ViewVC Help

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

root/OpenMD/trunk/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.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1930 by gezelter, Mon Aug 19 13:51:04 2013 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 42 | Line 35
35		*
36		* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37		* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	<	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	<	* [4]  Vardeman & Gezelter, in progress (2009).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42	+	#include "parallel/ForceMatrixDecomposition.hpp"
43	+	#include "math/SquareMatrix3.hpp"
44	+	#include "nonbonded/NonBondedInteraction.hpp"
45	+	#include "brains/SnapshotManager.hpp"
46	+	#include "brains/PairList.hpp"
47
48	+	using namespace std;
49	+	namespace OpenMD {
50
51	+	ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52
53	<	/*  -*- c++ -*-  */
54	<	#include "config.h"
55	<	#include <stdlib.h>
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_.clear();
58	>	cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59	>	cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60	>	cellOffsets_.push_back( Vector3i( 1,-1,-1) );
61	>	cellOffsets_.push_back( Vector3i(-1, 0,-1) );
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,-1, 0) );
68	>	cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69	>	cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70	>	cellOffsets_.push_back( Vector3i(-1, 0, 0) );
71	>	cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72	>	cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73	>	cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74	>	cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75	>	cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76	>	cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77	>	cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78	>	cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79	>	cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80	>	cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81	>	cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82	>	cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83	>	cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84	>	cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85	>	#endif
86	>	}
87
58	–	#include <iostream>
59	–	#include <vector>
60	–	#include <algorithm>
61	–	#include <cmath>
62	–	#include "parallel/ForceDecomposition.hpp"
88
89	+	/**
90	+	* distributeInitialData is essentially a copy of the older fortran
91	+	* SimulationSetup
92	+	*/
93	+	void ForceMatrixDecomposition::distributeInitialData() {
94	+	snap_ = sman_->getCurrentSnapshot();
95	+	storageLayout_ = sman_->getStorageLayout();
96	+	ff_ = info_->getForceField();
97	+	nLocal_ = snap_->getNumberOfAtoms();
98	+
99	+	nGroups_ = info_->getNLocalCutoffGroups();
100	+	// gather the information for atomtype IDs (atids):
101	+	idents = info_->getIdentArray();
102	+	regions = info_->getRegions();
103	+	AtomLocalToGlobal = info_->getGlobalAtomIndices();
104	+	cgLocalToGlobal = info_->getGlobalGroupIndices();
105	+	vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
106
107	<	using namespace std;
66	<	using namespace OpenMD;
107	>	massFactors = info_->getMassFactors();
108
109	<	//__static
109	>	PairList* excludes = info_->getExcludedInteractions();
110	>	PairList* oneTwo = info_->getOneTwoInteractions();
111	>	PairList* oneThree = info_->getOneThreeInteractions();
112	>	PairList* oneFour = info_->getOneFourInteractions();
113	>
114	>	if (needVelocities_)
115	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition |
116	>	DataStorage::dslVelocity);
117	>	else
118	>	snap_->cgData.setStorageLayout(DataStorage::dslPosition);
119	>
120		#ifdef IS_MPI
121	<	static vector<MPI:Comm> communictors;
122	<	#endif
121	>
122	>	MPI::Intracomm row = rowComm.getComm();
123	>	MPI::Intracomm col = colComm.getComm();
124
125	<	//____ MPITypeTraits
126	<	template<typename T>
127	<	struct MPITypeTraits;
125	>	AtomPlanIntRow = new Plan<int>(row, nLocal_);
126	>	AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
127	>	AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
128	>	AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
129	>	AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
130
131	<	#ifdef IS_MPI
132	<	template<>
133	<	struct MPITypeTraits<RealType> {
134	<	static const MPI::Datatype datatype;
135	<	};
82	<	const MPI_Datatype MPITypeTraits<RealType>::datatype = MY_MPI_REAL;
131	>	AtomPlanIntColumn = new Plan<int>(col, nLocal_);
132	>	AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
133	>	AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
134	>	AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
135	>	AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
136
137	<	template<>
138	<	struct MPITypeTraits<int> {
139	<	static const MPI::Datatype datatype;
140	<	};
88	<	const MPI::Datatype MPITypeTraits<int>::datatype = MPI_INT;
89	<	#endif
137	>	cgPlanIntRow = new Plan<int>(row, nGroups_);
138	>	cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
139	>	cgPlanIntColumn = new Plan<int>(col, nGroups_);
140	>	cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
141
142	<	/**
143	<	* Constructor for ForceDecomposition Parallel Decomposition Method
144	<	* Will try to construct a symmetric grid of processors. Ideally, the
145	<	* number of processors will be a square ex: 4, 9, 16, 25.
95	<	*
96	<	*/
142	>	nAtomsInRow_ = AtomPlanIntRow->getSize();
143	>	nAtomsInCol_ = AtomPlanIntColumn->getSize();
144	>	nGroupsInRow_ = cgPlanIntRow->getSize();
145	>	nGroupsInCol_ = cgPlanIntColumn->getSize();
146
147	<	ForceDecomposition::ForceDecomposition() {
147	>	// Modify the data storage objects with the correct layouts and sizes:
148	>	atomRowData.resize(nAtomsInRow_);
149	>	atomRowData.setStorageLayout(storageLayout_);
150	>	atomColData.resize(nAtomsInCol_);
151	>	atomColData.setStorageLayout(storageLayout_);
152	>	cgRowData.resize(nGroupsInRow_);
153	>	cgRowData.setStorageLayout(DataStorage::dslPosition);
154	>	cgColData.resize(nGroupsInCol_);
155	>	if (needVelocities_)
156	>	// we only need column velocities if we need them.
157	>	cgColData.setStorageLayout(DataStorage::dslPosition |
158	>	DataStorage::dslVelocity);
159	>	else
160	>	cgColData.setStorageLayout(DataStorage::dslPosition);
161	>
162	>	identsRow.resize(nAtomsInRow_);
163	>	identsCol.resize(nAtomsInCol_);
164	>
165	>	AtomPlanIntRow->gather(idents, identsRow);
166	>	AtomPlanIntColumn->gather(idents, identsCol);
167
168	<	#ifdef IS_MPI
169	<	int nProcs = MPI::COMM_WORLD.Get_size();
170	<	int worldRank = MPI::COMM_WORLD.Get_rank();
171	<	#endif
168	>	regionsRow.resize(nAtomsInRow_);
169	>	regionsCol.resize(nAtomsInCol_);
170	>
171	>	AtomPlanIntRow->gather(regions, regionsRow);
172	>	AtomPlanIntColumn->gather(regions, regionsCol);
173	>
174	>	// allocate memory for the parallel objects
175	>	atypesRow.resize(nAtomsInRow_);
176	>	atypesCol.resize(nAtomsInCol_);
177
178	<	// First time through, construct column stride.
179	<	if (communicators.size() == 0)
180	<	{
181	<	int nColumnsMax = (int) round(sqrt((float) nProcs));
109	<	for (int i = 0; i < nProcs; ++i)
110	<	{
111	<	if (nProcs%i==0) nColumns=i;
112	<	}
178	>	for (int i = 0; i < nAtomsInRow_; i++)
179	>	atypesRow[i] = ff_->getAtomType(identsRow[i]);
180	>	for (int i = 0; i < nAtomsInCol_; i++)
181	>	atypesCol[i] = ff_->getAtomType(identsCol[i]);
182
183	<	int nRows = nProcs/nColumns;
184	<	myRank_ = (int) worldRank%nColumns;
116	<	}
117	<	else
118	<	{
119	<	myRank_ = myRank/nColumns;
120	<	}
121	<	MPI::Comm newComm = MPI:COMM_WORLD.Split(myRank_,0);
122	<
123	<	isColumn_ = false;
124	<
125	<	}
183	>	pot_row.resize(nAtomsInRow_);
184	>	pot_col.resize(nAtomsInCol_);
185
186	<	ForceDecomposition::gather(sendbuf, receivebuf){
187	<	communicators(myIndex_).Allgatherv();
188	<	}
186	>	expot_row.resize(nAtomsInRow_);
187	>	expot_col.resize(nAtomsInCol_);
188	>
189	>	AtomRowToGlobal.resize(nAtomsInRow_);
190	>	AtomColToGlobal.resize(nAtomsInCol_);
191	>	AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
192	>	AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
193
194	+	cgRowToGlobal.resize(nGroupsInRow_);
195	+	cgColToGlobal.resize(nGroupsInCol_);
196	+	cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
197	+	cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
198
199	+	massFactorsRow.resize(nAtomsInRow_);
200	+	massFactorsCol.resize(nAtomsInCol_);
201	+	AtomPlanRealRow->gather(massFactors, massFactorsRow);
202	+	AtomPlanRealColumn->gather(massFactors, massFactorsCol);
203	+
204	+	groupListRow_.clear();
205	+	groupListRow_.resize(nGroupsInRow_);
206	+	for (int i = 0; i < nGroupsInRow_; i++) {
207	+	int gid = cgRowToGlobal[i];
208	+	for (int j = 0; j < nAtomsInRow_; j++) {
209	+	int aid = AtomRowToGlobal[j];
210	+	if (globalGroupMembership[aid] == gid)
211	+	groupListRow_[i].push_back(j);
212	+	}
213	+	}
214	+
215	+	groupListCol_.clear();
216	+	groupListCol_.resize(nGroupsInCol_);
217	+	for (int i = 0; i < nGroupsInCol_; i++) {
218	+	int gid = cgColToGlobal[i];
219	+	for (int j = 0; j < nAtomsInCol_; j++) {
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	+	int iglob = AtomRowToGlobal[i];
234	+
235	+	for (int j = 0; j < nAtomsInCol_; j++) {
236	+	int jglob = AtomColToGlobal[j];
237	+
238	+	if (excludes->hasPair(iglob, jglob))
239	+	excludesForAtom[i].push_back(j);
240	+
241	+	if (oneTwo->hasPair(iglob, jglob)) {
242	+	toposForAtom[i].push_back(j);
243	+	topoDist[i].push_back(1);
244	+	} else {
245	+	if (oneThree->hasPair(iglob, jglob)) {
246	+	toposForAtom[i].push_back(j);
247	+	topoDist[i].push_back(2);
248	+	} else {
249	+	if (oneFour->hasPair(iglob, jglob)) {
250	+	toposForAtom[i].push_back(j);
251	+	topoDist[i].push_back(3);
252	+	}
253	+	}
254	+	}
255	+	}
256	+	}
257	+
258	+	#else
259	+	excludesForAtom.clear();
260	+	excludesForAtom.resize(nLocal_);
261	+	toposForAtom.clear();
262	+	toposForAtom.resize(nLocal_);
263	+	topoDist.clear();
264	+	topoDist.resize(nLocal_);
265	+
266	+	for (int i = 0; i < nLocal_; i++) {
267	+	int iglob = AtomLocalToGlobal[i];
268	+
269	+	for (int j = 0; j < nLocal_; j++) {
270	+	int jglob = AtomLocalToGlobal[j];
271	+
272	+	if (excludes->hasPair(iglob, jglob))
273	+	excludesForAtom[i].push_back(j);
274	+
275	+	if (oneTwo->hasPair(iglob, jglob)) {
276	+	toposForAtom[i].push_back(j);
277	+	topoDist[i].push_back(1);
278	+	} else {
279	+	if (oneThree->hasPair(iglob, jglob)) {
280	+	toposForAtom[i].push_back(j);
281	+	topoDist[i].push_back(2);
282	+	} else {
283	+	if (oneFour->hasPair(iglob, jglob)) {
284	+	toposForAtom[i].push_back(j);
285	+	topoDist[i].push_back(3);
286	+	}
287	+	}
288	+	}
289	+	}
290	+	}
291	+	#endif
292	+
293	+	// allocate memory for the parallel objects
294	+	atypesLocal.resize(nLocal_);
295	+
296	+	for (int i = 0; i < nLocal_; i++)
297	+	atypesLocal[i] = ff_->getAtomType(idents[i]);
298	+
299	+	groupList_.clear();
300	+	groupList_.resize(nGroups_);
301	+	for (int i = 0; i < nGroups_; i++) {
302	+	int gid = cgLocalToGlobal[i];
303	+	for (int j = 0; j < nLocal_; j++) {
304	+	int aid = AtomLocalToGlobal[j];
305	+	if (globalGroupMembership[aid] == gid) {
306	+	groupList_[i].push_back(j);
307	+	}
308	+	}
309	+	}
310	+
311	+
312	+	createGtypeCutoffMap();
313	+
314	+	}
315	+
316	+	void ForceMatrixDecomposition::createGtypeCutoffMap() {
317	+
318	+	GrCut.clear();
319	+	GrCutSq.clear();
320	+	GrlistSq.clear();
321	+
322	+	RealType tol = 1e-6;
323	+	largestRcut_ = 0.0;
324	+	int atid;
325	+	set<AtomType*> atypes = info_->getSimulatedAtomTypes();
326	+
327	+	map<int, RealType> atypeCutoff;
328	+
329	+	for (set<AtomType*>::iterator at = atypes.begin();
330	+	at != atypes.end(); ++at){
331	+	atid = (*at)->getIdent();
332	+	if (userChoseCutoff_)
333	+	atypeCutoff[atid] = userCutoff_;
334	+	else
335	+	atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
336	+	}
337	+
338	+	vector<RealType> gTypeCutoffs;
339	+	// first we do a single loop over the cutoff groups to find the
340	+	// largest cutoff for any atypes present in this group.
341	+	#ifdef IS_MPI
342	+	vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
343	+	groupRowToGtype.resize(nGroupsInRow_);
344	+	for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
345	+	vector<int> atomListRow = getAtomsInGroupRow(cg1);
346	+	for (vector<int>::iterator ia = atomListRow.begin();
347	+	ia != atomListRow.end(); ++ia) {
348	+	int atom1 = (*ia);
349	+	atid = identsRow[atom1];
350	+	if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
351	+	groupCutoffRow[cg1] = atypeCutoff[atid];
352	+	}
353	+	}
354	+
355	+	bool gTypeFound = false;
356	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
357	+	if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
358	+	groupRowToGtype[cg1] = gt;
359	+	gTypeFound = true;
360	+	}
361	+	}
362	+	if (!gTypeFound) {
363	+	gTypeCutoffs.push_back( groupCutoffRow[cg1] );
364	+	groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
365	+	}
366	+
367	+	}
368	+	vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
369	+	groupColToGtype.resize(nGroupsInCol_);
370	+	for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
371	+	vector<int> atomListCol = getAtomsInGroupColumn(cg2);
372	+	for (vector<int>::iterator jb = atomListCol.begin();
373	+	jb != atomListCol.end(); ++jb) {
374	+	int atom2 = (*jb);
375	+	atid = identsCol[atom2];
376	+	if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
377	+	groupCutoffCol[cg2] = atypeCutoff[atid];
378	+	}
379	+	}
380	+	bool gTypeFound = false;
381	+	for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
382	+	if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
383	+	groupColToGtype[cg2] = gt;
384	+	gTypeFound = true;
385	+	}
386	+	}
387	+	if (!gTypeFound) {
388	+	gTypeCutoffs.push_back( groupCutoffCol[cg2] );
389	+	groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
390	+	}
391	+	}
392	+	#else
393	+
394	+	vector<RealType> groupCutoff(nGroups_, 0.0);
395	+	groupToGtype.resize(nGroups_);
396	+	for (int cg1 = 0; cg1 < nGroups_; cg1++) {
397	+	groupCutoff[cg1] = 0.0;
398	+	vector<int> atomList = getAtomsInGroupRow(cg1);
399	+	for (vector<int>::iterator ia = atomList.begin();
400	+	ia != atomList.end(); ++ia) {
401	+	int atom1 = (*ia);
402	+	atid = idents[atom1];
403	+	if (atypeCutoff[atid] > groupCutoff[cg1])
404	+	groupCutoff[cg1] = atypeCutoff[atid];
405	+	}
406	+
407	+	bool gTypeFound = false;
408	+	for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
409	+	if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
410	+	groupToGtype[cg1] = gt;
411	+	gTypeFound = true;
412	+	}
413	+	}
414	+	if (!gTypeFound) {
415	+	gTypeCutoffs.push_back( groupCutoff[cg1] );
416	+	groupToGtype[cg1] = gTypeCutoffs.size() - 1;
417	+	}
418	+	}
419	+	#endif
420
421	<	ForceDecomposition::scatter(sbuffer, rbuffer){
422	<	communicators(myIndex_).Reduce_scatter(sbuffer, recevbuf. recvcounts, MPI::DOUBLE, MPI::SUM);
423	<	}
421	>	// Now we find the maximum group cutoff value present in the simulation
422	>
423	>	RealType groupMax = *max_element(gTypeCutoffs.begin(),
424	>	gTypeCutoffs.end());
425	>
426	>	#ifdef IS_MPI
427	>	MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
428	>	MPI::MAX);
429	>	#endif
430	>
431	>	RealType tradRcut = groupMax;
432	>
433	>	GrCut.resize( gTypeCutoffs.size() );
434	>	GrCutSq.resize( gTypeCutoffs.size() );
435	>	GrlistSq.resize( gTypeCutoffs.size() );
436	>
437	>
438	>	for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
439	>	GrCut[i].resize( gTypeCutoffs.size() , 0.0);
440	>	GrCutSq[i].resize( gTypeCutoffs.size(), 0.0 );
441	>	GrlistSq[i].resize( gTypeCutoffs.size(), 0.0 );
442	>
443	>	for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {
444	>	RealType thisRcut;
445	>	switch(cutoffPolicy_) {
446	>	case TRADITIONAL:
447	>	thisRcut = tradRcut;
448	>	break;
449	>	case MIX:
450	>	thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
451	>	break;
452	>	case MAX:
453	>	thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
454	>	break;
455	>	default:
456	>	sprintf(painCave.errMsg,
457	>	"ForceMatrixDecomposition::createGtypeCutoffMap "
458	>	"hit an unknown cutoff policy!\n");
459	>	painCave.severity = OPENMD_ERROR;
460	>	painCave.isFatal = 1;
461	>	simError();
462	>	break;
463	>	}
464	>
465	>	GrCut[i][j] = thisRcut;
466	>	if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
467	>	GrCutSq[i][j] = thisRcut * thisRcut;
468	>	GrlistSq[i][j] = pow(thisRcut + skinThickness_, 2);
469	>
470	>	// pair<int,int> key = make_pair(i,j);
471	>	// gTypeCutoffMap[key].first = thisRcut;
472	>	// gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
473	>	// sanity check
474	>
475	>	if (userChoseCutoff_) {
476	>	if (abs(GrCut[i][j] - userCutoff_) > 0.0001) {
477	>	sprintf(painCave.errMsg,
478	>	"ForceMatrixDecomposition::createGtypeCutoffMap "
479	>	"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
480	>	painCave.severity = OPENMD_ERROR;
481	>	painCave.isFatal = 1;
482	>	simError();
483	>	}
484	>	}
485	>	}
486	>	}
487	>	}
488	>
489	>	void ForceMatrixDecomposition::getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) {
490	>	int i, j;
491	>	#ifdef IS_MPI
492	>	i = groupRowToGtype[cg1];
493	>	j = groupColToGtype[cg2];
494	>	#else
495	>	i = groupToGtype[cg1];
496	>	j = groupToGtype[cg2];
497	>	#endif
498	>	rcut = GrCut[i][j];
499	>	rcutsq = GrCutSq[i][j];
500	>	rlistsq = GrlistSq[i][j];
501	>	return;
502	>	//return gTypeCutoffMap[make_pair(i,j)];
503	>	}
504	>
505	>	int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
506	>	for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
507	>	if (toposForAtom[atom1][j] == atom2)
508	>	return topoDist[atom1][j];
509	>	}
510	>	return 0;
511	>	}
512	>
513	>	void ForceMatrixDecomposition::zeroWorkArrays() {
514	>	pairwisePot = 0.0;
515	>	embeddingPot = 0.0;
516	>	excludedPot = 0.0;
517	>	excludedSelfPot = 0.0;
518	>
519	>	#ifdef IS_MPI
520	>	if (storageLayout_ & DataStorage::dslForce) {
521	>	fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
522	>	fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
523	>	}
524	>
525	>	if (storageLayout_ & DataStorage::dslTorque) {
526	>	fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
527	>	fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
528	>	}
529	>
530	>	fill(pot_row.begin(), pot_row.end(),
531	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
532	>
533	>	fill(pot_col.begin(), pot_col.end(),
534	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
535	>
536	>	fill(expot_row.begin(), expot_row.end(),
537	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
538	>
539	>	fill(expot_col.begin(), expot_col.end(),
540	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
541	>
542	>	if (storageLayout_ & DataStorage::dslParticlePot) {
543	>	fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
544	>	0.0);
545	>	fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
546	>	0.0);
547	>	}
548	>
549	>	if (storageLayout_ & DataStorage::dslDensity) {
550	>	fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
551	>	fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
552	>	}
553	>
554	>	if (storageLayout_ & DataStorage::dslFunctional) {
555	>	fill(atomRowData.functional.begin(), atomRowData.functional.end(),
556	>	0.0);
557	>	fill(atomColData.functional.begin(), atomColData.functional.end(),
558	>	0.0);
559	>	}
560	>
561	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
562	>	fill(atomRowData.functionalDerivative.begin(),
563	>	atomRowData.functionalDerivative.end(), 0.0);
564	>	fill(atomColData.functionalDerivative.begin(),
565	>	atomColData.functionalDerivative.end(), 0.0);
566	>	}
567	>
568	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
569	>	fill(atomRowData.skippedCharge.begin(),
570	>	atomRowData.skippedCharge.end(), 0.0);
571	>	fill(atomColData.skippedCharge.begin(),
572	>	atomColData.skippedCharge.end(), 0.0);
573	>	}
574	>
575	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
576	>	fill(atomRowData.flucQFrc.begin(),
577	>	atomRowData.flucQFrc.end(), 0.0);
578	>	fill(atomColData.flucQFrc.begin(),
579	>	atomColData.flucQFrc.end(), 0.0);
580	>	}
581	>
582	>	if (storageLayout_ & DataStorage::dslElectricField) {
583	>	fill(atomRowData.electricField.begin(),
584	>	atomRowData.electricField.end(), V3Zero);
585	>	fill(atomColData.electricField.begin(),
586	>	atomColData.electricField.end(), V3Zero);
587	>	}
588	>
589	>	#endif
590	>	// even in parallel, we need to zero out the local arrays:
591	>
592	>	if (storageLayout_ & DataStorage::dslParticlePot) {
593	>	fill(snap_->atomData.particlePot.begin(),
594	>	snap_->atomData.particlePot.end(), 0.0);
595	>	}
596	>
597	>	if (storageLayout_ & DataStorage::dslDensity) {
598	>	fill(snap_->atomData.density.begin(),
599	>	snap_->atomData.density.end(), 0.0);
600	>	}
601	>
602	>	if (storageLayout_ & DataStorage::dslFunctional) {
603	>	fill(snap_->atomData.functional.begin(),
604	>	snap_->atomData.functional.end(), 0.0);
605	>	}
606	>
607	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
608	>	fill(snap_->atomData.functionalDerivative.begin(),
609	>	snap_->atomData.functionalDerivative.end(), 0.0);
610	>	}
611	>
612	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
613	>	fill(snap_->atomData.skippedCharge.begin(),
614	>	snap_->atomData.skippedCharge.end(), 0.0);
615	>	}
616	>
617	>	if (storageLayout_ & DataStorage::dslElectricField) {
618	>	fill(snap_->atomData.electricField.begin(),
619	>	snap_->atomData.electricField.end(), V3Zero);
620	>	}
621	>	}
622	>
623	>
624	>	void ForceMatrixDecomposition::distributeData()  {
625	>	snap_ = sman_->getCurrentSnapshot();
626	>	storageLayout_ = sman_->getStorageLayout();
627	>	#ifdef IS_MPI
628	>
629	>	// gather up the atomic positions
630	>	AtomPlanVectorRow->gather(snap_->atomData.position,
631	>	atomRowData.position);
632	>	AtomPlanVectorColumn->gather(snap_->atomData.position,
633	>	atomColData.position);
634	>
635	>	// gather up the cutoff group positions
636	>
637	>	cgPlanVectorRow->gather(snap_->cgData.position,
638	>	cgRowData.position);
639	>
640	>	cgPlanVectorColumn->gather(snap_->cgData.position,
641	>	cgColData.position);
642	>
643	>
644	>
645	>	if (needVelocities_) {
646	>	// gather up the atomic velocities
647	>	AtomPlanVectorColumn->gather(snap_->atomData.velocity,
648	>	atomColData.velocity);
649	>
650	>	cgPlanVectorColumn->gather(snap_->cgData.velocity,
651	>	cgColData.velocity);
652	>	}
653	>
654	>
655	>	// if needed, gather the atomic rotation matrices
656	>	if (storageLayout_ & DataStorage::dslAmat) {
657	>	AtomPlanMatrixRow->gather(snap_->atomData.aMat,
658	>	atomRowData.aMat);
659	>	AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
660	>	atomColData.aMat);
661	>	}
662	>
663	>	// if needed, gather the atomic eletrostatic information
664	>	if (storageLayout_ & DataStorage::dslDipole) {
665	>	AtomPlanVectorRow->gather(snap_->atomData.dipole,
666	>	atomRowData.dipole);
667	>	AtomPlanVectorColumn->gather(snap_->atomData.dipole,
668	>	atomColData.dipole);
669	>	}
670	>
671	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
672	>	AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
673	>	atomRowData.quadrupole);
674	>	AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
675	>	atomColData.quadrupole);
676	>	}
677	>
678	>	// if needed, gather the atomic fluctuating charge values
679	>	if (storageLayout_ & DataStorage::dslFlucQPosition) {
680	>	AtomPlanRealRow->gather(snap_->atomData.flucQPos,
681	>	atomRowData.flucQPos);
682	>	AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
683	>	atomColData.flucQPos);
684	>	}
685	>
686	>	#endif
687	>	}
688	>
689	>	/* collects information obtained during the pre-pair loop onto local
690	>	* data structures.
691	>	*/
692	>	void ForceMatrixDecomposition::collectIntermediateData() {
693	>	snap_ = sman_->getCurrentSnapshot();
694	>	storageLayout_ = sman_->getStorageLayout();
695	>	#ifdef IS_MPI
696	>
697	>	if (storageLayout_ & DataStorage::dslDensity) {
698	>
699	>	AtomPlanRealRow->scatter(atomRowData.density,
700	>	snap_->atomData.density);
701	>
702	>	int n = snap_->atomData.density.size();
703	>	vector<RealType> rho_tmp(n, 0.0);
704	>	AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
705	>	for (int i = 0; i < n; i++)
706	>	snap_->atomData.density[i] += rho_tmp[i];
707	>	}
708	>
709	>	// this isn't necessary if we don't have polarizable atoms, but
710	>	// we'll leave it here for now.
711	>	if (storageLayout_ & DataStorage::dslElectricField) {
712	>
713	>	AtomPlanVectorRow->scatter(atomRowData.electricField,
714	>	snap_->atomData.electricField);
715	>
716	>	int n = snap_->atomData.electricField.size();
717	>	vector<Vector3d> field_tmp(n, V3Zero);
718	>	AtomPlanVectorColumn->scatter(atomColData.electricField,
719	>	field_tmp);
720	>	for (int i = 0; i < n; i++)
721	>	snap_->atomData.electricField[i] += field_tmp[i];
722	>	}
723	>	#endif
724	>	}
725	>
726	>	/*
727	>	* redistributes information obtained during the pre-pair loop out to
728	>	* row and column-indexed data structures
729	>	*/
730	>	void ForceMatrixDecomposition::distributeIntermediateData() {
731	>	snap_ = sman_->getCurrentSnapshot();
732	>	storageLayout_ = sman_->getStorageLayout();
733	>	#ifdef IS_MPI
734	>	if (storageLayout_ & DataStorage::dslFunctional) {
735	>	AtomPlanRealRow->gather(snap_->atomData.functional,
736	>	atomRowData.functional);
737	>	AtomPlanRealColumn->gather(snap_->atomData.functional,
738	>	atomColData.functional);
739	>	}
740	>
741	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
742	>	AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
743	>	atomRowData.functionalDerivative);
744	>	AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
745	>	atomColData.functionalDerivative);
746	>	}
747	>	#endif
748	>	}
749	>
750	>
751	>	void ForceMatrixDecomposition::collectData() {
752	>	snap_ = sman_->getCurrentSnapshot();
753	>	storageLayout_ = sman_->getStorageLayout();
754	>	#ifdef IS_MPI
755	>	int n = snap_->atomData.force.size();
756	>	vector<Vector3d> frc_tmp(n, V3Zero);
757	>
758	>	AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
759	>	for (int i = 0; i < n; i++) {
760	>	snap_->atomData.force[i] += frc_tmp[i];
761	>	frc_tmp[i] = 0.0;
762	>	}
763	>
764	>	AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
765	>	for (int i = 0; i < n; i++) {
766	>	snap_->atomData.force[i] += frc_tmp[i];
767	>	}
768	>
769	>	if (storageLayout_ & DataStorage::dslTorque) {
770	>
771	>	int nt = snap_->atomData.torque.size();
772	>	vector<Vector3d> trq_tmp(nt, V3Zero);
773	>
774	>	AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
775	>	for (int i = 0; i < nt; i++) {
776	>	snap_->atomData.torque[i] += trq_tmp[i];
777	>	trq_tmp[i] = 0.0;
778	>	}
779	>
780	>	AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
781	>	for (int i = 0; i < nt; i++)
782	>	snap_->atomData.torque[i] += trq_tmp[i];
783	>	}
784	>
785	>	if (storageLayout_ & DataStorage::dslSkippedCharge) {
786	>
787	>	int ns = snap_->atomData.skippedCharge.size();
788	>	vector<RealType> skch_tmp(ns, 0.0);
789	>
790	>	AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
791	>	for (int i = 0; i < ns; i++) {
792	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
793	>	skch_tmp[i] = 0.0;
794	>	}
795	>
796	>	AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
797	>	for (int i = 0; i < ns; i++)
798	>	snap_->atomData.skippedCharge[i] += skch_tmp[i];
799	>
800	>	}
801	>
802	>	if (storageLayout_ & DataStorage::dslFlucQForce) {
803	>
804	>	int nq = snap_->atomData.flucQFrc.size();
805	>	vector<RealType> fqfrc_tmp(nq, 0.0);
806	>
807	>	AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
808	>	for (int i = 0; i < nq; i++) {
809	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
810	>	fqfrc_tmp[i] = 0.0;
811	>	}
812	>
813	>	AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
814	>	for (int i = 0; i < nq; i++)
815	>	snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
816	>
817	>	}
818	>
819	>	if (storageLayout_ & DataStorage::dslElectricField) {
820	>
821	>	int nef = snap_->atomData.electricField.size();
822	>	vector<Vector3d> efield_tmp(nef, V3Zero);
823	>
824	>	AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
825	>	for (int i = 0; i < nef; i++) {
826	>	snap_->atomData.electricField[i] += efield_tmp[i];
827	>	efield_tmp[i] = 0.0;
828	>	}
829	>
830	>	AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
831	>	for (int i = 0; i < nef; i++)
832	>	snap_->atomData.electricField[i] += efield_tmp[i];
833	>	}
834	>
835	>
836	>	nLocal_ = snap_->getNumberOfAtoms();
837	>
838	>	vector<potVec> pot_temp(nLocal_,
839	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
840	>	vector<potVec> expot_temp(nLocal_,
841	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
842	>
843	>	// scatter/gather pot_row into the members of my column
844	>
845	>	AtomPlanPotRow->scatter(pot_row, pot_temp);
846	>	AtomPlanPotRow->scatter(expot_row, expot_temp);
847	>
848	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
849	>	pairwisePot += pot_temp[ii];
850	>
851	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
852	>	excludedPot += expot_temp[ii];
853	>
854	>	if (storageLayout_ & DataStorage::dslParticlePot) {
855	>	// This is the pairwise contribution to the particle pot.  The
856	>	// embedding contribution is added in each of the low level
857	>	// non-bonded routines.  In single processor, this is done in
858	>	// unpackInteractionData, not in collectData.
859	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
860	>	for (int i = 0; i < nLocal_; i++) {
861	>	// factor of two is because the total potential terms are divided
862	>	// by 2 in parallel due to row/ column scatter
863	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
864	>	}
865	>	}
866	>	}
867	>
868	>	fill(pot_temp.begin(), pot_temp.end(),
869	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
870	>	fill(expot_temp.begin(), expot_temp.end(),
871	>	Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
872	>
873	>	AtomPlanPotColumn->scatter(pot_col, pot_temp);
874	>	AtomPlanPotColumn->scatter(expot_col, expot_temp);
875	>
876	>	for (int ii = 0;  ii < pot_temp.size(); ii++ )
877	>	pairwisePot += pot_temp[ii];
878	>
879	>	for (int ii = 0;  ii < expot_temp.size(); ii++ )
880	>	excludedPot += expot_temp[ii];
881	>
882	>	if (storageLayout_ & DataStorage::dslParticlePot) {
883	>	// This is the pairwise contribution to the particle pot.  The
884	>	// embedding contribution is added in each of the low level
885	>	// non-bonded routines.  In single processor, this is done in
886	>	// unpackInteractionData, not in collectData.
887	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
888	>	for (int i = 0; i < nLocal_; i++) {
889	>	// factor of two is because the total potential terms are divided
890	>	// by 2 in parallel due to row/ column scatter
891	>	snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
892	>	}
893	>	}
894	>	}
895	>
896	>	if (storageLayout_ & DataStorage::dslParticlePot) {
897	>	int npp = snap_->atomData.particlePot.size();
898	>	vector<RealType> ppot_temp(npp, 0.0);
899	>
900	>	// This is the direct or embedding contribution to the particle
901	>	// pot.
902	>
903	>	AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
904	>	for (int i = 0; i < npp; i++) {
905	>	snap_->atomData.particlePot[i] += ppot_temp[i];
906	>	}
907	>
908	>	fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
909	>
910	>	AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
911	>	for (int i = 0; i < npp; i++) {
912	>	snap_->atomData.particlePot[i] += ppot_temp[i];
913	>	}
914	>	}
915	>
916	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
917	>	RealType ploc1 = pairwisePot[ii];
918	>	RealType ploc2 = 0.0;
919	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
920	>	pairwisePot[ii] = ploc2;
921	>	}
922	>
923	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
924	>	RealType ploc1 = excludedPot[ii];
925	>	RealType ploc2 = 0.0;
926	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
927	>	excludedPot[ii] = ploc2;
928	>	}
929	>
930	>	// Here be dragons.
931	>	MPI::Intracomm col = colComm.getComm();
932	>
933	>	col.Allreduce(MPI::IN_PLACE,
934	>	&snap_->frameData.conductiveHeatFlux[0], 3,
935	>	MPI::REALTYPE, MPI::SUM);
936	>
937	>
938	>	#endif
939	>
940	>	}
941	>
942	>	/**
943	>	* Collects information obtained during the post-pair (and embedding
944	>	* functional) loops onto local data structures.
945	>	*/
946	>	void ForceMatrixDecomposition::collectSelfData() {
947	>	snap_ = sman_->getCurrentSnapshot();
948	>	storageLayout_ = sman_->getStorageLayout();
949	>
950	>	#ifdef IS_MPI
951	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
952	>	RealType ploc1 = embeddingPot[ii];
953	>	RealType ploc2 = 0.0;
954	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
955	>	embeddingPot[ii] = ploc2;
956	>	}
957	>	for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
958	>	RealType ploc1 = excludedSelfPot[ii];
959	>	RealType ploc2 = 0.0;
960	>	MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
961	>	excludedSelfPot[ii] = ploc2;
962	>	}
963	>	#endif
964	>
965	>	}
966	>
967	>
968	>
969	>	int& ForceMatrixDecomposition::getNAtomsInRow() {
970	>	#ifdef IS_MPI
971	>	return nAtomsInRow_;
972	>	#else
973	>	return nLocal_;
974	>	#endif
975	>	}
976	>
977	>	/**
978	>	* returns the list of atoms belonging to this group.
979	>	*/
980	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
981	>	#ifdef IS_MPI
982	>	return groupListRow_[cg1];
983	>	#else
984	>	return groupList_[cg1];
985	>	#endif
986	>	}
987	>
988	>	vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
989	>	#ifdef IS_MPI
990	>	return groupListCol_[cg2];
991	>	#else
992	>	return groupList_[cg2];
993	>	#endif
994	>	}
995	>
996	>	Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
997	>	Vector3d d;
998	>
999	>	#ifdef IS_MPI
1000	>	d = cgColData.position[cg2] - cgRowData.position[cg1];
1001	>	#else
1002	>	d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
1003	>	#endif
1004	>
1005	>	if (usePeriodicBoundaryConditions_) {
1006	>	snap_->wrapVector(d);
1007	>	}
1008	>	return d;
1009	>	}
1010	>
1011	>	Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
1012	>	#ifdef IS_MPI
1013	>	return cgColData.velocity[cg2];
1014	>	#else
1015	>	return snap_->cgData.velocity[cg2];
1016	>	#endif
1017	>	}
1018	>
1019	>	Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
1020	>	#ifdef IS_MPI
1021	>	return atomColData.velocity[atom2];
1022	>	#else
1023	>	return snap_->atomData.velocity[atom2];
1024	>	#endif
1025	>	}
1026	>
1027	>
1028	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
1029	>
1030	>	Vector3d d;
1031	>
1032	>	#ifdef IS_MPI
1033	>	d = cgRowData.position[cg1] - atomRowData.position[atom1];
1034	>	#else
1035	>	d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1036	>	#endif
1037	>	if (usePeriodicBoundaryConditions_) {
1038	>	snap_->wrapVector(d);
1039	>	}
1040	>	return d;
1041	>	}
1042	>
1043	>	Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
1044	>	Vector3d d;
1045	>
1046	>	#ifdef IS_MPI
1047	>	d = cgColData.position[cg2] - atomColData.position[atom2];
1048	>	#else
1049	>	d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1050	>	#endif
1051	>	if (usePeriodicBoundaryConditions_) {
1052	>	snap_->wrapVector(d);
1053	>	}
1054	>	return d;
1055	>	}
1056	>
1057	>	RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1058	>	#ifdef IS_MPI
1059	>	return massFactorsRow[atom1];
1060	>	#else
1061	>	return massFactors[atom1];
1062	>	#endif
1063	>	}
1064	>
1065	>	RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1066	>	#ifdef IS_MPI
1067	>	return massFactorsCol[atom2];
1068	>	#else
1069	>	return massFactors[atom2];
1070	>	#endif
1071	>
1072	>	}
1073	>
1074	>	Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
1075	>	Vector3d d;
1076	>
1077	>	#ifdef IS_MPI
1078	>	d = atomColData.position[atom2] - atomRowData.position[atom1];
1079	>	#else
1080	>	d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1081	>	#endif
1082	>	if (usePeriodicBoundaryConditions_) {
1083	>	snap_->wrapVector(d);
1084	>	}
1085	>	return d;
1086	>	}
1087	>
1088	>	vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1089	>	return excludesForAtom[atom1];
1090	>	}
1091	>
1092	>	/**
1093	>	* We need to exclude some overcounted interactions that result from
1094	>	* the parallel decomposition.
1095	>	*/
1096	>	bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1097	>	int unique_id_1, unique_id_2;
1098	>
1099	>	#ifdef IS_MPI
1100	>	// in MPI, we have to look up the unique IDs for each atom
1101	>	unique_id_1 = AtomRowToGlobal[atom1];
1102	>	unique_id_2 = AtomColToGlobal[atom2];
1103	>	// group1 = cgRowToGlobal[cg1];
1104	>	// group2 = cgColToGlobal[cg2];
1105	>	#else
1106	>	unique_id_1 = AtomLocalToGlobal[atom1];
1107	>	unique_id_2 = AtomLocalToGlobal[atom2];
1108	>	int group1 = cgLocalToGlobal[cg1];
1109	>	int group2 = cgLocalToGlobal[cg2];
1110	>	#endif
1111	>
1112	>	if (unique_id_1 == unique_id_2) return true;
1113	>
1114	>	#ifdef IS_MPI
1115	>	// this prevents us from doing the pair on multiple processors
1116	>	if (unique_id_1 < unique_id_2) {
1117	>	if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1118	>	} else {
1119	>	if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1120	>	}
1121	>	#endif
1122	>
1123	>	#ifndef IS_MPI
1124	>	if (group1 == group2) {
1125	>	if (unique_id_1 < unique_id_2) return true;
1126	>	}
1127	>	#endif
1128	>
1129	>	return false;
1130	>	}
1131	>
1132	>	/**
1133	>	* We need to handle the interactions for atoms who are involved in
1134	>	* the same rigid body as well as some short range interactions
1135	>	* (bonds, bends, torsions) differently from other interactions.
1136	>	* We'll still visit the pairwise routines, but with a flag that
1137	>	* tells those routines to exclude the pair from direct long range
1138	>	* interactions.  Some indirect interactions (notably reaction
1139	>	* field) must still be handled for these pairs.
1140	>	*/
1141	>	bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1142	>
1143	>	// excludesForAtom was constructed to use row/column indices in the MPI
1144	>	// version, and to use local IDs in the non-MPI version:
1145	>
1146	>	for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1147	>	i != excludesForAtom[atom1].end(); ++i) {
1148	>	if ( (*i) == atom2 ) return true;
1149	>	}
1150	>
1151	>	return false;
1152	>	}
1153	>
1154	>
1155	>	void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
1156	>	#ifdef IS_MPI
1157	>	atomRowData.force[atom1] += fg;
1158	>	#else
1159	>	snap_->atomData.force[atom1] += fg;
1160	>	#endif
1161	>	}
1162	>
1163	>	void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
1164	>	#ifdef IS_MPI
1165	>	atomColData.force[atom2] += fg;
1166	>	#else
1167	>	snap_->atomData.force[atom2] += fg;
1168	>	#endif
1169	>	}
1170	>
1171	>	// filling interaction blocks with pointers
1172	>	void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
1173	>	int atom1, int atom2) {
1174	>
1175	>	idat.excluded = excludeAtomPair(atom1, atom2);
1176	>
1177	>	#ifdef IS_MPI
1178	>	//idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1179	>	idat.atid1 = identsRow[atom1];
1180	>	idat.atid2 = identsCol[atom2];
1181	>
1182	>	if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0)
1183	>	idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1184	>
1185	>	if (storageLayout_ & DataStorage::dslAmat) {
1186	>	idat.A1 = &(atomRowData.aMat[atom1]);
1187	>	idat.A2 = &(atomColData.aMat[atom2]);
1188	>	}
1189	>
1190	>	if (storageLayout_ & DataStorage::dslTorque) {
1191	>	idat.t1 = &(atomRowData.torque[atom1]);
1192	>	idat.t2 = &(atomColData.torque[atom2]);
1193	>	}
1194	>
1195	>	if (storageLayout_ & DataStorage::dslDipole) {
1196	>	idat.dipole1 = &(atomRowData.dipole[atom1]);
1197	>	idat.dipole2 = &(atomColData.dipole[atom2]);
1198	>	}
1199	>
1200	>	if (storageLayout_ & DataStorage::dslQuadrupole) {
1201	>	idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1202	>	idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1203	>	}
1204	>
1205	>	if (storageLayout_ & DataStorage::dslDensity) {
1206	>	idat.rho1 = &(atomRowData.density[atom1]);
1207	>	idat.rho2 = &(atomColData.density[atom2]);
1208	>	}
1209	>
1210	>	if (storageLayout_ & DataStorage::dslFunctional) {
1211	>	idat.frho1 = &(atomRowData.functional[atom1]);
1212	>	idat.frho2 = &(atomColData.functional[atom2]);
1213	>	}
1214	>
1215	>	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1216	>	idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
1217	>	idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
1218	>	}
1219
1220	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1221	+	idat.particlePot1 = &(atomRowData.particlePot[atom1]);
1222	+	idat.particlePot2 = &(atomColData.particlePot[atom2]);
1223	+	}
1224
1225	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1226	+	idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
1227	+	idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1228	+	}
1229	+
1230	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1231	+	idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1232	+	idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1233	+	}
1234	+
1235	+	#else
1236	+
1237	+	//idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1238	+	idat.atid1 = idents[atom1];
1239	+	idat.atid2 = idents[atom2];
1240	+
1241	+	if (regions[atom1] >= 0 && regions[atom2] >= 0)
1242	+	idat.sameRegion = (regions[atom1] == regions[atom2]);
1243	+
1244	+	if (storageLayout_ & DataStorage::dslAmat) {
1245	+	idat.A1 = &(snap_->atomData.aMat[atom1]);
1246	+	idat.A2 = &(snap_->atomData.aMat[atom2]);
1247	+	}
1248	+
1249	+	if (storageLayout_ & DataStorage::dslTorque) {
1250	+	idat.t1 = &(snap_->atomData.torque[atom1]);
1251	+	idat.t2 = &(snap_->atomData.torque[atom2]);
1252	+	}
1253	+
1254	+	if (storageLayout_ & DataStorage::dslDipole) {
1255	+	idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1256	+	idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1257	+	}
1258	+
1259	+	if (storageLayout_ & DataStorage::dslQuadrupole) {
1260	+	idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1261	+	idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1262	+	}
1263	+
1264	+	if (storageLayout_ & DataStorage::dslDensity) {
1265	+	idat.rho1 = &(snap_->atomData.density[atom1]);
1266	+	idat.rho2 = &(snap_->atomData.density[atom2]);
1267	+	}
1268	+
1269	+	if (storageLayout_ & DataStorage::dslFunctional) {
1270	+	idat.frho1 = &(snap_->atomData.functional[atom1]);
1271	+	idat.frho2 = &(snap_->atomData.functional[atom2]);
1272	+	}
1273	+
1274	+	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
1275	+	idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
1276	+	idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
1277	+	}
1278	+
1279	+	if (storageLayout_ & DataStorage::dslParticlePot) {
1280	+	idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
1281	+	idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
1282	+	}
1283	+
1284	+	if (storageLayout_ & DataStorage::dslSkippedCharge) {
1285	+	idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1286	+	idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1287	+	}
1288	+
1289	+	if (storageLayout_ & DataStorage::dslFlucQPosition) {
1290	+	idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1291	+	idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1292	+	}
1293	+
1294	+	#endif
1295	+	}
1296	+
1297	+
1298	+	void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {
1299	+	#ifdef IS_MPI
1300	+	pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1301	+	pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1302	+	expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1303	+	expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1304	+
1305	+	atomRowData.force[atom1] += *(idat.f1);
1306	+	atomColData.force[atom2] -= *(idat.f1);
1307	+
1308	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1309	+	atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1310	+	atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1311	+	}
1312	+
1313	+	if (storageLayout_ & DataStorage::dslElectricField) {
1314	+	atomRowData.electricField[atom1] += *(idat.eField1);
1315	+	atomColData.electricField[atom2] += *(idat.eField2);
1316	+	}
1317	+
1318	+	#else
1319	+	pairwisePot += *(idat.pot);
1320	+	excludedPot += *(idat.excludedPot);
1321	+
1322	+	snap_->atomData.force[atom1] += *(idat.f1);
1323	+	snap_->atomData.force[atom2] -= *(idat.f1);
1324	+
1325	+	if (idat.doParticlePot) {
1326	+	// This is the pairwise contribution to the particle pot.  The
1327	+	// embedding contribution is added in each of the low level
1328	+	// non-bonded routines.  In parallel, this calculation is done
1329	+	// in collectData, not in unpackInteractionData.
1330	+	snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1331	+	snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1332	+	}
1333	+
1334	+	if (storageLayout_ & DataStorage::dslFlucQForce) {
1335	+	snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1336	+	snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1337	+	}
1338	+
1339	+	if (storageLayout_ & DataStorage::dslElectricField) {
1340	+	snap_->atomData.electricField[atom1] += *(idat.eField1);
1341	+	snap_->atomData.electricField[atom2] += *(idat.eField2);
1342	+	}
1343	+
1344	+	#endif
1345	+
1346	+	}
1347	+
1348	+	/*
1349	+	* buildNeighborList
1350	+	*
1351	+	* first element of pair is row-indexed CutoffGroup
1352	+	* second element of pair is column-indexed CutoffGroup
1353	+	*/
1354	+	void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1355	+
1356	+	neighborList.clear();
1357	+	groupCutoffs cuts;
1358	+	bool doAllPairs = false;
1359	+
1360	+	RealType rList_ = (largestRcut_ + skinThickness_);
1361	+	RealType rcut, rcutsq, rlistsq;
1362	+	Snapshot* snap_ = sman_->getCurrentSnapshot();
1363	+	Mat3x3d box;
1364	+	Mat3x3d invBox;
1365	+
1366	+	Vector3d rs, scaled, dr;
1367	+	Vector3i whichCell;
1368	+	int cellIndex;
1369	+
1370	+	#ifdef IS_MPI
1371	+	cellListRow_.clear();
1372	+	cellListCol_.clear();
1373	+	#else
1374	+	cellList_.clear();
1375	+	#endif
1376	+
1377	+	if (!usePeriodicBoundaryConditions_) {
1378	+	box = snap_->getBoundingBox();
1379	+	invBox = snap_->getInvBoundingBox();
1380	+	} else {
1381	+	box = snap_->getHmat();
1382	+	invBox = snap_->getInvHmat();
1383	+	}
1384	+
1385	+	Vector3d boxX = box.getColumn(0);
1386	+	Vector3d boxY = box.getColumn(1);
1387	+	Vector3d boxZ = box.getColumn(2);
1388	+
1389	+	nCells_.x() = (int) ( boxX.length() )/ rList_;
1390	+	nCells_.y() = (int) ( boxY.length() )/ rList_;
1391	+	nCells_.z() = (int) ( boxZ.length() )/ rList_;
1392	+
1393	+	// handle small boxes where the cell offsets can end up repeating cells
1394	+
1395	+	if (nCells_.x() < 3) doAllPairs = true;
1396	+	if (nCells_.y() < 3) doAllPairs = true;
1397	+	if (nCells_.z() < 3) doAllPairs = true;
1398	+
1399	+	int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1400	+
1401	+	#ifdef IS_MPI
1402	+	cellListRow_.resize(nCtot);
1403	+	cellListCol_.resize(nCtot);
1404	+	#else
1405	+	cellList_.resize(nCtot);
1406	+	#endif
1407	+
1408	+	if (!doAllPairs) {
1409	+	#ifdef IS_MPI
1410	+
1411	+	for (int i = 0; i < nGroupsInRow_; i++) {
1412	+	rs = cgRowData.position[i];
1413	+
1414	+	// scaled positions relative to the box vectors
1415	+	scaled = invBox * rs;
1416	+
1417	+	// wrap the vector back into the unit box by subtracting integer box
1418	+	// numbers
1419	+	for (int j = 0; j < 3; j++) {
1420	+	scaled[j] -= roundMe(scaled[j]);
1421	+	scaled[j] += 0.5;
1422	+	// Handle the special case when an object is exactly on the
1423	+	// boundary (a scaled coordinate of 1.0 is the same as
1424	+	// scaled coordinate of 0.0)
1425	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1426	+	}
1427	+
1428	+	// find xyz-indices of cell that cutoffGroup is in.
1429	+	whichCell.x() = nCells_.x() * scaled.x();
1430	+	whichCell.y() = nCells_.y() * scaled.y();
1431	+	whichCell.z() = nCells_.z() * scaled.z();
1432	+
1433	+	// find single index of this cell:
1434	+	cellIndex = Vlinear(whichCell, nCells_);
1435	+
1436	+	// add this cutoff group to the list of groups in this cell;
1437	+	cellListRow_[cellIndex].push_back(i);
1438	+	}
1439	+	for (int i = 0; i < nGroupsInCol_; i++) {
1440	+	rs = cgColData.position[i];
1441	+
1442	+	// scaled positions relative to the box vectors
1443	+	scaled = invBox * rs;
1444	+
1445	+	// wrap the vector back into the unit box by subtracting integer box
1446	+	// numbers
1447	+	for (int j = 0; j < 3; j++) {
1448	+	scaled[j] -= roundMe(scaled[j]);
1449	+	scaled[j] += 0.5;
1450	+	// Handle the special case when an object is exactly on the
1451	+	// boundary (a scaled coordinate of 1.0 is the same as
1452	+	// scaled coordinate of 0.0)
1453	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1454	+	}
1455	+
1456	+	// find xyz-indices of cell that cutoffGroup is in.
1457	+	whichCell.x() = nCells_.x() * scaled.x();
1458	+	whichCell.y() = nCells_.y() * scaled.y();
1459	+	whichCell.z() = nCells_.z() * scaled.z();
1460	+
1461	+	// find single index of this cell:
1462	+	cellIndex = Vlinear(whichCell, nCells_);
1463	+
1464	+	// add this cutoff group to the list of groups in this cell;
1465	+	cellListCol_[cellIndex].push_back(i);
1466	+	}
1467	+
1468	+	#else
1469	+	for (int i = 0; i < nGroups_; i++) {
1470	+	rs = snap_->cgData.position[i];
1471	+
1472	+	// scaled positions relative to the box vectors
1473	+	scaled = invBox * 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	+	scaled[j] -= roundMe(scaled[j]);
1479	+	scaled[j] += 0.5;
1480	+	// Handle the special case when an object is exactly on the
1481	+	// boundary (a scaled coordinate of 1.0 is the same as
1482	+	// scaled coordinate of 0.0)
1483	+	if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1484	+	}
1485	+
1486	+	// find xyz-indices of cell that cutoffGroup is in.
1487	+	whichCell.x() = nCells_.x() * scaled.x();
1488	+	whichCell.y() = nCells_.y() * scaled.y();
1489	+	whichCell.z() = nCells_.z() * scaled.z();
1490	+
1491	+	// find single index of this cell:
1492	+	cellIndex = Vlinear(whichCell, nCells_);
1493	+
1494	+	// add this cutoff group to the list of groups in this cell;
1495	+	cellList_[cellIndex].push_back(i);
1496	+	}
1497	+
1498	+	#endif
1499	+
1500	+	for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1501	+	for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1502	+	for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1503	+	Vector3i m1v(m1x, m1y, m1z);
1504	+	int m1 = Vlinear(m1v, nCells_);
1505	+
1506	+	for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1507	+	os != cellOffsets_.end(); ++os) {
1508	+
1509	+	Vector3i m2v = m1v + (*os);
1510	+
1511	+
1512	+	if (m2v.x() >= nCells_.x()) {
1513	+	m2v.x() = 0;
1514	+	} else if (m2v.x() < 0) {
1515	+	m2v.x() = nCells_.x() - 1;
1516	+	}
1517	+
1518	+	if (m2v.y() >= nCells_.y()) {
1519	+	m2v.y() = 0;
1520	+	} else if (m2v.y() < 0) {
1521	+	m2v.y() = nCells_.y() - 1;
1522	+	}
1523	+
1524	+	if (m2v.z() >= nCells_.z()) {
1525	+	m2v.z() = 0;
1526	+	} else if (m2v.z() < 0) {
1527	+	m2v.z() = nCells_.z() - 1;
1528	+	}
1529	+
1530	+	int m2 = Vlinear (m2v, nCells_);
1531	+
1532	+	#ifdef IS_MPI
1533	+	for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1534	+	j1 != cellListRow_[m1].end(); ++j1) {
1535	+	for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1536	+	j2 != cellListCol_[m2].end(); ++j2) {
1537	+
1538	+	// In parallel, we need to visit *all* pairs of row
1539	+	// & column indicies and will divide labor in the
1540	+	// force evaluation later.
1541	+	dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1542	+	if (usePeriodicBoundaryConditions_) {
1543	+	snap_->wrapVector(dr);
1544	+	}
1545	+	getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1546	+	if (dr.lengthSquare() < rlistsq) {
1547	+	neighborList.push_back(make_pair((*j1), (*j2)));
1548	+	}
1549	+	}
1550	+	}
1551	+	#else
1552	+	for (vector<int>::iterator j1 = cellList_[m1].begin();
1553	+	j1 != cellList_[m1].end(); ++j1) {
1554	+	for (vector<int>::iterator j2 = cellList_[m2].begin();
1555	+	j2 != cellList_[m2].end(); ++j2) {
1556	+
1557	+	// Always do this if we're in different cells or if
1558	+	// we're in the same cell and the global index of
1559	+	// the j2 cutoff group is greater than or equal to
1560	+	// the j1 cutoff group.  Note that Rappaport's code
1561	+	// has a "less than" conditional here, but that
1562	+	// deals with atom-by-atom computation.  OpenMD
1563	+	// allows atoms within a single cutoff group to
1564	+	// interact with each other.
1565	+
1566	+	if (m2 != m1 || (*j2) >= (*j1) ) {
1567	+
1568	+	dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1569	+	if (usePeriodicBoundaryConditions_) {
1570	+	snap_->wrapVector(dr);
1571	+	}
1572	+	getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1573	+	if (dr.lengthSquare() < rlistsq) {
1574	+	neighborList.push_back(make_pair((*j1), (*j2)));
1575	+	}
1576	+	}
1577	+	}
1578	+	}
1579	+	#endif
1580	+	}
1581	+	}
1582	+	}
1583	+	}
1584	+	} else {
1585	+	// branch to do all cutoff group pairs
1586	+	#ifdef IS_MPI
1587	+	for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1588	+	for (int j2 = 0; j2 < nGroupsInCol_; j2++) {
1589	+	dr = cgColData.position[j2] - cgRowData.position[j1];
1590	+	if (usePeriodicBoundaryConditions_) {
1591	+	snap_->wrapVector(dr);
1592	+	}
1593	+	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1594	+	if (dr.lengthSquare() < rlistsq) {
1595	+	neighborList.push_back(make_pair(j1, j2));
1596	+	}
1597	+	}
1598	+	}
1599	+	#else
1600	+	// include all groups here.
1601	+	for (int j1 = 0; j1 < nGroups_; j1++) {
1602	+	// include self group interactions j2 == j1
1603	+	for (int j2 = j1; j2 < nGroups_; j2++) {
1604	+	dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1605	+	if (usePeriodicBoundaryConditions_) {
1606	+	snap_->wrapVector(dr);
1607	+	}
1608	+	getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1609	+	if (dr.lengthSquare() < rlistsq) {
1610	+	neighborList.push_back(make_pair(j1, j2));
1611	+	}
1612	+	}
1613	+	}
1614	+	#endif
1615	+	}
1616	+
1617	+	// save the local cutoff group positions for the check that is
1618	+	// done on each loop:
1619	+	saved_CG_positions_.clear();
1620	+	for (int i = 0; i < nGroups_; i++)
1621	+	saved_CG_positions_.push_back(snap_->cgData.position[i]);
1622	+	}
1623	+	} //end namespace OpenMD

Diff Legend

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