if (storageLayout_ & DataStorage::dslElectroFrame)
1064	+	{
1065	+	idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1066	+	idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1067	+	}
1068	+
1069	+	if (storageLayout_ & DataStorage::dslTorque)
1070	+	{
1071	+	idat.t1 = &(snap_->atomData.torque[atom1]);
1072	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1073	+	}
1074	+
1075	+	if (storageLayout_ & DataStorage::dslDensity)
1076	+	{
1077	+	idat.rho1 = &(snap_->atomData.density[atom1]);
1078	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1079	+	}
1080	+
1081	+	if (storageLayout_ & DataStorage::dslFunctional)
1082	+	{
1083	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1084	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1085	+	}
1086	+
1087	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative)
1088	+	{
1089	+	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1090	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1091	+	}
1092	+
1093	+	if (storageLayout_ & DataStorage::dslParticlePot)
1094	+	{
1095	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1096	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1097	+	}
1098	+
1099	+	if (storageLayout_ & DataStorage::dslSkippedCharge)
1100	+	{
1101	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1102	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1103	+	}
1104	+	#endif
1105	+	}
1106	+
1107	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1108	+	#ifdef IS_MPI
1109	+	pot_row[atom1] += 0.5 * *(idat.pot);
1110	+	pot_col[atom2] += 0.5 * *(idat.pot);
1111	+
1112	+	atomRowData.force[atom1] += *(idat.f1);
1113	+	atomColData.force[atom2] -= *(idat.f1);
1114	+	#else
1115	+	pairwisePot += *(idat.pot);
1116	+
1117	+	snap_->atomData.force[atom1] += *(idat.f1);
1118	+	snap_->atomData.force[atom2] -= *(idat.f1);
1119	+	#endif
1120	+
1121	+	}
1122	+
1123	+	void ForceMatrixDecomposition::reorderGroupCutoffs(vector<int> &order) {
1124	+	vector<int> tmp = vector<int> (groupToGtype.size());
1125	+
1126	+	for (int i = 0; i < groupToGtype.size(); ++i)
1127	+	{
1128	+	tmp[i] = groupToGtype[i];
1129	+	}
1130	+
1131	+	for (int i = 0; i < groupToGtype.size(); ++i)
1132	+	{
1133	+	groupToGtype[i] = tmp[order[i]];
1134	+	}
1135	+	}
1136	+
1137	+	void ForceMatrixDecomposition::reorderPosition(vector<int> &order) {
1138	+	Snapshot* snap_ = info_->getSnapshotManager()->getCurrentSnapshot();
1139	+	DataStorage* cgConfig = &(snap_->cgData);
1140	+	vector<Vector3d> tmp = vector<Vector3d> (nGroups_);
1141	+
1142	+	for (int i = 0; i < nGroups_; ++i)
1143	+	{
1144	+	tmp[i] = snap_->cgData.position[i];
1145	+	}
1146	+
1147	+	vector<int> mapPos = vector<int>(nGroups_);
1148	+	for (int i = 0; i < nGroups_; ++i)
1149	+	{
1150	+	snap_->cgData.position[i] = tmp[order[i]];
1151	+	mapPos[order[i]] = i;
1152	+	}
1153	+
1154	+	SimInfo::MoleculeIterator mi;
1155	+	Molecule* mol;
1156	+	Molecule::CutoffGroupIterator ci;
1157	+	CutoffGroup* cg;
1158	+
1159	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1160	+	{
1161	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1162	+	{
1163	+	cg->setLocalIndex(mapPos[cg->getLocalIndex()]);
1164	+	}
1165	+	}
1166	+
1167	+	/*      if (info_->getNCutoffGroups() > 0)
1168	+	{
1169	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1170	+	{
1171	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1172	+	{
1173	+	printf("gbI:%d locI:%d x:%f y:%f z:%f\n", cg->getGlobalIndex(), cg->getLocalIndex(),
1174	+	cgConfig->position[cg->getLocalIndex()].x(), cgConfig->position[cg->getLocalIndex()].y(),
1175	+	cgConfig->position[cg->getLocalIndex()].z());
1176	+	}
1177	+	}
1178	+	} else
1179	+	{
1180	+	// center of mass of the group is the same as position of the atom
1181	+	// if cutoff group does not exist
1182	+	printf("ERROR!!!!!!!!!!!!!!!!!!!!!!!!!!!\n");
1183	+	//                      cgConfig->position = config->position;
1184	+	}*/
1185	+	}
1186	+
1187	+	void ForceMatrixDecomposition::reorderGroupList(vector<int> &order) {
1188	+	vector<vector<int> > tmp = vector<vector<int> > (groupList_.size());
1189	+
1190	+	for (int i = 0; i < groupList_.size(); ++i)
1191	+	{
1192	+	tmp[i] = groupList_[i];
1193	+	}
1194	+
1195	+	for (int i = 0; i < groupList_.size(); ++i)
1196	+	{
1197	+	groupList_[i] = tmp[order[i]];
1198	+	}
1199	+	}
1200	+
1201	+	void ForceMatrixDecomposition::reorderMemory(vector<vector<CutoffGroup *> > &H_c_l) {
1202	+	int n = 0;
1203	+	//      printf("Reorder memory time:%f!!!!!!!!!!!!!!!!!!!!!!!!!!!\n",
1204	+	//                      info_->getSnapshotManager()->getCurrentSnapshot()->getTime());
1205	+
1206	+	/* record the reordered atom indices */
1207	+	vector<int> k = vector<int> (nGroups_);
1208	+
1209	+	for (int c = 0; c < H_c_l.size(); ++c)
1210	+	{
1211	+	for (vector<CutoffGroup *>::iterator cg = H_c_l[c].begin(); cg != H_c_l[c].end(); ++cg)
1212	+	{
1213	+	int i = (*cg)->getGlobalIndex();
1214	+	k[n] = i;
1215	+	++n;
1216	+	}
1217	+	}
1218	+
1219	+	//      reorderGroupCutoffs(k);
1220	+	//      reorderGroupList(k);
1221	+	reorderPosition(k);
1222	+	}
1223	+
1224	+	vector<vector<CutoffGroup *> > ForceMatrixDecomposition::buildLayerBasedNeighborList() {
1225	+	//      printf("buildLayerBasedNeighborList; nGroups:%d\n", nGroups_);
1226	+	// Na = nGroups_
1227	+	/* cell occupancy counter */
1228	+	//      vector<int> k_c;
1229	+	/* c_i - has cell containing atom i (size Na) */
1230	+	vector<int> c = vector<int> (nGroups_);
1231	+	/* l_i - layer containing atom i (size Na) */
1232	+	//      vector<int> l;
1233	+
1234	+	RealType rList_ = (largestRcut_ + skinThickness_);
1235	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1236	+	Mat3x3d Hmat = snap_->getHmat();
1237	+	Vector3d Hx = Hmat.getColumn(0);
1238	+	Vector3d Hy = Hmat.getColumn(1);
1239	+	Vector3d Hz = Hmat.getColumn(2);
1240	+
1241	+	nCells_.x() = (int) (Hx.length()) / rList_;
1242	+	nCells_.y() = (int) (Hy.length()) / rList_;
1243	+	nCells_.z() = (int) (Hz.length()) / rList_;
1244	+
1245	+	Mat3x3d invHmat = snap_->getInvHmat();
1246	+	Vector3d rs, scaled, dr;
1247	+	Vector3i whichCell;
1248	+	int cellIndex;
1249	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1250	+
1251	+	//      k_c = vector<int> (nCtot, 0);
1252	+
1253	+	SimInfo::MoleculeIterator mi;
1254	+	Molecule* mol;
1255	+	Molecule::CutoffGroupIterator ci;
1256	+	CutoffGroup* cg;
1257	+
1258	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1259	+	{
1260	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1261	+	{
1262	+	rs = snap_->cgData.position[cg->getLocalIndex()];
1263	+
1264	+	// scaled positions relative to the box vectors
1265	+	scaled = invHmat * rs;
1266	+
1267	+	// wrap the vector back into the unit box by subtracting integer box
1268	+	// numbers
1269	+	for (int j = 0; j < 3; j++)
1270	+	{
1271	+	scaled[j] -= roundMe(scaled[j]);
1272	+	scaled[j] += 0.5;
1273	+	}
1274	+
1275	+	// find xyz-indices of cell that cutoffGroup is in.
1276	+	whichCell.x() = nCells_.x() * scaled.x();
1277	+	whichCell.y() = nCells_.y() * scaled.y();
1278	+	whichCell.z() = nCells_.z() * scaled.z();
1279	+
1280	+	//                      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(),
1281	+	//                                      whichCell.z());
1282	+
1283	+	// find single index of this cell:
1284	+	cellIndex = Vlinear(whichCell, nCells_);
1285	+
1286	+	c[cg->getGlobalIndex()] = cellIndex;
1287	+	}
1288	+	}
1289	+
1290	+	//      int k_c_curr;
1291	+	//      int k_c_max = 0;
1292	+	/* the cell-layer occupancy matrix */
1293	+	vector<vector<CutoffGroup *> > H_c_l = vector<vector<CutoffGroup *> > (nCtot);
1294	+
1295	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1296	+	{
1297	+	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1298	+
1299	+	{
1300	+	//                      k_c_curr = ++k_c[c[cg1->getGlobalIndex()]];
1301	+	//                      l.push_back(k_c_curr);
1302	+	//
1303	+	//                      /* determines the number of layers in use */
1304	+	//                      if (k_c_max < k_c_curr)
1305	+	//                      {
1306	+	//                              k_c_max = k_c_curr;
1307	+	//                      }
1308	+
1309	+	H_c_l[c[cg->getGlobalIndex()]].push_back(/*l[*/cg/*]*/);
1310	+	}
1311	+	}
1312	+
1313	+	reorderMemory(H_c_l);
1314	+
1315	+	int m;
1316	+	/* the neighbor matrix */
1317	+	vector<vector<CutoffGroup *> > neighborMatW = vector<vector<CutoffGroup *> > (nGroups_);
1318	+
1319	+	groupCutoffs cuts;
1320	+	CutoffGroup *cg1;
1321	+
1322	+	/* loops over objects(atoms, rigidBodies, cutoffGroups, etc.) */
1323	+	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1324	+	{
1325	+	for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
1326	+	{
1327	+	/* c' */
1328	+	int c1 = c[cg1->getGlobalIndex()];
1329	+	Vector3i c1v = idxToV(c1, nCells_);
1330	+
1331	+	/* loops over the neighboring cells c'' */
1332	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1333	+	{
1334	+	Vector3i c2v = c1v + (*os);
1335	+
1336	+	if (c2v.x() >= nCells_.x())
1337	+	{
1338	+	c2v.x() = 0;
1339	+	} else if (c2v.x() < 0)
1340	+	{
1341	+	c2v.x() = nCells_.x() - 1;
1342	+	}
1343	+
1344	+	if (c2v.y() >= nCells_.y())
1345	+	{
1346	+	c2v.y() = 0;
1347	+	} else if (c2v.y() < 0)
1348	+	{
1349	+	c2v.y() = nCells_.y() - 1;
1350	+	}
1351	+
1352	+	if (c2v.z() >= nCells_.z())
1353	+	{
1354	+	c2v.z() = 0;
1355	+	} else if (c2v.z() < 0)
1356	+	{
1357	+	c2v.z() = nCells_.z() - 1;
1358	+	}
1359	+
1360	+	int c2 = Vlinear(c2v, nCells_);
1361	+	/* loops over layers l to access the neighbor atoms */
1362	+	for (vector<CutoffGroup *>::iterator cg2 = H_c_l[c2].begin(); cg2 != H_c_l[c2].end(); ++cg2)
1363	+	{
1364	+	//                              if i'' = 0 then break // doesn't apply to vector implementation of matrix
1365	+	//                              if(i != *j)
1366	+	if (c2 != c1 || (*cg2)->getGlobalIndex() < cg1->getGlobalIndex())
1367	+	{
1368	+	dr = snap_->cgData.position[(*cg2)->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()];
1369	+	snap_->wrapVector(dr);
1370	+	cuts = getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex());
1371	+	if (dr.lengthSquare() < cuts.third)
1372	+	{
1373	+	/* transposed version of Rapaport W mat, to occupy successive memory locations on CPU */
1374	+	neighborMatW[cg1->getGlobalIndex()].push_back((*cg2));
1375	+	}
1376	+	}
1377	+	}
1378	+	}
1379	+	}
1380	+	}
1381	+
1382	+	// save the local cutoff group positions for the check that is
1383	+	// done on each loop:
1384	+	saved_CG_positions_.clear();
1385	+	for (int i = 0; i < nGroups_; i++)
1386	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1387	+
1388	+	return neighborMatW;
1389	+	}
1390	+
1391	+	/*
1392	+	* buildNeighborList
1393	+	*
1394	+	* first element of pair is row-indexed CutoffGroup
1395	+	* second element of pair is column-indexed CutoffGroup
1396	+	*/
1397	+	vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1398	+
1399	+	vector<pair<int, int> > neighborList;
1400	+	groupCutoffs cuts;
1401	+	bool doAllPairs = false;
1402	+
1403	+	#ifdef IS_MPI
1404	+	cellListRow_.clear();
1405	+	cellListCol_.clear();
1406	+	#else
1407	+	cellList_.clear();
1408	+	#endif
1409	+
1410	+	RealType rList_ = (largestRcut_ + skinThickness_);
1411	+	RealType rl2 = rList_ * rList_;
1412	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1413	+	Mat3x3d Hmat = snap_->getHmat();
1414	+	Vector3d Hx = Hmat.getColumn(0);
1415	+	Vector3d Hy = Hmat.getColumn(1);
1416	+	Vector3d Hz = Hmat.getColumn(2);
1417	+
1418	+	nCells_.x() = (int) (Hx.length()) / rList_;
1419	+	nCells_.y() = (int) (Hy.length()) / rList_;
1420	+	nCells_.z() = (int) (Hz.length()) / rList_;
1421	+
1422	+	// handle small boxes where the cell offsets can end up repeating cells
1423	+
1424	+	if (nCells_.x() < 3)
1425	+	doAllPairs = true;
1426	+	if (nCells_.y() < 3)
1427	+	doAllPairs = true;
1428	+	if (nCells_.z() < 3)
1429	+	doAllPairs = true;
1430	+
1431	+	Mat3x3d invHmat = snap_->getInvHmat();
1432	+	Vector3d rs, scaled, dr;
1433	+	Vector3i whichCell;
1434	+	int cellIndex;
1435	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1436	+
1437	+	#ifdef IS_MPI
1438	+	cellListRow_.resize(nCtot);
1439	+	cellListCol_.resize(nCtot);
1440	+	#else
1441	+	cellList_.resize(nCtot);
1442	+	#endif
1443	+
1444	+	if (!doAllPairs)
1445	+	{
1446	+	#ifdef IS_MPI
1447	+
1448	+	for (int i = 0; i < nGroupsInRow_; i++)
1449	+	{
1450	+	rs = cgRowData.position[i];
1451	+
1452	+	// scaled positions relative to the box vectors
1453	+	scaled = invHmat * rs;
1454	+
1455	+	// wrap the vector back into the unit box by subtracting integer box
1456	+	// numbers
1457	+	for (int j = 0; j < 3; j++)
1458	+	{
1459	+	scaled[j] -= roundMe(scaled[j]);
1460	+	scaled[j] += 0.5;
1461	+	}
1462	+
1463	+	// find xyz-indices of cell that cutoffGroup is in.
1464	+	whichCell.x() = nCells_.x() * scaled.x();
1465	+	whichCell.y() = nCells_.y() * scaled.y();
1466	+	whichCell.z() = nCells_.z() * scaled.z();
1467	+
1468	+	// find single index of this cell:
1469	+	cellIndex = Vlinear(whichCell, nCells_);
1470	+
1471	+	// add this cutoff group to the list of groups in this cell;
1472	+	cellListRow_[cellIndex].push_back(i);
1473	+	}
1474	+	for (int i = 0; i < nGroupsInCol_; i++)
1475	+	{
1476	+	rs = cgColData.position[i];
1477	+
1478	+	// scaled positions relative to the box vectors
1479	+	scaled = invHmat * rs;
1480	+
1481	+	// wrap the vector back into the unit box by subtracting integer box
1482	+	// numbers
1483	+	for (int j = 0; j < 3; j++)
1484	+	{
1485	+	scaled[j] -= roundMe(scaled[j]);
1486	+	scaled[j] += 0.5;
1487	+	}
1488	+
1489	+	// find xyz-indices of cell that cutoffGroup is in.
1490	+	whichCell.x() = nCells_.x() * scaled.x();
1491	+	whichCell.y() = nCells_.y() * scaled.y();
1492	+	whichCell.z() = nCells_.z() * scaled.z();
1493	+
1494	+	// find single index of this cell:
1495	+	cellIndex = Vlinear(whichCell, nCells_);
1496	+
1497	+	// add this cutoff group to the list of groups in this cell;
1498	+	cellListCol_[cellIndex].push_back(i);
1499	+	}
1500	+	#else
1501	+	for (int i = 0; i < nGroups_; i++)
1502	+	{
1503	+	rs = snap_->cgData.position[i];
1504	+
1505	+	// scaled positions relative to the box vectors
1506	+	scaled = invHmat * rs;
1507	+
1508	+	// wrap the vector back into the unit box by subtracting integer box
1509	+	// numbers
1510	+	for (int j = 0; j < 3; j++)
1511	+	{
1512	+	scaled[j] -= roundMe(scaled[j]);
1513	+	scaled[j] += 0.5;
1514	+	}
1515	+
1516	+	// find xyz-indices of cell that cutoffGroup is in.
1517	+	whichCell.x() = nCells_.x() * scaled.x();
1518	+	whichCell.y() = nCells_.y() * scaled.y();
1519	+	whichCell.z() = nCells_.z() * scaled.z();
1520	+
1521	+	// find single index of this cell:
1522	+	cellIndex = Vlinear(whichCell, nCells_);
1523	+
1524	+	// add this cutoff group to the list of groups in this cell;
1525	+	cellList_[cellIndex].push_back(i);
1526	+	}
1527	+	#endif
1528	+
1529	+	for (int m1z = 0; m1z < nCells_.z(); m1z++)
1530	+	{
1531	+	for (int m1y = 0; m1y < nCells_.y(); m1y++)
1532	+	{
1533	+	for (int m1x = 0; m1x < nCells_.x(); m1x++)
1534	+	{
1535	+	Vector3i m1v(m1x, m1y, m1z);
1536	+	int m1 = Vlinear(m1v, nCells_);
1537	+
1538	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os)
1539	+	{
1540	+
1541	+	Vector3i m2v = m1v + (*os);
1542	+
1543	+	if (m2v.x() >= nCells_.x())
1544	+	{
1545	+	m2v.x() = 0;
1546	+	} else if (m2v.x() < 0)
1547	+	{
1548	+	m2v.x() = nCells_.x() - 1;
1549	+	}
1550	+
1551	+	if (m2v.y() >= nCells_.y())
1552	+	{
1553	+	m2v.y() = 0;
1554	+	} else if (m2v.y() < 0)
1555	+	{
1556	+	m2v.y() = nCells_.y() - 1;
1557	+	}
1558	+
1559	+	if (m2v.z() >= nCells_.z())
1560	+	{
1561	+	m2v.z() = 0;
1562	+	} else if (m2v.z() < 0)
1563	+	{
1564	+	m2v.z() = nCells_.z() - 1;
1565	+	}
1566	+
1567	+	int m2 = Vlinear(m2v, nCells_);
1568	+
1569	+	#ifdef IS_MPI
1570	+	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1571	+	j1 != cellListRow_[m1].end(); ++j1)
1572	+	{
1573	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1574	+	j2 != cellListCol_[m2].end(); ++j2)
1575	+	{
1576	+
1577	+	// In parallel, we need to visit *all* pairs of row &
1578	+	// column indicies and will truncate later on.
1579	+	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1580	+	snap_->wrapVector(dr);
1581	+	cuts = getGroupCutoffs( (*j1), (*j2) );
1582	+	if (dr.lengthSquare() < cuts.third)
1583	+	{
1584	+	neighborList.push_back(make_pair((*j1), (*j2)));
1585	+	}
1586	+	}
1587	+	}
1588	+	#else
1589	+
1590	+	for (vector<int>::iterator j1 = cellList_[m1].begin(); j1 != cellList_[m1].end(); ++j1)
1591	+	{
1592	+	for (vector<int>::iterator j2 = cellList_[m2].begin(); j2 != cellList_[m2].end(); ++j2)
1593	+	{
1594	+
1595	+	// Always do this if we're in different cells or if
1596	+	// we're in the same cell and the global index of the
1597	+	// j2 cutoff group is less than the j1 cutoff group
1598	+
1599	+	if (m2 != m1 || (*j2) < (*j1))
1600	+	{
1601	+	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1602	+	snap_->wrapVector(dr);
1603	+	cuts = getGroupCutoffs((*j1), (*j2));
1604	+	if (dr.lengthSquare() < cuts.third)
1605	+	{
1606	+	neighborList.push_back(make_pair((*j1), (*j2)));
1607	+	}
1608	+	}
1609	+	}
1610	+	}
1611	+	#endif
1612	+	}
1613	+	}
1614	+	}
1615	+	}
1616	+	} else
1617	+	{
1618	+	// branch to do all cutoff group pairs
1619	+	#ifdef IS_MPI
1620	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++)
1621	+	{
1622	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++)
1623	+	{
1624	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1625	+	snap_->wrapVector(dr);
1626	+	cuts = getGroupCutoffs( j1, j2 );
1627	+	if (dr.lengthSquare() < cuts.third)
1628	+	{
1629	+	neighborList.push_back(make_pair(j1, j2));
1630	+	}
1631	+	}
1632	+	}
1633	+	#else
1634	+	for (int j1 = 0; j1 < nGroups_ - 1; j1++)
1635	+	{
1636	+	for (int j2 = j1 + 1; j2 < nGroups_; j2++)
1637	+	{
1638	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1639	+	snap_->wrapVector(dr);
1640	+	cuts = getGroupCutoffs(j1, j2);
1641	+	if (dr.lengthSquare() < cuts.third)
1642	+	{
1643	+	neighborList.push_back(make_pair(j1, j2));
1644	+	}
1645	+	}
1646	+	}
1647	+	#endif
1648	+	}
1649	+
1650	+	// save the local cutoff group positions for the check that is
1651	+	// done on each loop:
1652	+	saved_CG_positions_.clear();
1653	+	for (int i = 0; i < nGroups_; i++)
1654	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1655	+
1656	+	return neighborList;
1657	+	}
1658	+	} //end namespace OpenMD

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines