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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1538 by chuckv, Tue Jan 11 18:58:12 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1586 by gezelter, Tue Jun 21 06:34:35 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  
47 + using namespace std;
48 + namespace OpenMD {
49  
50 +  /**
51 +   * distributeInitialData is essentially a copy of the older fortran
52 +   * SimulationSetup
53 +   */
54 +  
55 +  void ForceMatrixDecomposition::distributeInitialData() {
56 +    snap_ = sman_->getCurrentSnapshot();
57 +    storageLayout_ = sman_->getStorageLayout();
58 +    ff_ = info_->getForceField();
59 +    nLocal_ = snap_->getNumberOfAtoms();
60  
61 < /*  -*- c++ -*-  */
62 < #include "config.h"
63 < #include <stdlib.h>
61 >    nGroups_ = info_->getNLocalCutoffGroups();
62 >    // gather the information for atomtype IDs (atids):
63 >    idents = info_->getIdentArray();
64 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
65 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
66 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67 >
68 >    massFactors = info_->getMassFactors();
69 >
70 >    PairList excludes = info_->getExcludedInteractions();
71 >    PairList oneTwo = info_->getOneTwoInteractions();
72 >    PairList oneThree = info_->getOneThreeInteractions();
73 >    PairList oneFour = info_->getOneFourInteractions();
74 >
75   #ifdef IS_MPI
76 < #include <mpi.h>
77 < #endif
76 >
77 >    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
78 >    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
79 >    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
80 >    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
81 >    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
82  
83 < #include <iostream>
84 < #include <vector>
85 < #include <algorithm>
86 < #include <cmath>
87 < #include "parallel/ForceDecomposition.hpp"
83 >    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
84 >    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
85 >    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
86 >    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
87 >    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
88  
89 +    cgCommIntRow = new Communicator<Row,int>(nGroups_);
90 +    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
91 +    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
92 +    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
93  
94 < using namespace std;
95 < using namespace OpenMD;
94 >    nAtomsInRow_ = AtomCommIntRow->getSize();
95 >    nAtomsInCol_ = AtomCommIntColumn->getSize();
96 >    nGroupsInRow_ = cgCommIntRow->getSize();
97 >    nGroupsInCol_ = cgCommIntColumn->getSize();
98  
99 < //__static
100 < #ifdef IS_MPI
101 < static vector<MPI:Comm> communictors;
102 < #endif
99 >    // Modify the data storage objects with the correct layouts and sizes:
100 >    atomRowData.resize(nAtomsInRow_);
101 >    atomRowData.setStorageLayout(storageLayout_);
102 >    atomColData.resize(nAtomsInCol_);
103 >    atomColData.setStorageLayout(storageLayout_);
104 >    cgRowData.resize(nGroupsInRow_);
105 >    cgRowData.setStorageLayout(DataStorage::dslPosition);
106 >    cgColData.resize(nGroupsInCol_);
107 >    cgColData.setStorageLayout(DataStorage::dslPosition);
108 >        
109 >    identsRow.resize(nAtomsInRow_);
110 >    identsCol.resize(nAtomsInCol_);
111 >    
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114 >    
115 >    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116 >    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
117 >    
118 >    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119 >    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120  
121 < //____ MPITypeTraits
122 < template<typename T>
75 < struct MPITypeTraits;
121 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
122 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
123  
124 < #ifdef IS_MPI
125 < template<>
126 < struct MPITypeTraits<RealType> {
127 <  static const MPI::Datatype datatype;
128 < };
129 < const MPI_Datatype MPITypeTraits<RealType>::datatype = MY_MPI_REAL;
124 >    groupListRow_.clear();
125 >    groupListRow_.resize(nGroupsInRow_);
126 >    for (int i = 0; i < nGroupsInRow_; i++) {
127 >      int gid = cgRowToGlobal[i];
128 >      for (int j = 0; j < nAtomsInRow_; j++) {
129 >        int aid = AtomRowToGlobal[j];
130 >        if (globalGroupMembership[aid] == gid)
131 >          groupListRow_[i].push_back(j);
132 >      }      
133 >    }
134  
135 < template<>
136 < struct MPITypeTraits<int> {
137 <  static const MPI::Datatype datatype;
138 < };
139 < const MPI::Datatype MPITypeTraits<int>::datatype = MPI_INT;
140 < #endif
135 >    groupListCol_.clear();
136 >    groupListCol_.resize(nGroupsInCol_);
137 >    for (int i = 0; i < nGroupsInCol_; i++) {
138 >      int gid = cgColToGlobal[i];
139 >      for (int j = 0; j < nAtomsInCol_; j++) {
140 >        int aid = AtomColToGlobal[j];
141 >        if (globalGroupMembership[aid] == gid)
142 >          groupListCol_[i].push_back(j);
143 >      }      
144 >    }
145  
146 < /**
147 < * Constructor for ForceDecomposition Parallel Decomposition Method
148 < * Will try to construct a symmetric grid of processors. Ideally, the
149 < * number of processors will be a square ex: 4, 9, 16, 25.
150 < *
151 < */
146 >    skipsForAtom.clear();
147 >    skipsForAtom.resize(nAtomsInRow_);
148 >    toposForAtom.clear();
149 >    toposForAtom.resize(nAtomsInRow_);
150 >    topoDist.clear();
151 >    topoDist.resize(nAtomsInRow_);
152 >    for (int i = 0; i < nAtomsInRow_; i++) {
153 >      int iglob = AtomRowToGlobal[i];
154  
155 < ForceDecomposition::ForceDecomposition() {
155 >      for (int j = 0; j < nAtomsInCol_; j++) {
156 >        int jglob = AtomColToGlobal[j];
157  
158 < #ifdef IS_MPI
159 <  int nProcs = MPI::COMM_WORLD.Get_size();
160 <  int worldRank = MPI::COMM_WORLD.Get_rank();
158 >        if (excludes.hasPair(iglob, jglob))
159 >          skipsForAtom[i].push_back(j);      
160 >        
161 >        if (oneTwo.hasPair(iglob, jglob)) {
162 >          toposForAtom[i].push_back(j);
163 >          topoDist[i].push_back(1);
164 >        } else {
165 >          if (oneThree.hasPair(iglob, jglob)) {
166 >            toposForAtom[i].push_back(j);
167 >            topoDist[i].push_back(2);
168 >          } else {
169 >            if (oneFour.hasPair(iglob, jglob)) {
170 >              toposForAtom[i].push_back(j);
171 >              topoDist[i].push_back(3);
172 >            }
173 >          }
174 >        }
175 >      }      
176 >    }
177 >
178   #endif
179  
180 <  // First time through, construct column stride.
181 <  if (communicators.size() == 0)
182 <  {
183 <    int nColumnsMax = (int) round(sqrt((float) nProcs));
184 <    for (int i = 0; i < nProcs; ++i)
185 <    {
186 <      if (nProcs%i==0) nColumns=i;
180 >    groupList_.clear();
181 >    groupList_.resize(nGroups_);
182 >    for (int i = 0; i < nGroups_; i++) {
183 >      int gid = cgLocalToGlobal[i];
184 >      for (int j = 0; j < nLocal_; j++) {
185 >        int aid = AtomLocalToGlobal[j];
186 >        if (globalGroupMembership[aid] == gid) {
187 >          groupList_[i].push_back(j);
188 >        }
189 >      }      
190      }
191  
192 <    int nRows = nProcs/nColumns;    
193 <    myRank_ = (int) worldRank%nColumns;
192 >    skipsForAtom.clear();
193 >    skipsForAtom.resize(nLocal_);
194 >    toposForAtom.clear();
195 >    toposForAtom.resize(nLocal_);
196 >    topoDist.clear();
197 >    topoDist.resize(nLocal_);
198 >
199 >    for (int i = 0; i < nLocal_; i++) {
200 >      int iglob = AtomLocalToGlobal[i];
201 >
202 >      for (int j = 0; j < nLocal_; j++) {
203 >        int jglob = AtomLocalToGlobal[j];
204 >
205 >        if (excludes.hasPair(iglob, jglob))
206 >          skipsForAtom[i].push_back(j);              
207 >        
208 >        if (oneTwo.hasPair(iglob, jglob)) {
209 >          toposForAtom[i].push_back(j);
210 >          topoDist[i].push_back(1);
211 >        } else {
212 >          if (oneThree.hasPair(iglob, jglob)) {
213 >            toposForAtom[i].push_back(j);
214 >            topoDist[i].push_back(2);
215 >          } else {
216 >            if (oneFour.hasPair(iglob, jglob)) {
217 >              toposForAtom[i].push_back(j);
218 >              topoDist[i].push_back(3);
219 >            }
220 >          }
221 >        }
222 >      }      
223 >    }
224 >    
225 >    createGtypeCutoffMap();
226    }
227 <  else
228 <  {
229 <    myRank_ = myRank/nColumns;
230 <  }
231 <  MPI::Comm newComm = MPI:COMM_WORLD.Split(myRank_,0);
232 <  
233 <  isColumn_ = false;
234 <  
235 < }
227 >  
228 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
229 >    
230 >    RealType tol = 1e-6;
231 >    RealType rc;
232 >    int atid;
233 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
234 >    vector<RealType> atypeCutoff;
235 >    atypeCutoff.resize( atypes.size() );
236 >      
237 >    for (set<AtomType*>::iterator at = atypes.begin();
238 >         at != atypes.end(); ++at){
239 >      atid = (*at)->getIdent();
240  
241 < ForceDecomposition::gather(sendbuf, receivebuf){
242 <  communicators(myIndex_).Allgatherv();
243 < }
241 >      if (userChoseCutoff_)
242 >        atypeCutoff[atid] = userCutoff_;
243 >      else
244 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
245 >    }
246  
247 +    vector<RealType> gTypeCutoffs;
248  
249 +    // first we do a single loop over the cutoff groups to find the
250 +    // largest cutoff for any atypes present in this group.
251 + #ifdef IS_MPI
252 +    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
253 +    groupRowToGtype.resize(nGroupsInRow_);
254 +    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
255 +      vector<int> atomListRow = getAtomsInGroupRow(cg1);
256 +      for (vector<int>::iterator ia = atomListRow.begin();
257 +           ia != atomListRow.end(); ++ia) {            
258 +        int atom1 = (*ia);
259 +        atid = identsRow[atom1];
260 +        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
261 +          groupCutoffRow[cg1] = atypeCutoff[atid];
262 +        }
263 +      }
264  
265 < ForceDecomposition::scatter(sbuffer, rbuffer){
266 <  communicators(myIndex_).Reduce_scatter(sbuffer, recevbuf. recvcounts, MPI::DOUBLE, MPI::SUM);
267 < }
265 >      bool gTypeFound = false;
266 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
267 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
268 >          groupRowToGtype[cg1] = gt;
269 >          gTypeFound = true;
270 >        }
271 >      }
272 >      if (!gTypeFound) {
273 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
274 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
275 >      }
276 >      
277 >    }
278 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
279 >    groupColToGtype.resize(nGroupsInCol_);
280 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
281 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
282 >      for (vector<int>::iterator jb = atomListCol.begin();
283 >           jb != atomListCol.end(); ++jb) {            
284 >        int atom2 = (*jb);
285 >        atid = identsCol[atom2];
286 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
287 >          groupCutoffCol[cg2] = atypeCutoff[atid];
288 >        }
289 >      }
290 >      bool gTypeFound = false;
291 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
292 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
293 >          groupColToGtype[cg2] = gt;
294 >          gTypeFound = true;
295 >        }
296 >      }
297 >      if (!gTypeFound) {
298 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
299 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
300 >      }
301 >    }
302 > #else
303  
304 +    vector<RealType> groupCutoff(nGroups_, 0.0);
305 +    groupToGtype.resize(nGroups_);
306  
307 +    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
308 +
309 +      groupCutoff[cg1] = 0.0;
310 +      vector<int> atomList = getAtomsInGroupRow(cg1);
311 +
312 +      for (vector<int>::iterator ia = atomList.begin();
313 +           ia != atomList.end(); ++ia) {            
314 +        int atom1 = (*ia);
315 +        atid = idents[atom1];
316 +        if (atypeCutoff[atid] > groupCutoff[cg1]) {
317 +          groupCutoff[cg1] = atypeCutoff[atid];
318 +        }
319 +      }
320 +
321 +      bool gTypeFound = false;
322 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
323 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
324 +          groupToGtype[cg1] = gt;
325 +          gTypeFound = true;
326 +        }
327 +      }
328 +      if (!gTypeFound) {
329 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
330 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
331 +      }      
332 +    }
333 + #endif
334 +
335 +    // Now we find the maximum group cutoff value present in the simulation
336 +
337 +    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
338 +
339 + #ifdef IS_MPI
340 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
341 + #endif
342 +    
343 +    RealType tradRcut = groupMax;
344 +
345 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
346 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
347 +        RealType thisRcut;
348 +        switch(cutoffPolicy_) {
349 +        case TRADITIONAL:
350 +          thisRcut = tradRcut;
351 +          break;
352 +        case MIX:
353 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
354 +          break;
355 +        case MAX:
356 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
357 +          break;
358 +        default:
359 +          sprintf(painCave.errMsg,
360 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
361 +                  "hit an unknown cutoff policy!\n");
362 +          painCave.severity = OPENMD_ERROR;
363 +          painCave.isFatal = 1;
364 +          simError();
365 +          break;
366 +        }
367 +
368 +        pair<int,int> key = make_pair(i,j);
369 +        gTypeCutoffMap[key].first = thisRcut;
370 +
371 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
372 +
373 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
374 +        
375 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
376 +
377 +        // sanity check
378 +        
379 +        if (userChoseCutoff_) {
380 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
381 +            sprintf(painCave.errMsg,
382 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
383 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
384 +            painCave.severity = OPENMD_ERROR;
385 +            painCave.isFatal = 1;
386 +            simError();            
387 +          }
388 +        }
389 +      }
390 +    }
391 +  }
392 +
393 +
394 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
395 +    int i, j;  
396 + #ifdef IS_MPI
397 +    i = groupRowToGtype[cg1];
398 +    j = groupColToGtype[cg2];
399 + #else
400 +    i = groupToGtype[cg1];
401 +    j = groupToGtype[cg2];
402 + #endif    
403 +    return gTypeCutoffMap[make_pair(i,j)];
404 +  }
405 +
406 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
407 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
408 +      if (toposForAtom[atom1][j] == atom2)
409 +        return topoDist[atom1][j];
410 +    }
411 +    return 0;
412 +  }
413 +
414 +  void ForceMatrixDecomposition::zeroWorkArrays() {
415 +    pairwisePot = 0.0;
416 +    embeddingPot = 0.0;
417 +
418 + #ifdef IS_MPI
419 +    if (storageLayout_ & DataStorage::dslForce) {
420 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
421 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
422 +    }
423 +
424 +    if (storageLayout_ & DataStorage::dslTorque) {
425 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
426 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
427 +    }
428 +    
429 +    fill(pot_row.begin(), pot_row.end(),
430 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
431 +
432 +    fill(pot_col.begin(), pot_col.end(),
433 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
434 +
435 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
436 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
437 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
438 +    }
439 +
440 +    if (storageLayout_ & DataStorage::dslDensity) {      
441 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
442 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
443 +    }
444 +
445 +    if (storageLayout_ & DataStorage::dslFunctional) {  
446 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
447 +      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
448 +    }
449 +
450 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
451 +      fill(atomRowData.functionalDerivative.begin(),
452 +           atomRowData.functionalDerivative.end(), 0.0);
453 +      fill(atomColData.functionalDerivative.begin(),
454 +           atomColData.functionalDerivative.end(), 0.0);
455 +    }
456 +
457 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
458 +      fill(atomRowData.skippedCharge.begin(), atomRowData.skippedCharge.end(), 0.0);
459 +      fill(atomColData.skippedCharge.begin(), atomColData.skippedCharge.end(), 0.0);
460 +    }
461 +
462 + #else
463 +    
464 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
465 +      fill(snap_->atomData.particlePot.begin(),
466 +           snap_->atomData.particlePot.end(), 0.0);
467 +    }
468 +    
469 +    if (storageLayout_ & DataStorage::dslDensity) {      
470 +      fill(snap_->atomData.density.begin(),
471 +           snap_->atomData.density.end(), 0.0);
472 +    }
473 +    if (storageLayout_ & DataStorage::dslFunctional) {
474 +      fill(snap_->atomData.functional.begin(),
475 +           snap_->atomData.functional.end(), 0.0);
476 +    }
477 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
478 +      fill(snap_->atomData.functionalDerivative.begin(),
479 +           snap_->atomData.functionalDerivative.end(), 0.0);
480 +    }
481 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
482 +      fill(snap_->atomData.skippedCharge.begin(),
483 +           snap_->atomData.skippedCharge.end(), 0.0);
484 +    }
485 + #endif
486 +    
487 +  }
488 +
489 +
490 +  void ForceMatrixDecomposition::distributeData()  {
491 +    snap_ = sman_->getCurrentSnapshot();
492 +    storageLayout_ = sman_->getStorageLayout();
493 + #ifdef IS_MPI
494 +    
495 +    // gather up the atomic positions
496 +    AtomCommVectorRow->gather(snap_->atomData.position,
497 +                              atomRowData.position);
498 +    AtomCommVectorColumn->gather(snap_->atomData.position,
499 +                                 atomColData.position);
500 +    
501 +    // gather up the cutoff group positions
502 +    cgCommVectorRow->gather(snap_->cgData.position,
503 +                            cgRowData.position);
504 +    cgCommVectorColumn->gather(snap_->cgData.position,
505 +                               cgColData.position);
506 +    
507 +    // if needed, gather the atomic rotation matrices
508 +    if (storageLayout_ & DataStorage::dslAmat) {
509 +      AtomCommMatrixRow->gather(snap_->atomData.aMat,
510 +                                atomRowData.aMat);
511 +      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
512 +                                   atomColData.aMat);
513 +    }
514 +    
515 +    // if needed, gather the atomic eletrostatic frames
516 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
517 +      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
518 +                                atomRowData.electroFrame);
519 +      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
520 +                                   atomColData.electroFrame);
521 +    }
522 + #endif      
523 +  }
524 +  
525 +  /* collects information obtained during the pre-pair loop onto local
526 +   * data structures.
527 +   */
528 +  void ForceMatrixDecomposition::collectIntermediateData() {
529 +    snap_ = sman_->getCurrentSnapshot();
530 +    storageLayout_ = sman_->getStorageLayout();
531 + #ifdef IS_MPI
532 +    
533 +    if (storageLayout_ & DataStorage::dslDensity) {
534 +      
535 +      AtomCommRealRow->scatter(atomRowData.density,
536 +                               snap_->atomData.density);
537 +      
538 +      int n = snap_->atomData.density.size();
539 +      vector<RealType> rho_tmp(n, 0.0);
540 +      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
541 +      for (int i = 0; i < n; i++)
542 +        snap_->atomData.density[i] += rho_tmp[i];
543 +    }
544 + #endif
545 +  }
546 +
547 +  /*
548 +   * redistributes information obtained during the pre-pair loop out to
549 +   * row and column-indexed data structures
550 +   */
551 +  void ForceMatrixDecomposition::distributeIntermediateData() {
552 +    snap_ = sman_->getCurrentSnapshot();
553 +    storageLayout_ = sman_->getStorageLayout();
554 + #ifdef IS_MPI
555 +    if (storageLayout_ & DataStorage::dslFunctional) {
556 +      AtomCommRealRow->gather(snap_->atomData.functional,
557 +                              atomRowData.functional);
558 +      AtomCommRealColumn->gather(snap_->atomData.functional,
559 +                                 atomColData.functional);
560 +    }
561 +    
562 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
563 +      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
564 +                              atomRowData.functionalDerivative);
565 +      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
566 +                                 atomColData.functionalDerivative);
567 +    }
568 + #endif
569 +  }
570 +  
571 +  
572 +  void ForceMatrixDecomposition::collectData() {
573 +    snap_ = sman_->getCurrentSnapshot();
574 +    storageLayout_ = sman_->getStorageLayout();
575 + #ifdef IS_MPI    
576 +    int n = snap_->atomData.force.size();
577 +    vector<Vector3d> frc_tmp(n, V3Zero);
578 +    
579 +    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
580 +    for (int i = 0; i < n; i++) {
581 +      snap_->atomData.force[i] += frc_tmp[i];
582 +      frc_tmp[i] = 0.0;
583 +    }
584 +    
585 +    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
586 +    for (int i = 0; i < n; i++)
587 +      snap_->atomData.force[i] += frc_tmp[i];
588 +    
589 +    
590 +    if (storageLayout_ & DataStorage::dslTorque) {
591 +
592 +      int nt = snap_->atomData.force.size();
593 +      vector<Vector3d> trq_tmp(nt, V3Zero);
594 +
595 +      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
596 +      for (int i = 0; i < n; i++) {
597 +        snap_->atomData.torque[i] += trq_tmp[i];
598 +        trq_tmp[i] = 0.0;
599 +      }
600 +      
601 +      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
602 +      for (int i = 0; i < n; i++)
603 +        snap_->atomData.torque[i] += trq_tmp[i];
604 +    }
605 +    
606 +    nLocal_ = snap_->getNumberOfAtoms();
607 +
608 +    vector<potVec> pot_temp(nLocal_,
609 +                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
610 +
611 +    // scatter/gather pot_row into the members of my column
612 +          
613 +    AtomCommPotRow->scatter(pot_row, pot_temp);
614 +
615 +    for (int ii = 0;  ii < pot_temp.size(); ii++ )
616 +      pairwisePot += pot_temp[ii];
617 +    
618 +    fill(pot_temp.begin(), pot_temp.end(),
619 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
620 +      
621 +    AtomCommPotColumn->scatter(pot_col, pot_temp);    
622 +    
623 +    for (int ii = 0;  ii < pot_temp.size(); ii++ )
624 +      pairwisePot += pot_temp[ii];    
625 + #endif
626 +
627 +  }
628 +
629 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
630 + #ifdef IS_MPI
631 +    return nAtomsInRow_;
632 + #else
633 +    return nLocal_;
634 + #endif
635 +  }
636 +
637 +  /**
638 +   * returns the list of atoms belonging to this group.  
639 +   */
640 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
641 + #ifdef IS_MPI
642 +    return groupListRow_[cg1];
643 + #else
644 +    return groupList_[cg1];
645 + #endif
646 +  }
647 +
648 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
649 + #ifdef IS_MPI
650 +    return groupListCol_[cg2];
651 + #else
652 +    return groupList_[cg2];
653 + #endif
654 +  }
655 +  
656 +  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
657 +    Vector3d d;
658 +    
659 + #ifdef IS_MPI
660 +    d = cgColData.position[cg2] - cgRowData.position[cg1];
661 + #else
662 +    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
663 + #endif
664 +    
665 +    snap_->wrapVector(d);
666 +    return d;    
667 +  }
668 +
669 +
670 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
671 +
672 +    Vector3d d;
673 +    
674 + #ifdef IS_MPI
675 +    d = cgRowData.position[cg1] - atomRowData.position[atom1];
676 + #else
677 +    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
678 + #endif
679 +
680 +    snap_->wrapVector(d);
681 +    return d;    
682 +  }
683 +  
684 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
685 +    Vector3d d;
686 +    
687 + #ifdef IS_MPI
688 +    d = cgColData.position[cg2] - atomColData.position[atom2];
689 + #else
690 +    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
691 + #endif
692 +    
693 +    snap_->wrapVector(d);
694 +    return d;    
695 +  }
696 +
697 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
698 + #ifdef IS_MPI
699 +    return massFactorsRow[atom1];
700 + #else
701 +    return massFactors[atom1];
702 + #endif
703 +  }
704 +
705 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
706 + #ifdef IS_MPI
707 +    return massFactorsCol[atom2];
708 + #else
709 +    return massFactors[atom2];
710 + #endif
711 +
712 +  }
713 +    
714 +  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
715 +    Vector3d d;
716 +    
717 + #ifdef IS_MPI
718 +    d = atomColData.position[atom2] - atomRowData.position[atom1];
719 + #else
720 +    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
721 + #endif
722 +
723 +    snap_->wrapVector(d);
724 +    return d;    
725 +  }
726 +
727 +  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
728 +    return skipsForAtom[atom1];
729 +  }
730 +
731 +  /**
732 +   * There are a number of reasons to skip a pair or a
733 +   * particle. Mostly we do this to exclude atoms who are involved in
734 +   * short range interactions (bonds, bends, torsions), but we also
735 +   * need to exclude some overcounted interactions that result from
736 +   * the parallel decomposition.
737 +   */
738 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
739 +    int unique_id_1, unique_id_2;
740 +
741 + #ifdef IS_MPI
742 +    // in MPI, we have to look up the unique IDs for each atom
743 +    unique_id_1 = AtomRowToGlobal[atom1];
744 +    unique_id_2 = AtomColToGlobal[atom2];
745 +
746 +    // this situation should only arise in MPI simulations
747 +    if (unique_id_1 == unique_id_2) return true;
748 +    
749 +    // this prevents us from doing the pair on multiple processors
750 +    if (unique_id_1 < unique_id_2) {
751 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
752 +    } else {
753 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
754 +    }
755 + #else
756 +    // in the normal loop, the atom numbers are unique
757 +    unique_id_1 = atom1;
758 +    unique_id_2 = atom2;
759 + #endif
760 +    
761 +    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
762 +         i != skipsForAtom[atom1].end(); ++i) {
763 +      if ( (*i) == unique_id_2 ) return true;
764 +    }
765 +
766 +    return false;
767 +  }
768 +
769 +
770 +  void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
771 + #ifdef IS_MPI
772 +    atomRowData.force[atom1] += fg;
773 + #else
774 +    snap_->atomData.force[atom1] += fg;
775 + #endif
776 +  }
777 +
778 +  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
779 + #ifdef IS_MPI
780 +    atomColData.force[atom2] += fg;
781 + #else
782 +    snap_->atomData.force[atom2] += fg;
783 + #endif
784 +  }
785 +
786 +    // filling interaction blocks with pointers
787 +  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
788 +                                                     int atom1, int atom2) {    
789 + #ifdef IS_MPI
790 +    
791 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
792 +                             ff_->getAtomType(identsCol[atom2]) );
793 +    
794 +    if (storageLayout_ & DataStorage::dslAmat) {
795 +      idat.A1 = &(atomRowData.aMat[atom1]);
796 +      idat.A2 = &(atomColData.aMat[atom2]);
797 +    }
798 +    
799 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
800 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
801 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
802 +    }
803 +
804 +    if (storageLayout_ & DataStorage::dslTorque) {
805 +      idat.t1 = &(atomRowData.torque[atom1]);
806 +      idat.t2 = &(atomColData.torque[atom2]);
807 +    }
808 +
809 +    if (storageLayout_ & DataStorage::dslDensity) {
810 +      idat.rho1 = &(atomRowData.density[atom1]);
811 +      idat.rho2 = &(atomColData.density[atom2]);
812 +    }
813 +
814 +    if (storageLayout_ & DataStorage::dslFunctional) {
815 +      idat.frho1 = &(atomRowData.functional[atom1]);
816 +      idat.frho2 = &(atomColData.functional[atom2]);
817 +    }
818 +
819 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
820 +      idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
821 +      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
822 +    }
823 +
824 +    if (storageLayout_ & DataStorage::dslParticlePot) {
825 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
826 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
827 +    }
828 +
829 + #else
830 +
831 +    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
832 +                             ff_->getAtomType(idents[atom2]) );
833 +
834 +    if (storageLayout_ & DataStorage::dslAmat) {
835 +      idat.A1 = &(snap_->atomData.aMat[atom1]);
836 +      idat.A2 = &(snap_->atomData.aMat[atom2]);
837 +    }
838 +
839 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
840 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
841 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
842 +    }
843 +
844 +    if (storageLayout_ & DataStorage::dslTorque) {
845 +      idat.t1 = &(snap_->atomData.torque[atom1]);
846 +      idat.t2 = &(snap_->atomData.torque[atom2]);
847 +    }
848 +
849 +    if (storageLayout_ & DataStorage::dslDensity) {    
850 +      idat.rho1 = &(snap_->atomData.density[atom1]);
851 +      idat.rho2 = &(snap_->atomData.density[atom2]);
852 +    }
853 +
854 +    if (storageLayout_ & DataStorage::dslFunctional) {
855 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
856 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
857 +    }
858 +
859 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
860 +      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
861 +      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
862 +    }
863 +
864 +    if (storageLayout_ & DataStorage::dslParticlePot) {
865 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
866 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
867 +    }
868 +
869 + #endif
870 +  }
871 +
872 +  
873 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
874 + #ifdef IS_MPI
875 +    pot_row[atom1] += 0.5 *  *(idat.pot);
876 +    pot_col[atom2] += 0.5 *  *(idat.pot);
877 +
878 +    atomRowData.force[atom1] += *(idat.f1);
879 +    atomColData.force[atom2] -= *(idat.f1);
880 + #else
881 +    pairwisePot += *(idat.pot);
882 +
883 +    snap_->atomData.force[atom1] += *(idat.f1);
884 +    snap_->atomData.force[atom2] -= *(idat.f1);
885 + #endif
886 +    
887 +  }
888 +
889 +
890 +  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
891 +                                              int atom1, int atom2) {
892 + #ifdef IS_MPI
893 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
894 +                             ff_->getAtomType(identsCol[atom2]) );
895 +
896 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
897 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
898 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
899 +    }
900 +
901 +    if (storageLayout_ & DataStorage::dslTorque) {
902 +      idat.t1 = &(atomRowData.torque[atom1]);
903 +      idat.t2 = &(atomColData.torque[atom2]);
904 +    }
905 +
906 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
907 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
908 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
909 +    }
910 + #else
911 +    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
912 +                             ff_->getAtomType(idents[atom2]) );
913 +
914 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
915 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
916 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
917 +    }
918 +
919 +    if (storageLayout_ & DataStorage::dslTorque) {
920 +      idat.t1 = &(snap_->atomData.torque[atom1]);
921 +      idat.t2 = &(snap_->atomData.torque[atom2]);
922 +    }
923 +
924 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
925 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
926 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
927 +    }
928 + #endif    
929 +  }
930 +
931 +
932 +  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
933 + #ifdef IS_MPI
934 +    pot_row[atom1] += 0.5 *  *(idat.pot);
935 +    pot_col[atom2] += 0.5 *  *(idat.pot);
936 + #else
937 +    pairwisePot += *(idat.pot);  
938 + #endif
939 +
940 +  }
941 +
942 +
943 +  /*
944 +   * buildNeighborList
945 +   *
946 +   * first element of pair is row-indexed CutoffGroup
947 +   * second element of pair is column-indexed CutoffGroup
948 +   */
949 +  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
950 +      
951 +    vector<pair<int, int> > neighborList;
952 +    groupCutoffs cuts;
953 + #ifdef IS_MPI
954 +    cellListRow_.clear();
955 +    cellListCol_.clear();
956 + #else
957 +    cellList_.clear();
958 + #endif
959 +
960 +    RealType rList_ = (largestRcut_ + skinThickness_);
961 +    RealType rl2 = rList_ * rList_;
962 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
963 +    Mat3x3d Hmat = snap_->getHmat();
964 +    Vector3d Hx = Hmat.getColumn(0);
965 +    Vector3d Hy = Hmat.getColumn(1);
966 +    Vector3d Hz = Hmat.getColumn(2);
967 +
968 +    nCells_.x() = (int) ( Hx.length() )/ rList_;
969 +    nCells_.y() = (int) ( Hy.length() )/ rList_;
970 +    nCells_.z() = (int) ( Hz.length() )/ rList_;
971 +
972 +    Mat3x3d invHmat = snap_->getInvHmat();
973 +    Vector3d rs, scaled, dr;
974 +    Vector3i whichCell;
975 +    int cellIndex;
976 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
977 +
978 + #ifdef IS_MPI
979 +    cellListRow_.resize(nCtot);
980 +    cellListCol_.resize(nCtot);
981 + #else
982 +    cellList_.resize(nCtot);
983 + #endif
984 +
985 + #ifdef IS_MPI
986 +    for (int i = 0; i < nGroupsInRow_; i++) {
987 +      rs = cgRowData.position[i];
988 +
989 +      // scaled positions relative to the box vectors
990 +      scaled = invHmat * rs;
991 +
992 +      // wrap the vector back into the unit box by subtracting integer box
993 +      // numbers
994 +      for (int j = 0; j < 3; j++) {
995 +        scaled[j] -= roundMe(scaled[j]);
996 +        scaled[j] += 0.5;
997 +      }
998 +    
999 +      // find xyz-indices of cell that cutoffGroup is in.
1000 +      whichCell.x() = nCells_.x() * scaled.x();
1001 +      whichCell.y() = nCells_.y() * scaled.y();
1002 +      whichCell.z() = nCells_.z() * scaled.z();
1003 +
1004 +      // find single index of this cell:
1005 +      cellIndex = Vlinear(whichCell, nCells_);
1006 +
1007 +      // add this cutoff group to the list of groups in this cell;
1008 +      cellListRow_[cellIndex].push_back(i);
1009 +    }
1010 +
1011 +    for (int i = 0; i < nGroupsInCol_; i++) {
1012 +      rs = cgColData.position[i];
1013 +
1014 +      // scaled positions relative to the box vectors
1015 +      scaled = invHmat * rs;
1016 +
1017 +      // wrap the vector back into the unit box by subtracting integer box
1018 +      // numbers
1019 +      for (int j = 0; j < 3; j++) {
1020 +        scaled[j] -= roundMe(scaled[j]);
1021 +        scaled[j] += 0.5;
1022 +      }
1023 +
1024 +      // find xyz-indices of cell that cutoffGroup is in.
1025 +      whichCell.x() = nCells_.x() * scaled.x();
1026 +      whichCell.y() = nCells_.y() * scaled.y();
1027 +      whichCell.z() = nCells_.z() * scaled.z();
1028 +
1029 +      // find single index of this cell:
1030 +      cellIndex = Vlinear(whichCell, nCells_);
1031 +
1032 +      // add this cutoff group to the list of groups in this cell;
1033 +      cellListCol_[cellIndex].push_back(i);
1034 +    }
1035 + #else
1036 +    for (int i = 0; i < nGroups_; i++) {
1037 +      rs = snap_->cgData.position[i];
1038 +
1039 +      // scaled positions relative to the box vectors
1040 +      scaled = invHmat * rs;
1041 +
1042 +      // wrap the vector back into the unit box by subtracting integer box
1043 +      // numbers
1044 +      for (int j = 0; j < 3; j++) {
1045 +        scaled[j] -= roundMe(scaled[j]);
1046 +        scaled[j] += 0.5;
1047 +      }
1048 +
1049 +      // find xyz-indices of cell that cutoffGroup is in.
1050 +      whichCell.x() = nCells_.x() * scaled.x();
1051 +      whichCell.y() = nCells_.y() * scaled.y();
1052 +      whichCell.z() = nCells_.z() * scaled.z();
1053 +
1054 +      // find single index of this cell:
1055 +      cellIndex = Vlinear(whichCell, nCells_);      
1056 +
1057 +      // add this cutoff group to the list of groups in this cell;
1058 +      cellList_[cellIndex].push_back(i);
1059 +    }
1060 + #endif
1061 +
1062 +    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1063 +      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1064 +        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1065 +          Vector3i m1v(m1x, m1y, m1z);
1066 +          int m1 = Vlinear(m1v, nCells_);
1067 +
1068 +          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1069 +               os != cellOffsets_.end(); ++os) {
1070 +            
1071 +            Vector3i m2v = m1v + (*os);
1072 +            
1073 +            if (m2v.x() >= nCells_.x()) {
1074 +              m2v.x() = 0;          
1075 +            } else if (m2v.x() < 0) {
1076 +              m2v.x() = nCells_.x() - 1;
1077 +            }
1078 +            
1079 +            if (m2v.y() >= nCells_.y()) {
1080 +              m2v.y() = 0;          
1081 +            } else if (m2v.y() < 0) {
1082 +              m2v.y() = nCells_.y() - 1;
1083 +            }
1084 +            
1085 +            if (m2v.z() >= nCells_.z()) {
1086 +              m2v.z() = 0;          
1087 +            } else if (m2v.z() < 0) {
1088 +              m2v.z() = nCells_.z() - 1;
1089 +            }
1090 +            
1091 +            int m2 = Vlinear (m2v, nCells_);
1092 +
1093 + #ifdef IS_MPI
1094 +            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1095 +                 j1 != cellListRow_[m1].end(); ++j1) {
1096 +              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1097 +                   j2 != cellListCol_[m2].end(); ++j2) {
1098 +                              
1099 +                // Always do this if we're in different cells or if
1100 +                // we're in the same cell and the global index of the
1101 +                // j2 cutoff group is less than the j1 cutoff group
1102 +
1103 +                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1104 +                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1105 +                  snap_->wrapVector(dr);
1106 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1107 +                  if (dr.lengthSquare() < cuts.third) {
1108 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1109 +                  }
1110 +                }
1111 +              }
1112 +            }
1113 + #else
1114 +
1115 +            for (vector<int>::iterator j1 = cellList_[m1].begin();
1116 +                 j1 != cellList_[m1].end(); ++j1) {
1117 +              for (vector<int>::iterator j2 = cellList_[m2].begin();
1118 +                   j2 != cellList_[m2].end(); ++j2) {
1119 +
1120 +                // Always do this if we're in different cells or if
1121 +                // we're in the same cell and the global index of the
1122 +                // j2 cutoff group is less than the j1 cutoff group
1123 +
1124 +                if (m2 != m1 || (*j2) < (*j1)) {
1125 +                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1126 +                  snap_->wrapVector(dr);
1127 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1128 +                  if (dr.lengthSquare() < cuts.third) {
1129 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1130 +                  }
1131 +                }
1132 +              }
1133 +            }
1134 + #endif
1135 +          }
1136 +        }
1137 +      }
1138 +    }
1139 +    
1140 +    // save the local cutoff group positions for the check that is
1141 +    // done on each loop:
1142 +    saved_CG_positions_.clear();
1143 +    for (int i = 0; i < nGroups_; i++)
1144 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1145 +  
1146 +    return neighborList;
1147 +  }
1148 + } //end namespace OpenMD

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