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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1554 by gezelter, Sat Apr 30 02:54:02 2011 UTC vs.
Revision 1601 by gezelter, Thu Aug 4 20:04:35 2011 UTC

# Line 42 | Line 42
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 +  ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
51 +
52 +    // In a parallel computation, row and colum scans must visit all
53 +    // surrounding cells (not just the 14 upper triangular blocks that
54 +    // are used when the processor can see all pairs)
55 + #ifdef IS_MPI
56 +    cellOffsets_.push_back( Vector3i(-1, 0, 0) );
57 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
58 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
59 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
60 +    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
61 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
62 +    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
63 +    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
64 +    cellOffsets_.push_back( Vector3i( 1,-1,-1) );
65 +    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
66 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );
68 +    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
69 + #endif    
70 +  }
71 +
72 +
73    /**
74     * distributeInitialData is essentially a copy of the older fortran
75     * SimulationSetup
76     */
53 –  
77    void ForceMatrixDecomposition::distributeInitialData() {
78      snap_ = sman_->getCurrentSnapshot();
79      storageLayout_ = sman_->getStorageLayout();
80 < #ifdef IS_MPI    
81 <    int nLocal = snap_->getNumberOfAtoms();
59 <    int nGroups = snap_->getNumberOfCutoffGroups();
80 >    ff_ = info_->getForceField();
81 >    nLocal_ = snap_->getNumberOfAtoms();
82      
83 <    AtomCommIntRow = new Communicator<Row,int>(nLocal);
84 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
85 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
86 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
83 >    nGroups_ = info_->getNLocalCutoffGroups();
84 >    // gather the information for atomtype IDs (atids):
85 >    idents = info_->getIdentArray();
86 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
87 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
88 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
89  
90 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
67 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
68 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
69 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
90 >    massFactors = info_->getMassFactors();
91  
92 <    cgCommIntRow = new Communicator<Row,int>(nGroups);
93 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
94 <    cgCommIntColumn = new Communicator<Column,int>(nGroups);
95 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
92 >    PairList* excludes = info_->getExcludedInteractions();
93 >    PairList* oneTwo = info_->getOneTwoInteractions();
94 >    PairList* oneThree = info_->getOneThreeInteractions();
95 >    PairList* oneFour = info_->getOneFourInteractions();
96  
97 <    int nAtomsInRow = AtomCommIntRow->getSize();
98 <    int nAtomsInCol = AtomCommIntColumn->getSize();
99 <    int nGroupsInRow = cgCommIntRow->getSize();
100 <    int nGroupsInCol = cgCommIntColumn->getSize();
97 > #ifdef IS_MPI
98 >
99 >    MPI::Intracomm row = rowComm.getComm();
100 >    MPI::Intracomm col = colComm.getComm();
101  
102 +    AtomPlanIntRow = new Plan<int>(row, nLocal_);
103 +    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
104 +    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
105 +    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
106 +    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
107 +
108 +    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
109 +    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
110 +    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
111 +    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
112 +    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
113 +
114 +    cgPlanIntRow = new Plan<int>(row, nGroups_);
115 +    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
116 +    cgPlanIntColumn = new Plan<int>(col, nGroups_);
117 +    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
118 +
119 +    nAtomsInRow_ = AtomPlanIntRow->getSize();
120 +    nAtomsInCol_ = AtomPlanIntColumn->getSize();
121 +    nGroupsInRow_ = cgPlanIntRow->getSize();
122 +    nGroupsInCol_ = cgPlanIntColumn->getSize();
123 +
124      // Modify the data storage objects with the correct layouts and sizes:
125 <    atomRowData.resize(nAtomsInRow);
125 >    atomRowData.resize(nAtomsInRow_);
126      atomRowData.setStorageLayout(storageLayout_);
127 <    atomColData.resize(nAtomsInCol);
127 >    atomColData.resize(nAtomsInCol_);
128      atomColData.setStorageLayout(storageLayout_);
129 <    cgRowData.resize(nGroupsInRow);
129 >    cgRowData.resize(nGroupsInRow_);
130      cgRowData.setStorageLayout(DataStorage::dslPosition);
131 <    cgColData.resize(nGroupsInCol);
131 >    cgColData.resize(nGroupsInCol_);
132      cgColData.setStorageLayout(DataStorage::dslPosition);
133 +        
134 +    identsRow.resize(nAtomsInRow_);
135 +    identsCol.resize(nAtomsInCol_);
136      
137 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
138 <                                      vector<RealType> (nAtomsInRow, 0.0));
139 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
140 <                                      vector<RealType> (nAtomsInCol, 0.0));
137 >    AtomPlanIntRow->gather(idents, identsRow);
138 >    AtomPlanIntColumn->gather(idents, identsCol);
139 >    
140 >    // allocate memory for the parallel objects
141 >    atypesRow.resize(nAtomsInRow_);
142 >    atypesCol.resize(nAtomsInCol_);
143  
144 +    for (int i = 0; i < nAtomsInRow_; i++)
145 +      atypesRow[i] = ff_->getAtomType(identsRow[i]);
146 +    for (int i = 0; i < nAtomsInCol_; i++)
147 +      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
148  
149 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
149 >    pot_row.resize(nAtomsInRow_);
150 >    pot_col.resize(nAtomsInCol_);
151 >
152 >    AtomRowToGlobal.resize(nAtomsInRow_);
153 >    AtomColToGlobal.resize(nAtomsInCol_);
154 >    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155 >    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156 >
157 >    cgRowToGlobal.resize(nGroupsInRow_);
158 >    cgColToGlobal.resize(nGroupsInCol_);
159 >    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
160 >    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
161 >
162 >    massFactorsRow.resize(nAtomsInRow_);
163 >    massFactorsCol.resize(nAtomsInCol_);
164 >    AtomPlanRealRow->gather(massFactors, massFactorsRow);
165 >    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
166 >
167 >    groupListRow_.clear();
168 >    groupListRow_.resize(nGroupsInRow_);
169 >    for (int i = 0; i < nGroupsInRow_; i++) {
170 >      int gid = cgRowToGlobal[i];
171 >      for (int j = 0; j < nAtomsInRow_; j++) {
172 >        int aid = AtomRowToGlobal[j];
173 >        if (globalGroupMembership[aid] == gid)
174 >          groupListRow_[i].push_back(j);
175 >      }      
176 >    }
177 >
178 >    groupListCol_.clear();
179 >    groupListCol_.resize(nGroupsInCol_);
180 >    for (int i = 0; i < nGroupsInCol_; i++) {
181 >      int gid = cgColToGlobal[i];
182 >      for (int j = 0; j < nAtomsInCol_; j++) {
183 >        int aid = AtomColToGlobal[j];
184 >        if (globalGroupMembership[aid] == gid)
185 >          groupListCol_[i].push_back(j);
186 >      }      
187 >    }
188 >
189 >    excludesForAtom.clear();
190 >    excludesForAtom.resize(nAtomsInRow_);
191 >    toposForAtom.clear();
192 >    toposForAtom.resize(nAtomsInRow_);
193 >    topoDist.clear();
194 >    topoDist.resize(nAtomsInRow_);
195 >    for (int i = 0; i < nAtomsInRow_; i++) {
196 >      int iglob = AtomRowToGlobal[i];
197 >
198 >      for (int j = 0; j < nAtomsInCol_; j++) {
199 >        int jglob = AtomColToGlobal[j];
200 >
201 >        if (excludes->hasPair(iglob, jglob))
202 >          excludesForAtom[i].push_back(j);      
203 >        
204 >        if (oneTwo->hasPair(iglob, jglob)) {
205 >          toposForAtom[i].push_back(j);
206 >          topoDist[i].push_back(1);
207 >        } else {
208 >          if (oneThree->hasPair(iglob, jglob)) {
209 >            toposForAtom[i].push_back(j);
210 >            topoDist[i].push_back(2);
211 >          } else {
212 >            if (oneFour->hasPair(iglob, jglob)) {
213 >              toposForAtom[i].push_back(j);
214 >              topoDist[i].push_back(3);
215 >            }
216 >          }
217 >        }
218 >      }      
219 >    }
220 >
221 > #endif
222 >
223 >    // allocate memory for the parallel objects
224 >    atypesLocal.resize(nLocal_);
225 >
226 >    for (int i = 0; i < nLocal_; i++)
227 >      atypesLocal[i] = ff_->getAtomType(idents[i]);
228 >
229 >    groupList_.clear();
230 >    groupList_.resize(nGroups_);
231 >    for (int i = 0; i < nGroups_; i++) {
232 >      int gid = cgLocalToGlobal[i];
233 >      for (int j = 0; j < nLocal_; j++) {
234 >        int aid = AtomLocalToGlobal[j];
235 >        if (globalGroupMembership[aid] == gid) {
236 >          groupList_[i].push_back(j);
237 >        }
238 >      }      
239 >    }
240 >
241 >    excludesForAtom.clear();
242 >    excludesForAtom.resize(nLocal_);
243 >    toposForAtom.clear();
244 >    toposForAtom.resize(nLocal_);
245 >    topoDist.clear();
246 >    topoDist.resize(nLocal_);
247 >
248 >    for (int i = 0; i < nLocal_; i++) {
249 >      int iglob = AtomLocalToGlobal[i];
250 >
251 >      for (int j = 0; j < nLocal_; j++) {
252 >        int jglob = AtomLocalToGlobal[j];
253 >
254 >        if (excludes->hasPair(iglob, jglob))
255 >          excludesForAtom[i].push_back(j);              
256 >        
257 >        if (oneTwo->hasPair(iglob, jglob)) {
258 >          toposForAtom[i].push_back(j);
259 >          topoDist[i].push_back(1);
260 >        } else {
261 >          if (oneThree->hasPair(iglob, jglob)) {
262 >            toposForAtom[i].push_back(j);
263 >            topoDist[i].push_back(2);
264 >          } else {
265 >            if (oneFour->hasPair(iglob, jglob)) {
266 >              toposForAtom[i].push_back(j);
267 >              topoDist[i].push_back(3);
268 >            }
269 >          }
270 >        }
271 >      }      
272 >    }
273      
274 <    // gather the information for atomtype IDs (atids):
275 <    vector<int> identsLocal = info_->getIdentArray();
276 <    identsRow.reserve(nAtomsInRow);
277 <    identsCol.reserve(nAtomsInCol);
274 >    createGtypeCutoffMap();
275 >
276 >  }
277 >  
278 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
279      
280 <    AtomCommIntRow->gather(identsLocal, identsRow);
281 <    AtomCommIntColumn->gather(identsLocal, identsCol);
280 >    RealType tol = 1e-6;
281 >    largestRcut_ = 0.0;
282 >    RealType rc;
283 >    int atid;
284 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
285      
286 <    AtomLocalToGlobal = info_->getGlobalAtomIndices();
287 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
288 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
286 >    map<int, RealType> atypeCutoff;
287 >      
288 >    for (set<AtomType*>::iterator at = atypes.begin();
289 >         at != atypes.end(); ++at){
290 >      atid = (*at)->getIdent();
291 >      if (userChoseCutoff_)
292 >        atypeCutoff[atid] = userCutoff_;
293 >      else
294 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
295 >    }
296      
297 <    cgLocalToGlobal = info_->getGlobalGroupIndices();
298 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
299 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
300 <
301 <    // still need:
302 <    // topoDist
303 <    // exclude
297 >    vector<RealType> gTypeCutoffs;
298 >    // first we do a single loop over the cutoff groups to find the
299 >    // largest cutoff for any atypes present in this group.
300 > #ifdef IS_MPI
301 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
302 >    groupRowToGtype.resize(nGroupsInRow_);
303 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
304 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
305 >      for (vector<int>::iterator ia = atomListRow.begin();
306 >           ia != atomListRow.end(); ++ia) {            
307 >        int atom1 = (*ia);
308 >        atid = identsRow[atom1];
309 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
310 >          groupCutoffRow[cg1] = atypeCutoff[atid];
311 >        }
312 >      }
313 >
314 >      bool gTypeFound = false;
315 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
316 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
317 >          groupRowToGtype[cg1] = gt;
318 >          gTypeFound = true;
319 >        }
320 >      }
321 >      if (!gTypeFound) {
322 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
323 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
324 >      }
325 >      
326 >    }
327 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
328 >    groupColToGtype.resize(nGroupsInCol_);
329 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
330 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
331 >      for (vector<int>::iterator jb = atomListCol.begin();
332 >           jb != atomListCol.end(); ++jb) {            
333 >        int atom2 = (*jb);
334 >        atid = identsCol[atom2];
335 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
336 >          groupCutoffCol[cg2] = atypeCutoff[atid];
337 >        }
338 >      }
339 >      bool gTypeFound = false;
340 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
341 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
342 >          groupColToGtype[cg2] = gt;
343 >          gTypeFound = true;
344 >        }
345 >      }
346 >      if (!gTypeFound) {
347 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
348 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
349 >      }
350 >    }
351 > #else
352 >
353 >    vector<RealType> groupCutoff(nGroups_, 0.0);
354 >    groupToGtype.resize(nGroups_);
355 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
356 >      groupCutoff[cg1] = 0.0;
357 >      vector<int> atomList = getAtomsInGroupRow(cg1);
358 >      for (vector<int>::iterator ia = atomList.begin();
359 >           ia != atomList.end(); ++ia) {            
360 >        int atom1 = (*ia);
361 >        atid = idents[atom1];
362 >        if (atypeCutoff[atid] > groupCutoff[cg1])
363 >          groupCutoff[cg1] = atypeCutoff[atid];
364 >      }
365 >      
366 >      bool gTypeFound = false;
367 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
368 >        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
369 >          groupToGtype[cg1] = gt;
370 >          gTypeFound = true;
371 >        }
372 >      }
373 >      if (!gTypeFound) {      
374 >        gTypeCutoffs.push_back( groupCutoff[cg1] );
375 >        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
376 >      }      
377 >    }
378   #endif
379 +
380 +    // Now we find the maximum group cutoff value present in the simulation
381 +
382 +    RealType groupMax = *max_element(gTypeCutoffs.begin(),
383 +                                     gTypeCutoffs.end());
384 +
385 + #ifdef IS_MPI
386 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
387 +                              MPI::MAX);
388 + #endif
389 +    
390 +    RealType tradRcut = groupMax;
391 +
392 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
393 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
394 +        RealType thisRcut;
395 +        switch(cutoffPolicy_) {
396 +        case TRADITIONAL:
397 +          thisRcut = tradRcut;
398 +          break;
399 +        case MIX:
400 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
401 +          break;
402 +        case MAX:
403 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
404 +          break;
405 +        default:
406 +          sprintf(painCave.errMsg,
407 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
408 +                  "hit an unknown cutoff policy!\n");
409 +          painCave.severity = OPENMD_ERROR;
410 +          painCave.isFatal = 1;
411 +          simError();
412 +          break;
413 +        }
414 +
415 +        pair<int,int> key = make_pair(i,j);
416 +        gTypeCutoffMap[key].first = thisRcut;
417 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
418 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
419 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
420 +        // sanity check
421 +        
422 +        if (userChoseCutoff_) {
423 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
424 +            sprintf(painCave.errMsg,
425 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
426 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
427 +            painCave.severity = OPENMD_ERROR;
428 +            painCave.isFatal = 1;
429 +            simError();            
430 +          }
431 +        }
432 +      }
433 +    }
434    }
435 +
436 +
437 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
438 +    int i, j;  
439 + #ifdef IS_MPI
440 +    i = groupRowToGtype[cg1];
441 +    j = groupColToGtype[cg2];
442 + #else
443 +    i = groupToGtype[cg1];
444 +    j = groupToGtype[cg2];
445 + #endif    
446 +    return gTypeCutoffMap[make_pair(i,j)];
447 +  }
448 +
449 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
450 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
451 +      if (toposForAtom[atom1][j] == atom2)
452 +        return topoDist[atom1][j];
453 +    }
454 +    return 0;
455 +  }
456 +
457 +  void ForceMatrixDecomposition::zeroWorkArrays() {
458 +    pairwisePot = 0.0;
459 +    embeddingPot = 0.0;
460 +
461 + #ifdef IS_MPI
462 +    if (storageLayout_ & DataStorage::dslForce) {
463 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
464 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
465 +    }
466 +
467 +    if (storageLayout_ & DataStorage::dslTorque) {
468 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
469 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
470 +    }
471      
472 +    fill(pot_row.begin(), pot_row.end(),
473 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
474  
475 +    fill(pot_col.begin(), pot_col.end(),
476 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
477  
478 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
479 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
480 +           0.0);
481 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
482 +           0.0);
483 +    }
484 +
485 +    if (storageLayout_ & DataStorage::dslDensity) {      
486 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
487 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
488 +    }
489 +
490 +    if (storageLayout_ & DataStorage::dslFunctional) {  
491 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
492 +           0.0);
493 +      fill(atomColData.functional.begin(), atomColData.functional.end(),
494 +           0.0);
495 +    }
496 +
497 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
498 +      fill(atomRowData.functionalDerivative.begin(),
499 +           atomRowData.functionalDerivative.end(), 0.0);
500 +      fill(atomColData.functionalDerivative.begin(),
501 +           atomColData.functionalDerivative.end(), 0.0);
502 +    }
503 +
504 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
505 +      fill(atomRowData.skippedCharge.begin(),
506 +           atomRowData.skippedCharge.end(), 0.0);
507 +      fill(atomColData.skippedCharge.begin(),
508 +           atomColData.skippedCharge.end(), 0.0);
509 +    }
510 +
511 + #endif
512 +    // even in parallel, we need to zero out the local arrays:
513 +
514 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
515 +      fill(snap_->atomData.particlePot.begin(),
516 +           snap_->atomData.particlePot.end(), 0.0);
517 +    }
518 +    
519 +    if (storageLayout_ & DataStorage::dslDensity) {      
520 +      fill(snap_->atomData.density.begin(),
521 +           snap_->atomData.density.end(), 0.0);
522 +    }
523 +    if (storageLayout_ & DataStorage::dslFunctional) {
524 +      fill(snap_->atomData.functional.begin(),
525 +           snap_->atomData.functional.end(), 0.0);
526 +    }
527 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
528 +      fill(snap_->atomData.functionalDerivative.begin(),
529 +           snap_->atomData.functionalDerivative.end(), 0.0);
530 +    }
531 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
532 +      fill(snap_->atomData.skippedCharge.begin(),
533 +           snap_->atomData.skippedCharge.end(), 0.0);
534 +    }
535 +    
536 +  }
537 +
538 +
539    void ForceMatrixDecomposition::distributeData()  {
540      snap_ = sman_->getCurrentSnapshot();
541      storageLayout_ = sman_->getStorageLayout();
542   #ifdef IS_MPI
543      
544      // gather up the atomic positions
545 <    AtomCommVectorRow->gather(snap_->atomData.position,
545 >    AtomPlanVectorRow->gather(snap_->atomData.position,
546                                atomRowData.position);
547 <    AtomCommVectorColumn->gather(snap_->atomData.position,
547 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
548                                   atomColData.position);
549      
550      // gather up the cutoff group positions
551 <    cgCommVectorRow->gather(snap_->cgData.position,
551 >
552 >    cgPlanVectorRow->gather(snap_->cgData.position,
553                              cgRowData.position);
554 <    cgCommVectorColumn->gather(snap_->cgData.position,
554 >
555 >    cgPlanVectorColumn->gather(snap_->cgData.position,
556                                 cgColData.position);
557 +
558      
559      // if needed, gather the atomic rotation matrices
560      if (storageLayout_ & DataStorage::dslAmat) {
561 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
561 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
562                                  atomRowData.aMat);
563 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
563 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
564                                     atomColData.aMat);
565      }
566      
567      // if needed, gather the atomic eletrostatic frames
568      if (storageLayout_ & DataStorage::dslElectroFrame) {
569 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
569 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
570                                  atomRowData.electroFrame);
571 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
571 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
572                                     atomColData.electroFrame);
573      }
574 +
575   #endif      
576    }
577    
578 +  /* collects information obtained during the pre-pair loop onto local
579 +   * data structures.
580 +   */
581    void ForceMatrixDecomposition::collectIntermediateData() {
582      snap_ = sman_->getCurrentSnapshot();
583      storageLayout_ = sman_->getStorageLayout();
# Line 162 | Line 585 | namespace OpenMD {
585      
586      if (storageLayout_ & DataStorage::dslDensity) {
587        
588 <      AtomCommRealRow->scatter(atomRowData.density,
588 >      AtomPlanRealRow->scatter(atomRowData.density,
589                                 snap_->atomData.density);
590        
591        int n = snap_->atomData.density.size();
592 <      std::vector<RealType> rho_tmp(n, 0.0);
593 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
592 >      vector<RealType> rho_tmp(n, 0.0);
593 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
594        for (int i = 0; i < n; i++)
595          snap_->atomData.density[i] += rho_tmp[i];
596      }
597   #endif
598    }
599 <  
599 >
600 >  /*
601 >   * redistributes information obtained during the pre-pair loop out to
602 >   * row and column-indexed data structures
603 >   */
604    void ForceMatrixDecomposition::distributeIntermediateData() {
605      snap_ = sman_->getCurrentSnapshot();
606      storageLayout_ = sman_->getStorageLayout();
607   #ifdef IS_MPI
608      if (storageLayout_ & DataStorage::dslFunctional) {
609 <      AtomCommRealRow->gather(snap_->atomData.functional,
609 >      AtomPlanRealRow->gather(snap_->atomData.functional,
610                                atomRowData.functional);
611 <      AtomCommRealColumn->gather(snap_->atomData.functional,
611 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
612                                   atomColData.functional);
613      }
614      
615      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
616 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
616 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
617                                atomRowData.functionalDerivative);
618 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
618 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
619                                   atomColData.functionalDerivative);
620      }
621   #endif
# Line 202 | Line 629 | namespace OpenMD {
629      int n = snap_->atomData.force.size();
630      vector<Vector3d> frc_tmp(n, V3Zero);
631      
632 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
632 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
633      for (int i = 0; i < n; i++) {
634        snap_->atomData.force[i] += frc_tmp[i];
635        frc_tmp[i] = 0.0;
636      }
637      
638 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
639 <    for (int i = 0; i < n; i++)
638 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
639 >    for (int i = 0; i < n; i++) {
640        snap_->atomData.force[i] += frc_tmp[i];
641 <    
642 <    
641 >    }
642 >        
643      if (storageLayout_ & DataStorage::dslTorque) {
644  
645 <      int nt = snap_->atomData.force.size();
645 >      int nt = snap_->atomData.torque.size();
646        vector<Vector3d> trq_tmp(nt, V3Zero);
647  
648 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
649 <      for (int i = 0; i < n; i++) {
648 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
649 >      for (int i = 0; i < nt; i++) {
650          snap_->atomData.torque[i] += trq_tmp[i];
651          trq_tmp[i] = 0.0;
652        }
653        
654 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
655 <      for (int i = 0; i < n; i++)
654 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
655 >      for (int i = 0; i < nt; i++)
656          snap_->atomData.torque[i] += trq_tmp[i];
657      }
658 +
659 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
660 +
661 +      int ns = snap_->atomData.skippedCharge.size();
662 +      vector<RealType> skch_tmp(ns, 0.0);
663 +
664 +      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
665 +      for (int i = 0; i < ns; i++) {
666 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
667 +        skch_tmp[i] = 0.0;
668 +      }
669 +      
670 +      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
671 +      for (int i = 0; i < ns; i++)
672 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
673 +    }
674      
675 <    int nLocal = snap_->getNumberOfAtoms();
675 >    nLocal_ = snap_->getNumberOfAtoms();
676  
677 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
678 <                                       vector<RealType> (nLocal, 0.0));
677 >    vector<potVec> pot_temp(nLocal_,
678 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
679 >
680 >    // scatter/gather pot_row into the members of my column
681 >          
682 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
683 >
684 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
685 >      pairwisePot += pot_temp[ii];
686      
687 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
688 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
689 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
690 <        pot_local[i] += pot_temp[i][ii];
691 <      }
687 >    fill(pot_temp.begin(), pot_temp.end(),
688 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
689 >      
690 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
691 >    
692 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
693 >      pairwisePot += pot_temp[ii];    
694 >    
695 >    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
696 >      RealType ploc1 = pairwisePot[ii];
697 >      RealType ploc2 = 0.0;
698 >      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
699 >      pairwisePot[ii] = ploc2;
700      }
701 +
702   #endif
703 +
704    }
705  
706 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
707 + #ifdef IS_MPI
708 +    return nAtomsInRow_;
709 + #else
710 +    return nLocal_;
711 + #endif
712 +  }
713 +
714 +  /**
715 +   * returns the list of atoms belonging to this group.  
716 +   */
717 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
718 + #ifdef IS_MPI
719 +    return groupListRow_[cg1];
720 + #else
721 +    return groupList_[cg1];
722 + #endif
723 +  }
724 +
725 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
726 + #ifdef IS_MPI
727 +    return groupListCol_[cg2];
728 + #else
729 +    return groupList_[cg2];
730 + #endif
731 +  }
732    
733    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
734      Vector3d d;
# Line 284 | Line 770 | namespace OpenMD {
770      snap_->wrapVector(d);
771      return d;    
772    }
773 +
774 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
775 + #ifdef IS_MPI
776 +    return massFactorsRow[atom1];
777 + #else
778 +    return massFactors[atom1];
779 + #endif
780 +  }
781 +
782 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
783 + #ifdef IS_MPI
784 +    return massFactorsCol[atom2];
785 + #else
786 +    return massFactors[atom2];
787 + #endif
788 +
789 +  }
790      
791    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
792      Vector3d d;
# Line 298 | Line 801 | namespace OpenMD {
801      return d;    
802    }
803  
804 +  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
805 +    return excludesForAtom[atom1];
806 +  }
807 +
808 +  /**
809 +   * We need to exclude some overcounted interactions that result from
810 +   * the parallel decomposition.
811 +   */
812 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
813 +    int unique_id_1, unique_id_2;
814 +    
815 + #ifdef IS_MPI
816 +    // in MPI, we have to look up the unique IDs for each atom
817 +    unique_id_1 = AtomRowToGlobal[atom1];
818 +    unique_id_2 = AtomColToGlobal[atom2];
819 +
820 +    // this situation should only arise in MPI simulations
821 +    if (unique_id_1 == unique_id_2) return true;
822 +    
823 +    // this prevents us from doing the pair on multiple processors
824 +    if (unique_id_1 < unique_id_2) {
825 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
826 +    } else {
827 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
828 +    }
829 + #endif
830 +    return false;
831 +  }
832 +
833 +  /**
834 +   * We need to handle the interactions for atoms who are involved in
835 +   * the same rigid body as well as some short range interactions
836 +   * (bonds, bends, torsions) differently from other interactions.
837 +   * We'll still visit the pairwise routines, but with a flag that
838 +   * tells those routines to exclude the pair from direct long range
839 +   * interactions.  Some indirect interactions (notably reaction
840 +   * field) must still be handled for these pairs.
841 +   */
842 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
843 +    int unique_id_2;
844 + #ifdef IS_MPI
845 +    // in MPI, we have to look up the unique IDs for the row atom.
846 +    unique_id_2 = AtomColToGlobal[atom2];
847 + #else
848 +    // in the normal loop, the atom numbers are unique
849 +    unique_id_2 = atom2;
850 + #endif
851 +    
852 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
853 +         i != excludesForAtom[atom1].end(); ++i) {
854 +      if ( (*i) == unique_id_2 ) return true;
855 +    }
856 +
857 +    return false;
858 +  }
859 +
860 +
861    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
862   #ifdef IS_MPI
863      atomRowData.force[atom1] += fg;
# Line 312 | Line 872 | namespace OpenMD {
872   #else
873      snap_->atomData.force[atom2] += fg;
874   #endif
315 –
875    }
876  
877      // filling interaction blocks with pointers
878 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
878 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
879 >                                                     int atom1, int atom2) {
880  
881 <    InteractionData idat;
881 >    idat.excluded = excludeAtomPair(atom1, atom2);
882 >  
883   #ifdef IS_MPI
884 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
885 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
886 +    //                         ff_->getAtomType(identsCol[atom2]) );
887 +    
888      if (storageLayout_ & DataStorage::dslAmat) {
889        idat.A1 = &(atomRowData.aMat[atom1]);
890        idat.A2 = &(atomColData.aMat[atom2]);
891      }
892 <
892 >    
893      if (storageLayout_ & DataStorage::dslElectroFrame) {
894        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
895        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
# Line 340 | Line 905 | namespace OpenMD {
905        idat.rho2 = &(atomColData.density[atom2]);
906      }
907  
908 +    if (storageLayout_ & DataStorage::dslFunctional) {
909 +      idat.frho1 = &(atomRowData.functional[atom1]);
910 +      idat.frho2 = &(atomColData.functional[atom2]);
911 +    }
912 +
913      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
914        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
915        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
916 +    }
917 +
918 +    if (storageLayout_ & DataStorage::dslParticlePot) {
919 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
920 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
921 +    }
922 +
923 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
924 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
925 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
926 +    }
927 +
928 + #else
929 +
930 +    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
931 +    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
932 +    //                         ff_->getAtomType(idents[atom2]) );
933 +
934 +    if (storageLayout_ & DataStorage::dslAmat) {
935 +      idat.A1 = &(snap_->atomData.aMat[atom1]);
936 +      idat.A2 = &(snap_->atomData.aMat[atom2]);
937 +    }
938 +
939 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
940 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
941 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
942 +    }
943 +
944 +    if (storageLayout_ & DataStorage::dslTorque) {
945 +      idat.t1 = &(snap_->atomData.torque[atom1]);
946 +      idat.t2 = &(snap_->atomData.torque[atom2]);
947 +    }
948 +
949 +    if (storageLayout_ & DataStorage::dslDensity) {    
950 +      idat.rho1 = &(snap_->atomData.density[atom1]);
951 +      idat.rho2 = &(snap_->atomData.density[atom2]);
952 +    }
953 +
954 +    if (storageLayout_ & DataStorage::dslFunctional) {
955 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
956 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
957 +    }
958 +
959 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
960 +      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
961 +      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
962 +    }
963 +
964 +    if (storageLayout_ & DataStorage::dslParticlePot) {
965 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
966 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
967 +    }
968 +
969 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
970 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
971 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
972      }
973   #endif
348 –    
974    }
350 –  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
351 –  }
352 –  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
353 –  }
975  
976    
977 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
978 + #ifdef IS_MPI
979 +    pot_row[atom1] += 0.5 *  *(idat.pot);
980 +    pot_col[atom2] += 0.5 *  *(idat.pot);
981 +
982 +    atomRowData.force[atom1] += *(idat.f1);
983 +    atomColData.force[atom2] -= *(idat.f1);
984 + #else
985 +    pairwisePot += *(idat.pot);
986 +
987 +    snap_->atomData.force[atom1] += *(idat.f1);
988 +    snap_->atomData.force[atom2] -= *(idat.f1);
989 + #endif
990 +    
991 +  }
992 +
993 +  /*
994 +   * buildNeighborList
995 +   *
996 +   * first element of pair is row-indexed CutoffGroup
997 +   * second element of pair is column-indexed CutoffGroup
998 +   */
999 +  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1000 +      
1001 +    vector<pair<int, int> > neighborList;
1002 +    groupCutoffs cuts;
1003 +    bool doAllPairs = false;
1004 +
1005 + #ifdef IS_MPI
1006 +    cellListRow_.clear();
1007 +    cellListCol_.clear();
1008 + #else
1009 +    cellList_.clear();
1010 + #endif
1011 +
1012 +    RealType rList_ = (largestRcut_ + skinThickness_);
1013 +    RealType rl2 = rList_ * rList_;
1014 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
1015 +    Mat3x3d Hmat = snap_->getHmat();
1016 +    Vector3d Hx = Hmat.getColumn(0);
1017 +    Vector3d Hy = Hmat.getColumn(1);
1018 +    Vector3d Hz = Hmat.getColumn(2);
1019 +
1020 +    nCells_.x() = (int) ( Hx.length() )/ rList_;
1021 +    nCells_.y() = (int) ( Hy.length() )/ rList_;
1022 +    nCells_.z() = (int) ( Hz.length() )/ rList_;
1023 +
1024 +    // handle small boxes where the cell offsets can end up repeating cells
1025 +    
1026 +    if (nCells_.x() < 3) doAllPairs = true;
1027 +    if (nCells_.y() < 3) doAllPairs = true;
1028 +    if (nCells_.z() < 3) doAllPairs = true;
1029 +
1030 +    Mat3x3d invHmat = snap_->getInvHmat();
1031 +    Vector3d rs, scaled, dr;
1032 +    Vector3i whichCell;
1033 +    int cellIndex;
1034 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1035 +
1036 + #ifdef IS_MPI
1037 +    cellListRow_.resize(nCtot);
1038 +    cellListCol_.resize(nCtot);
1039 + #else
1040 +    cellList_.resize(nCtot);
1041 + #endif
1042 +
1043 +    if (!doAllPairs) {
1044 + #ifdef IS_MPI
1045 +
1046 +      for (int i = 0; i < nGroupsInRow_; i++) {
1047 +        rs = cgRowData.position[i];
1048 +        
1049 +        // scaled positions relative to the box vectors
1050 +        scaled = invHmat * rs;
1051 +        
1052 +        // wrap the vector back into the unit box by subtracting integer box
1053 +        // numbers
1054 +        for (int j = 0; j < 3; j++) {
1055 +          scaled[j] -= roundMe(scaled[j]);
1056 +          scaled[j] += 0.5;
1057 +        }
1058 +        
1059 +        // find xyz-indices of cell that cutoffGroup is in.
1060 +        whichCell.x() = nCells_.x() * scaled.x();
1061 +        whichCell.y() = nCells_.y() * scaled.y();
1062 +        whichCell.z() = nCells_.z() * scaled.z();
1063 +        
1064 +        // find single index of this cell:
1065 +        cellIndex = Vlinear(whichCell, nCells_);
1066 +        
1067 +        // add this cutoff group to the list of groups in this cell;
1068 +        cellListRow_[cellIndex].push_back(i);
1069 +      }
1070 +      for (int i = 0; i < nGroupsInCol_; i++) {
1071 +        rs = cgColData.position[i];
1072 +        
1073 +        // scaled positions relative to the box vectors
1074 +        scaled = invHmat * rs;
1075 +        
1076 +        // wrap the vector back into the unit box by subtracting integer box
1077 +        // numbers
1078 +        for (int j = 0; j < 3; j++) {
1079 +          scaled[j] -= roundMe(scaled[j]);
1080 +          scaled[j] += 0.5;
1081 +        }
1082 +        
1083 +        // find xyz-indices of cell that cutoffGroup is in.
1084 +        whichCell.x() = nCells_.x() * scaled.x();
1085 +        whichCell.y() = nCells_.y() * scaled.y();
1086 +        whichCell.z() = nCells_.z() * scaled.z();
1087 +        
1088 +        // find single index of this cell:
1089 +        cellIndex = Vlinear(whichCell, nCells_);
1090 +        
1091 +        // add this cutoff group to the list of groups in this cell;
1092 +        cellListCol_[cellIndex].push_back(i);
1093 +      }
1094 + #else
1095 +      for (int i = 0; i < nGroups_; i++) {
1096 +        rs = snap_->cgData.position[i];
1097 +        
1098 +        // scaled positions relative to the box vectors
1099 +        scaled = invHmat * rs;
1100 +        
1101 +        // wrap the vector back into the unit box by subtracting integer box
1102 +        // numbers
1103 +        for (int j = 0; j < 3; j++) {
1104 +          scaled[j] -= roundMe(scaled[j]);
1105 +          scaled[j] += 0.5;
1106 +        }
1107 +        
1108 +        // find xyz-indices of cell that cutoffGroup is in.
1109 +        whichCell.x() = nCells_.x() * scaled.x();
1110 +        whichCell.y() = nCells_.y() * scaled.y();
1111 +        whichCell.z() = nCells_.z() * scaled.z();
1112 +        
1113 +        // find single index of this cell:
1114 +        cellIndex = Vlinear(whichCell, nCells_);
1115 +        
1116 +        // add this cutoff group to the list of groups in this cell;
1117 +        cellList_[cellIndex].push_back(i);
1118 +      }
1119 + #endif
1120 +
1121 +      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1122 +        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1123 +          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1124 +            Vector3i m1v(m1x, m1y, m1z);
1125 +            int m1 = Vlinear(m1v, nCells_);
1126 +            
1127 +            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1128 +                 os != cellOffsets_.end(); ++os) {
1129 +              
1130 +              Vector3i m2v = m1v + (*os);
1131 +              
1132 +              if (m2v.x() >= nCells_.x()) {
1133 +                m2v.x() = 0;          
1134 +              } else if (m2v.x() < 0) {
1135 +                m2v.x() = nCells_.x() - 1;
1136 +              }
1137 +              
1138 +              if (m2v.y() >= nCells_.y()) {
1139 +                m2v.y() = 0;          
1140 +              } else if (m2v.y() < 0) {
1141 +                m2v.y() = nCells_.y() - 1;
1142 +              }
1143 +              
1144 +              if (m2v.z() >= nCells_.z()) {
1145 +                m2v.z() = 0;          
1146 +              } else if (m2v.z() < 0) {
1147 +                m2v.z() = nCells_.z() - 1;
1148 +              }
1149 +              
1150 +              int m2 = Vlinear (m2v, nCells_);
1151 +              
1152 + #ifdef IS_MPI
1153 +              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1154 +                   j1 != cellListRow_[m1].end(); ++j1) {
1155 +                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1156 +                     j2 != cellListCol_[m2].end(); ++j2) {
1157 +                  
1158 +                  // In parallel, we need to visit *all* pairs of row &
1159 +                  // column indicies and will truncate later on.
1160 +                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1161 +                  snap_->wrapVector(dr);
1162 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1163 +                  if (dr.lengthSquare() < cuts.third) {
1164 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1165 +                  }                  
1166 +                }
1167 +              }
1168 + #else
1169 +              
1170 +              for (vector<int>::iterator j1 = cellList_[m1].begin();
1171 +                   j1 != cellList_[m1].end(); ++j1) {
1172 +                for (vector<int>::iterator j2 = cellList_[m2].begin();
1173 +                     j2 != cellList_[m2].end(); ++j2) {
1174 +                  
1175 +                  // Always do this if we're in different cells or if
1176 +                  // we're in the same cell and the global index of the
1177 +                  // j2 cutoff group is less than the j1 cutoff group
1178 +                  
1179 +                  if (m2 != m1 || (*j2) < (*j1)) {
1180 +                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1181 +                    snap_->wrapVector(dr);
1182 +                    cuts = getGroupCutoffs( (*j1), (*j2) );
1183 +                    if (dr.lengthSquare() < cuts.third) {
1184 +                      neighborList.push_back(make_pair((*j1), (*j2)));
1185 +                    }
1186 +                  }
1187 +                }
1188 +              }
1189 + #endif
1190 +            }
1191 +          }
1192 +        }
1193 +      }
1194 +    } else {
1195 +      // branch to do all cutoff group pairs
1196 + #ifdef IS_MPI
1197 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1198 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1199 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1200 +          snap_->wrapVector(dr);
1201 +          cuts = getGroupCutoffs( j1, j2 );
1202 +          if (dr.lengthSquare() < cuts.third) {
1203 +            neighborList.push_back(make_pair(j1, j2));
1204 +          }
1205 +        }
1206 +      }
1207 + #else
1208 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1209 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1210 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1211 +          snap_->wrapVector(dr);
1212 +          cuts = getGroupCutoffs( j1, j2 );
1213 +          if (dr.lengthSquare() < cuts.third) {
1214 +            neighborList.push_back(make_pair(j1, j2));
1215 +          }
1216 +        }
1217 +      }        
1218 + #endif
1219 +    }
1220 +      
1221 +    // save the local cutoff group positions for the check that is
1222 +    // done on each loop:
1223 +    saved_CG_positions_.clear();
1224 +    for (int i = 0; i < nGroups_; i++)
1225 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1226 +    
1227 +    return neighborList;
1228 +  }
1229   } //end namespace OpenMD

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