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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 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs.
Revision 1592 by gezelter, Tue Jul 12 20:33:14 2011 UTC

# Line 55 | Line 55 | namespace OpenMD {
55    void ForceMatrixDecomposition::distributeInitialData() {
56      snap_ = sman_->getCurrentSnapshot();
57      storageLayout_ = sman_->getStorageLayout();
58 +    ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
60 <    nGroups_ = snap_->getNumberOfCutoffGroups();
61 <
60 >    
61 >    nGroups_ = info_->getNLocalCutoffGroups();
62      // gather the information for atomtype IDs (atids):
63 <    vector<int> identsLocal = info_->getIdentArray();
63 >    idents = info_->getIdentArray();
64      AtomLocalToGlobal = info_->getGlobalAtomIndices();
65      cgLocalToGlobal = info_->getGlobalGroupIndices();
66      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
66 –    vector<RealType> massFactorsLocal = info_->getMassFactors();
67 –    PairList excludes = info_->getExcludedInteractions();
68 –    PairList oneTwo = info_->getOneTwoInteractions();
69 –    PairList oneThree = info_->getOneThreeInteractions();
70 –    PairList oneFour = info_->getOneFourInteractions();
71 –    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
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  
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      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_);
# Line 101 | Line 105 | namespace OpenMD {
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 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
113 <                                      vector<RealType> (nAtomsInRow_, 0.0));
107 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
108 <                                      vector<RealType> (nAtomsInCol_, 0.0));
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
115 <    identsRow.reserve(nAtomsInRow_);
116 <    identsCol.reserve(nAtomsInCol_);
117 <    
118 <    AtomCommIntRow->gather(identsLocal, identsRow);
119 <    AtomCommIntColumn->gather(identsLocal, identsCol);
120 <    
115 >    // allocate memory for the parallel objects
116 >    atypesRow.resize(nAtomsInRow_);
117 >    atypesCol.resize(nAtomsInCol_);
118 >
119 >    for (int i = 0; i < nAtomsInRow_; i++)
120 >      atypesRow[i] = ff_->getAtomType(identsRow[i]);
121 >    for (int i = 0; i < nAtomsInCol_; i++)
122 >      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
123 >
124 >    pot_row.resize(nAtomsInRow_);
125 >    pot_col.resize(nAtomsInCol_);
126 >
127 >    AtomRowToGlobal.resize(nAtomsInRow_);
128 >    AtomColToGlobal.resize(nAtomsInCol_);
129      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
130      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
131      
132 +    cgRowToGlobal.resize(nGroupsInRow_);
133 +    cgColToGlobal.resize(nGroupsInCol_);
134      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
135      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
136  
137 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
138 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
137 >    massFactorsRow.resize(nAtomsInRow_);
138 >    massFactorsCol.resize(nAtomsInCol_);
139 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
140 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
141  
142      groupListRow_.clear();
143 <    groupListRow_.reserve(nGroupsInRow_);
143 >    groupListRow_.resize(nGroupsInRow_);
144      for (int i = 0; i < nGroupsInRow_; i++) {
145        int gid = cgRowToGlobal[i];
146        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 134 | Line 151 | namespace OpenMD {
151      }
152  
153      groupListCol_.clear();
154 <    groupListCol_.reserve(nGroupsInCol_);
154 >    groupListCol_.resize(nGroupsInCol_);
155      for (int i = 0; i < nGroupsInCol_; i++) {
156        int gid = cgColToGlobal[i];
157        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 144 | Line 161 | namespace OpenMD {
161        }      
162      }
163  
164 <    skipsForRowAtom.clear();
165 <    skipsForRowAtom.reserve(nAtomsInRow_);
164 >    excludesForAtom.clear();
165 >    excludesForAtom.resize(nAtomsInRow_);
166 >    toposForAtom.clear();
167 >    toposForAtom.resize(nAtomsInRow_);
168 >    topoDist.clear();
169 >    topoDist.resize(nAtomsInRow_);
170      for (int i = 0; i < nAtomsInRow_; i++) {
171 <      int iglob = AtomColToGlobal[i];
151 <      for (int j = 0; j < nAtomsInCol_; j++) {
152 <        int jglob = AtomRowToGlobal[j];        
153 <        if (excludes.hasPair(iglob, jglob))
154 <          skipsForRowAtom[i].push_back(j);      
155 <      }      
156 <    }
171 >      int iglob = AtomRowToGlobal[i];
172  
158 –    toposForRowAtom.clear();
159 –    toposForRowAtom.reserve(nAtomsInRow_);
160 –    for (int i = 0; i < nAtomsInRow_; i++) {
161 –      int iglob = AtomColToGlobal[i];
162 –      int nTopos = 0;
173        for (int j = 0; j < nAtomsInCol_; j++) {
174 <        int jglob = AtomRowToGlobal[j];        
175 <        if (oneTwo.hasPair(iglob, jglob)) {
176 <          toposForRowAtom[i].push_back(j);
177 <          topoDistRow[i][nTopos] = 1;
178 <          nTopos++;
174 >        int jglob = AtomColToGlobal[j];
175 >
176 >        if (excludes->hasPair(iglob, jglob))
177 >          excludesForAtom[i].push_back(j);      
178 >        
179 >        if (oneTwo->hasPair(iglob, jglob)) {
180 >          toposForAtom[i].push_back(j);
181 >          topoDist[i].push_back(1);
182 >        } else {
183 >          if (oneThree->hasPair(iglob, jglob)) {
184 >            toposForAtom[i].push_back(j);
185 >            topoDist[i].push_back(2);
186 >          } else {
187 >            if (oneFour->hasPair(iglob, jglob)) {
188 >              toposForAtom[i].push_back(j);
189 >              topoDist[i].push_back(3);
190 >            }
191 >          }
192          }
170 –        if (oneThree.hasPair(iglob, jglob)) {
171 –          toposForRowAtom[i].push_back(j);
172 –          topoDistRow[i][nTopos] = 2;
173 –          nTopos++;
174 –        }
175 –        if (oneFour.hasPair(iglob, jglob)) {
176 –          toposForRowAtom[i].push_back(j);
177 –          topoDistRow[i][nTopos] = 3;
178 –          nTopos++;
179 –        }
193        }      
194      }
195  
196   #endif
197  
198 +    // allocate memory for the parallel objects
199 +    atypesLocal.resize(nLocal_);
200 +
201 +    for (int i = 0; i < nLocal_; i++)
202 +      atypesLocal[i] = ff_->getAtomType(idents[i]);
203 +
204      groupList_.clear();
205 <    groupList_.reserve(nGroups_);
205 >    groupList_.resize(nGroups_);
206      for (int i = 0; i < nGroups_; i++) {
207        int gid = cgLocalToGlobal[i];
208        for (int j = 0; j < nLocal_; j++) {
209          int aid = AtomLocalToGlobal[j];
210 <        if (globalGroupMembership[aid] == gid)
210 >        if (globalGroupMembership[aid] == gid) {
211            groupList_[i].push_back(j);
212 +        }
213        }      
214      }
215  
216 <    skipsForLocalAtom.clear();
217 <    skipsForLocalAtom.reserve(nLocal_);
216 >    excludesForAtom.clear();
217 >    excludesForAtom.resize(nLocal_);
218 >    toposForAtom.clear();
219 >    toposForAtom.resize(nLocal_);
220 >    topoDist.clear();
221 >    topoDist.resize(nLocal_);
222  
223      for (int i = 0; i < nLocal_; i++) {
224        int iglob = AtomLocalToGlobal[i];
225 +
226        for (int j = 0; j < nLocal_; j++) {
227 <        int jglob = AtomLocalToGlobal[j];        
228 <        if (excludes.hasPair(iglob, jglob))
229 <          skipsForLocalAtom[i].push_back(j);      
227 >        int jglob = AtomLocalToGlobal[j];
228 >
229 >        if (excludes->hasPair(iglob, jglob))
230 >          excludesForAtom[i].push_back(j);              
231 >        
232 >        if (oneTwo->hasPair(iglob, jglob)) {
233 >          toposForAtom[i].push_back(j);
234 >          topoDist[i].push_back(1);
235 >        } else {
236 >          if (oneThree->hasPair(iglob, jglob)) {
237 >            toposForAtom[i].push_back(j);
238 >            topoDist[i].push_back(2);
239 >          } else {
240 >            if (oneFour->hasPair(iglob, jglob)) {
241 >              toposForAtom[i].push_back(j);
242 >              topoDist[i].push_back(3);
243 >            }
244 >          }
245 >        }
246        }      
247      }
248 +    
249 +    createGtypeCutoffMap();
250  
251 <    toposForLocalAtom.clear();
252 <    toposForLocalAtom.reserve(nLocal_);
253 <    for (int i = 0; i < nLocal_; i++) {
254 <      int iglob = AtomLocalToGlobal[i];
255 <      int nTopos = 0;
256 <      for (int j = 0; j < nLocal_; j++) {
257 <        int jglob = AtomLocalToGlobal[j];        
258 <        if (oneTwo.hasPair(iglob, jglob)) {
259 <          toposForLocalAtom[i].push_back(j);
260 <          topoDistLocal[i][nTopos] = 1;
261 <          nTopos++;
251 >  }
252 >  
253 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
254 >    
255 >    RealType tol = 1e-6;
256 >    largestRcut_ = 0.0;
257 >    RealType rc;
258 >    int atid;
259 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
260 >    
261 >    map<int, RealType> atypeCutoff;
262 >      
263 >    for (set<AtomType*>::iterator at = atypes.begin();
264 >         at != atypes.end(); ++at){
265 >      atid = (*at)->getIdent();
266 >      if (userChoseCutoff_)
267 >        atypeCutoff[atid] = userCutoff_;
268 >      else
269 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
270 >    }
271 >    
272 >    vector<RealType> gTypeCutoffs;
273 >    // first we do a single loop over the cutoff groups to find the
274 >    // largest cutoff for any atypes present in this group.
275 > #ifdef IS_MPI
276 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
277 >    groupRowToGtype.resize(nGroupsInRow_);
278 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
279 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
280 >      for (vector<int>::iterator ia = atomListRow.begin();
281 >           ia != atomListRow.end(); ++ia) {            
282 >        int atom1 = (*ia);
283 >        atid = identsRow[atom1];
284 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
285 >          groupCutoffRow[cg1] = atypeCutoff[atid];
286          }
287 <        if (oneThree.hasPair(iglob, jglob)) {
288 <          toposForLocalAtom[i].push_back(j);
289 <          topoDistLocal[i][nTopos] = 2;
290 <          nTopos++;
287 >      }
288 >
289 >      bool gTypeFound = false;
290 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
291 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
292 >          groupRowToGtype[cg1] = gt;
293 >          gTypeFound = true;
294 >        }
295 >      }
296 >      if (!gTypeFound) {
297 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
298 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
299 >      }
300 >      
301 >    }
302 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
303 >    groupColToGtype.resize(nGroupsInCol_);
304 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
305 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
306 >      for (vector<int>::iterator jb = atomListCol.begin();
307 >           jb != atomListCol.end(); ++jb) {            
308 >        int atom2 = (*jb);
309 >        atid = identsCol[atom2];
310 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
311 >          groupCutoffCol[cg2] = atypeCutoff[atid];
312          }
313 <        if (oneFour.hasPair(iglob, jglob)) {
314 <          toposForLocalAtom[i].push_back(j);
315 <          topoDistLocal[i][nTopos] = 3;
316 <          nTopos++;
317 <        }
313 >      }
314 >      bool gTypeFound = false;
315 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
316 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
317 >          groupColToGtype[cg2] = gt;
318 >          gTypeFound = true;
319 >        }
320 >      }
321 >      if (!gTypeFound) {
322 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
323 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
324 >      }
325 >    }
326 > #else
327 >
328 >    vector<RealType> groupCutoff(nGroups_, 0.0);
329 >    groupToGtype.resize(nGroups_);
330 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
331 >      groupCutoff[cg1] = 0.0;
332 >      vector<int> atomList = getAtomsInGroupRow(cg1);
333 >      for (vector<int>::iterator ia = atomList.begin();
334 >           ia != atomList.end(); ++ia) {            
335 >        int atom1 = (*ia);
336 >        atid = idents[atom1];
337 >        if (atypeCutoff[atid] > groupCutoff[cg1])
338 >          groupCutoff[cg1] = atypeCutoff[atid];
339 >      }
340 >      
341 >      bool gTypeFound = false;
342 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
343 >        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
344 >          groupToGtype[cg1] = gt;
345 >          gTypeFound = true;
346 >        }
347 >      }
348 >      if (!gTypeFound) {      
349 >        gTypeCutoffs.push_back( groupCutoff[cg1] );
350 >        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
351        }      
352      }
353 + #endif
354 +
355 +    // Now we find the maximum group cutoff value present in the simulation
356 +
357 +    RealType groupMax = *max_element(gTypeCutoffs.begin(),
358 +                                     gTypeCutoffs.end());
359 +
360 + #ifdef IS_MPI
361 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
362 +                              MPI::MAX);
363 + #endif
364 +    
365 +    RealType tradRcut = groupMax;
366 +
367 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
368 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
369 +        RealType thisRcut;
370 +        switch(cutoffPolicy_) {
371 +        case TRADITIONAL:
372 +          thisRcut = tradRcut;
373 +          break;
374 +        case MIX:
375 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
376 +          break;
377 +        case MAX:
378 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
379 +          break;
380 +        default:
381 +          sprintf(painCave.errMsg,
382 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
383 +                  "hit an unknown cutoff policy!\n");
384 +          painCave.severity = OPENMD_ERROR;
385 +          painCave.isFatal = 1;
386 +          simError();
387 +          break;
388 +        }
389 +
390 +        pair<int,int> key = make_pair(i,j);
391 +        gTypeCutoffMap[key].first = thisRcut;
392 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
393 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
394 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
395 +        // sanity check
396 +        
397 +        if (userChoseCutoff_) {
398 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
399 +            sprintf(painCave.errMsg,
400 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
401 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
402 +            painCave.severity = OPENMD_ERROR;
403 +            painCave.isFatal = 1;
404 +            simError();            
405 +          }
406 +        }
407 +      }
408 +    }
409    }
410 <  
410 >
411 >
412 >  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
413 >    int i, j;  
414 > #ifdef IS_MPI
415 >    i = groupRowToGtype[cg1];
416 >    j = groupColToGtype[cg2];
417 > #else
418 >    i = groupToGtype[cg1];
419 >    j = groupToGtype[cg2];
420 > #endif    
421 >    return gTypeCutoffMap[make_pair(i,j)];
422 >  }
423 >
424 >  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
425 >    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
426 >      if (toposForAtom[atom1][j] == atom2)
427 >        return topoDist[atom1][j];
428 >    }
429 >    return 0;
430 >  }
431 >
432 >  void ForceMatrixDecomposition::zeroWorkArrays() {
433 >    pairwisePot = 0.0;
434 >    embeddingPot = 0.0;
435 >
436 > #ifdef IS_MPI
437 >    if (storageLayout_ & DataStorage::dslForce) {
438 >      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
439 >      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
440 >    }
441 >
442 >    if (storageLayout_ & DataStorage::dslTorque) {
443 >      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
444 >      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
445 >    }
446 >    
447 >    fill(pot_row.begin(), pot_row.end(),
448 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
449 >
450 >    fill(pot_col.begin(), pot_col.end(),
451 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
452 >
453 >    if (storageLayout_ & DataStorage::dslParticlePot) {    
454 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
455 >           0.0);
456 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
457 >           0.0);
458 >    }
459 >
460 >    if (storageLayout_ & DataStorage::dslDensity) {      
461 >      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
462 >      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
463 >    }
464 >
465 >    if (storageLayout_ & DataStorage::dslFunctional) {  
466 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
467 >           0.0);
468 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
469 >           0.0);
470 >    }
471 >
472 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
473 >      fill(atomRowData.functionalDerivative.begin(),
474 >           atomRowData.functionalDerivative.end(), 0.0);
475 >      fill(atomColData.functionalDerivative.begin(),
476 >           atomColData.functionalDerivative.end(), 0.0);
477 >    }
478 >
479 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
480 >      fill(atomRowData.skippedCharge.begin(),
481 >           atomRowData.skippedCharge.end(), 0.0);
482 >      fill(atomColData.skippedCharge.begin(),
483 >           atomColData.skippedCharge.end(), 0.0);
484 >    }
485 >
486 > #endif
487 >    // even in parallel, we need to zero out the local arrays:
488 >
489 >    if (storageLayout_ & DataStorage::dslParticlePot) {      
490 >      fill(snap_->atomData.particlePot.begin(),
491 >           snap_->atomData.particlePot.end(), 0.0);
492 >    }
493 >    
494 >    if (storageLayout_ & DataStorage::dslDensity) {      
495 >      fill(snap_->atomData.density.begin(),
496 >           snap_->atomData.density.end(), 0.0);
497 >    }
498 >    if (storageLayout_ & DataStorage::dslFunctional) {
499 >      fill(snap_->atomData.functional.begin(),
500 >           snap_->atomData.functional.end(), 0.0);
501 >    }
502 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
503 >      fill(snap_->atomData.functionalDerivative.begin(),
504 >           snap_->atomData.functionalDerivative.end(), 0.0);
505 >    }
506 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
507 >      fill(snap_->atomData.skippedCharge.begin(),
508 >           snap_->atomData.skippedCharge.end(), 0.0);
509 >    }
510 >    
511 >  }
512 >
513 >
514    void ForceMatrixDecomposition::distributeData()  {
515      snap_ = sman_->getCurrentSnapshot();
516      storageLayout_ = sman_->getStorageLayout();
# Line 263 | Line 543 | namespace OpenMD {
543        AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
544                                     atomColData.electroFrame);
545      }
546 +
547   #endif      
548    }
549    
550 +  /* collects information obtained during the pre-pair loop onto local
551 +   * data structures.
552 +   */
553    void ForceMatrixDecomposition::collectIntermediateData() {
554      snap_ = sman_->getCurrentSnapshot();
555      storageLayout_ = sman_->getStorageLayout();
# Line 277 | Line 561 | namespace OpenMD {
561                                 snap_->atomData.density);
562        
563        int n = snap_->atomData.density.size();
564 <      std::vector<RealType> rho_tmp(n, 0.0);
564 >      vector<RealType> rho_tmp(n, 0.0);
565        AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
566        for (int i = 0; i < n; i++)
567          snap_->atomData.density[i] += rho_tmp[i];
568      }
569   #endif
570    }
571 <  
571 >
572 >  /*
573 >   * redistributes information obtained during the pre-pair loop out to
574 >   * row and column-indexed data structures
575 >   */
576    void ForceMatrixDecomposition::distributeIntermediateData() {
577      snap_ = sman_->getCurrentSnapshot();
578      storageLayout_ = sman_->getStorageLayout();
# Line 322 | Line 610 | namespace OpenMD {
610      AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
611      for (int i = 0; i < n; i++)
612        snap_->atomData.force[i] += frc_tmp[i];
613 <    
326 <    
613 >        
614      if (storageLayout_ & DataStorage::dslTorque) {
615  
616 <      int nt = snap_->atomData.force.size();
616 >      int nt = snap_->atomData.torque.size();
617        vector<Vector3d> trq_tmp(nt, V3Zero);
618  
619        AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
620 <      for (int i = 0; i < n; i++) {
620 >      for (int i = 0; i < nt; i++) {
621          snap_->atomData.torque[i] += trq_tmp[i];
622          trq_tmp[i] = 0.0;
623        }
624        
625        AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
626 <      for (int i = 0; i < n; i++)
626 >      for (int i = 0; i < nt; i++)
627          snap_->atomData.torque[i] += trq_tmp[i];
628      }
342 –    
343 –    nLocal_ = snap_->getNumberOfAtoms();
629  
630 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
631 <                                       vector<RealType> (nLocal_, 0.0));
632 <    
633 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
634 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
635 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
636 <        pot_local[i] += pot_temp[i][ii];
630 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {
631 >
632 >      int ns = snap_->atomData.skippedCharge.size();
633 >      vector<RealType> skch_tmp(ns, 0.0);
634 >
635 >      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
636 >      for (int i = 0; i < ns; i++) {
637 >        snap_->atomData.skippedCharge[i] += skch_tmp[i];
638 >        skch_tmp[i] = 0.0;
639        }
640 +      
641 +      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
642 +      for (int i = 0; i < ns; i++)
643 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
644      }
645 +    
646 +    nLocal_ = snap_->getNumberOfAtoms();
647 +
648 +    vector<potVec> pot_temp(nLocal_,
649 +                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
650 +
651 +    // scatter/gather pot_row into the members of my column
652 +          
653 +    AtomCommPotRow->scatter(pot_row, pot_temp);
654 +
655 +    for (int ii = 0;  ii < pot_temp.size(); ii++ )
656 +      pairwisePot += pot_temp[ii];
657 +    
658 +    fill(pot_temp.begin(), pot_temp.end(),
659 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
660 +      
661 +    AtomCommPotColumn->scatter(pot_col, pot_temp);    
662 +    
663 +    for (int ii = 0;  ii < pot_temp.size(); ii++ )
664 +      pairwisePot += pot_temp[ii];    
665   #endif
666 +
667    }
668  
669    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 426 | Line 738 | namespace OpenMD {
738   #ifdef IS_MPI
739      return massFactorsRow[atom1];
740   #else
741 <    return massFactorsLocal[atom1];
741 >    return massFactors[atom1];
742   #endif
743    }
744  
# Line 434 | Line 746 | namespace OpenMD {
746   #ifdef IS_MPI
747      return massFactorsCol[atom2];
748   #else
749 <    return massFactorsLocal[atom2];
749 >    return massFactors[atom2];
750   #endif
751  
752    }
# Line 452 | Line 764 | namespace OpenMD {
764      return d;    
765    }
766  
767 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
768 < #ifdef IS_MPI
457 <    return skipsForRowAtom[atom1];
458 < #else
459 <    return skipsForLocalAtom[atom1];
460 < #endif
767 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
768 >    return excludesForAtom[atom1];
769    }
770  
771    /**
772 <   * there are a number of reasons to skip a pair or a particle mostly
773 <   * we do this to exclude atoms who are involved in short range
466 <   * interactions (bonds, bends, torsions), but we also need to
467 <   * exclude some overcounted interactions that result from the
468 <   * parallel decomposition.
772 >   * We need to exclude some overcounted interactions that result from
773 >   * the parallel decomposition.
774     */
775    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
776      int unique_id_1, unique_id_2;
# Line 484 | Line 789 | namespace OpenMD {
789      } else {
790        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
791      }
792 + #endif
793 +    return false;
794 +  }
795 +
796 +  /**
797 +   * We need to handle the interactions for atoms who are involved in
798 +   * the same rigid body as well as some short range interactions
799 +   * (bonds, bends, torsions) differently from other interactions.
800 +   * We'll still visit the pairwise routines, but with a flag that
801 +   * tells those routines to exclude the pair from direct long range
802 +   * interactions.  Some indirect interactions (notably reaction
803 +   * field) must still be handled for these pairs.
804 +   */
805 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
806 +    int unique_id_2;
807 +    
808 + #ifdef IS_MPI
809 +    // in MPI, we have to look up the unique IDs for the row atom.
810 +    unique_id_2 = AtomColToGlobal[atom2];
811   #else
812      // in the normal loop, the atom numbers are unique
489 –    unique_id_1 = atom1;
813      unique_id_2 = atom2;
814   #endif
815      
816 < #ifdef IS_MPI
817 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
495 <         i != skipsForRowAtom[atom1].end(); ++i) {
816 >    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
817 >         i != excludesForAtom[atom1].end(); ++i) {
818        if ( (*i) == unique_id_2 ) return true;
497 –    }    
498 – #else
499 –    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
500 –         i != skipsForLocalAtom[atom1].end(); ++i) {
501 –      if ( (*i) == unique_id_2 ) return true;
502 –    }    
503 – #endif
504 –  }
505 –
506 –  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
507 –    
508 – #ifdef IS_MPI
509 –    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
510 –      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
819      }
512 – #else
513 –    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
514 –      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
515 –    }
516 – #endif
820  
821 <    // zero is default for unconnected (i.e. normal) pair interactions
519 <    return 0;
821 >    return false;
822    }
823  
824 +
825    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
826   #ifdef IS_MPI
827      atomRowData.force[atom1] += fg;
# Line 536 | Line 839 | namespace OpenMD {
839    }
840  
841      // filling interaction blocks with pointers
842 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
843 <    InteractionData idat;
842 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
843 >                                                     int atom1, int atom2) {
844  
845 +    idat.excluded = excludeAtomPair(atom1, atom2);
846 +  
847   #ifdef IS_MPI
848 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
849 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
850 +    //                         ff_->getAtomType(identsCol[atom2]) );
851 +    
852      if (storageLayout_ & DataStorage::dslAmat) {
853        idat.A1 = &(atomRowData.aMat[atom1]);
854        idat.A2 = &(atomColData.aMat[atom2]);
# Line 560 | Line 869 | namespace OpenMD {
869        idat.rho2 = &(atomColData.density[atom2]);
870      }
871  
872 +    if (storageLayout_ & DataStorage::dslFunctional) {
873 +      idat.frho1 = &(atomRowData.functional[atom1]);
874 +      idat.frho2 = &(atomColData.functional[atom2]);
875 +    }
876 +
877      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
878        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
879        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
880      }
881  
882 +    if (storageLayout_ & DataStorage::dslParticlePot) {
883 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
884 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
885 +    }
886 +
887 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
888 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
889 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
890 +    }
891 +
892   #else
893 +
894 +    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
895 +    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
896 +    //                         ff_->getAtomType(idents[atom2]) );
897 +
898      if (storageLayout_ & DataStorage::dslAmat) {
899        idat.A1 = &(snap_->atomData.aMat[atom1]);
900        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 581 | Line 910 | namespace OpenMD {
910        idat.t2 = &(snap_->atomData.torque[atom2]);
911      }
912  
913 <    if (storageLayout_ & DataStorage::dslDensity) {
913 >    if (storageLayout_ & DataStorage::dslDensity) {    
914        idat.rho1 = &(snap_->atomData.density[atom1]);
915        idat.rho2 = &(snap_->atomData.density[atom2]);
916      }
917  
918 +    if (storageLayout_ & DataStorage::dslFunctional) {
919 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
920 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
921 +    }
922 +
923      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
924        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
925        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
926      }
593 – #endif
594 –    return idat;
595 –  }
927  
928 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
928 >    if (storageLayout_ & DataStorage::dslParticlePot) {
929 >      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
930 >      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
931 >    }
932  
933 <    InteractionData idat;
934 < #ifdef IS_MPI
935 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
602 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
603 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
933 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {
934 >      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
935 >      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
936      }
605 –    if (storageLayout_ & DataStorage::dslTorque) {
606 –      idat.t1 = &(atomRowData.torque[atom1]);
607 –      idat.t2 = &(atomColData.torque[atom2]);
608 –    }
609 –    if (storageLayout_ & DataStorage::dslForce) {
610 –      idat.t1 = &(atomRowData.force[atom1]);
611 –      idat.t2 = &(atomColData.force[atom2]);
612 –    }
613 – #else
614 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
615 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
616 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
617 –    }
618 –    if (storageLayout_ & DataStorage::dslTorque) {
619 –      idat.t1 = &(snap_->atomData.torque[atom1]);
620 –      idat.t2 = &(snap_->atomData.torque[atom2]);
621 –    }
622 –    if (storageLayout_ & DataStorage::dslForce) {
623 –      idat.t1 = &(snap_->atomData.force[atom1]);
624 –      idat.t2 = &(snap_->atomData.force[atom2]);
625 –    }
937   #endif
627 –    
938    }
939  
940 +  
941 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
942 + #ifdef IS_MPI
943 +    pot_row[atom1] += 0.5 *  *(idat.pot);
944 +    pot_col[atom2] += 0.5 *  *(idat.pot);
945  
946 +    atomRowData.force[atom1] += *(idat.f1);
947 +    atomColData.force[atom2] -= *(idat.f1);
948 + #else
949 +    pairwisePot += *(idat.pot);
950  
951 +    snap_->atomData.force[atom1] += *(idat.f1);
952 +    snap_->atomData.force[atom2] -= *(idat.f1);
953 + #endif
954 +    
955 +  }
956  
957    /*
958     * buildNeighborList
# Line 639 | Line 963 | namespace OpenMD {
963    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
964        
965      vector<pair<int, int> > neighborList;
966 +    groupCutoffs cuts;
967 +    bool doAllPairs = false;
968 +
969   #ifdef IS_MPI
970      cellListRow_.clear();
971      cellListCol_.clear();
# Line 646 | Line 973 | namespace OpenMD {
973      cellList_.clear();
974   #endif
975  
976 <    // dangerous to not do error checking.
650 <    RealType rCut_;
651 <
652 <    RealType rList_ = (rCut_ + skinThickness_);
976 >    RealType rList_ = (largestRcut_ + skinThickness_);
977      RealType rl2 = rList_ * rList_;
978      Snapshot* snap_ = sman_->getCurrentSnapshot();
979      Mat3x3d Hmat = snap_->getHmat();
# Line 661 | Line 985 | namespace OpenMD {
985      nCells_.y() = (int) ( Hy.length() )/ rList_;
986      nCells_.z() = (int) ( Hz.length() )/ rList_;
987  
988 +    // handle small boxes where the cell offsets can end up repeating cells
989 +    
990 +    if (nCells_.x() < 3) doAllPairs = true;
991 +    if (nCells_.y() < 3) doAllPairs = true;
992 +    if (nCells_.z() < 3) doAllPairs = true;
993 +
994      Mat3x3d invHmat = snap_->getInvHmat();
995      Vector3d rs, scaled, dr;
996      Vector3i whichCell;
997      int cellIndex;
998 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
999  
1000   #ifdef IS_MPI
1001 <    for (int i = 0; i < nGroupsInRow_; i++) {
1002 <      rs = cgRowData.position[i];
672 <      // scaled positions relative to the box vectors
673 <      scaled = invHmat * rs;
674 <      // wrap the vector back into the unit box by subtracting integer box
675 <      // numbers
676 <      for (int j = 0; j < 3; j++)
677 <        scaled[j] -= roundMe(scaled[j]);
678 <    
679 <      // find xyz-indices of cell that cutoffGroup is in.
680 <      whichCell.x() = nCells_.x() * scaled.x();
681 <      whichCell.y() = nCells_.y() * scaled.y();
682 <      whichCell.z() = nCells_.z() * scaled.z();
683 <
684 <      // find single index of this cell:
685 <      cellIndex = Vlinear(whichCell, nCells_);
686 <      // add this cutoff group to the list of groups in this cell;
687 <      cellListRow_[cellIndex].push_back(i);
688 <    }
689 <
690 <    for (int i = 0; i < nGroupsInCol_; i++) {
691 <      rs = cgColData.position[i];
692 <      // scaled positions relative to the box vectors
693 <      scaled = invHmat * rs;
694 <      // wrap the vector back into the unit box by subtracting integer box
695 <      // numbers
696 <      for (int j = 0; j < 3; j++)
697 <        scaled[j] -= roundMe(scaled[j]);
698 <
699 <      // find xyz-indices of cell that cutoffGroup is in.
700 <      whichCell.x() = nCells_.x() * scaled.x();
701 <      whichCell.y() = nCells_.y() * scaled.y();
702 <      whichCell.z() = nCells_.z() * scaled.z();
703 <
704 <      // find single index of this cell:
705 <      cellIndex = Vlinear(whichCell, nCells_);
706 <      // add this cutoff group to the list of groups in this cell;
707 <      cellListCol_[cellIndex].push_back(i);
708 <    }
1001 >    cellListRow_.resize(nCtot);
1002 >    cellListCol_.resize(nCtot);
1003   #else
1004 <    for (int i = 0; i < nGroups_; i++) {
711 <      rs = snap_->cgData.position[i];
712 <      // scaled positions relative to the box vectors
713 <      scaled = invHmat * rs;
714 <      // wrap the vector back into the unit box by subtracting integer box
715 <      // numbers
716 <      for (int j = 0; j < 3; j++)
717 <        scaled[j] -= roundMe(scaled[j]);
718 <
719 <      // find xyz-indices of cell that cutoffGroup is in.
720 <      whichCell.x() = nCells_.x() * scaled.x();
721 <      whichCell.y() = nCells_.y() * scaled.y();
722 <      whichCell.z() = nCells_.z() * scaled.z();
723 <
724 <      // find single index of this cell:
725 <      cellIndex = Vlinear(whichCell, nCells_);
726 <      // add this cutoff group to the list of groups in this cell;
727 <      cellList_[cellIndex].push_back(i);
728 <    }
1004 >    cellList_.resize(nCtot);
1005   #endif
1006  
1007 +    if (!doAllPairs) {
1008 + #ifdef IS_MPI
1009  
1010 +      for (int i = 0; i < nGroupsInRow_; i++) {
1011 +        rs = cgRowData.position[i];
1012 +        
1013 +        // scaled positions relative to the box vectors
1014 +        scaled = invHmat * rs;
1015 +        
1016 +        // wrap the vector back into the unit box by subtracting integer box
1017 +        // numbers
1018 +        for (int j = 0; j < 3; j++) {
1019 +          scaled[j] -= roundMe(scaled[j]);
1020 +          scaled[j] += 0.5;
1021 +        }
1022 +        
1023 +        // find xyz-indices of cell that cutoffGroup is in.
1024 +        whichCell.x() = nCells_.x() * scaled.x();
1025 +        whichCell.y() = nCells_.y() * scaled.y();
1026 +        whichCell.z() = nCells_.z() * scaled.z();
1027 +        
1028 +        // find single index of this cell:
1029 +        cellIndex = Vlinear(whichCell, nCells_);
1030 +        
1031 +        // add this cutoff group to the list of groups in this cell;
1032 +        cellListRow_[cellIndex].push_back(i);
1033 +      }
1034 +      
1035 +      for (int i = 0; i < nGroupsInCol_; i++) {
1036 +        rs = cgColData.position[i];
1037 +        
1038 +        // scaled positions relative to the box vectors
1039 +        scaled = invHmat * rs;
1040 +        
1041 +        // wrap the vector back into the unit box by subtracting integer box
1042 +        // numbers
1043 +        for (int j = 0; j < 3; j++) {
1044 +          scaled[j] -= roundMe(scaled[j]);
1045 +          scaled[j] += 0.5;
1046 +        }
1047 +        
1048 +        // find xyz-indices of cell that cutoffGroup is in.
1049 +        whichCell.x() = nCells_.x() * scaled.x();
1050 +        whichCell.y() = nCells_.y() * scaled.y();
1051 +        whichCell.z() = nCells_.z() * scaled.z();
1052 +        
1053 +        // find single index of this cell:
1054 +        cellIndex = Vlinear(whichCell, nCells_);
1055 +        
1056 +        // add this cutoff group to the list of groups in this cell;
1057 +        cellListCol_[cellIndex].push_back(i);
1058 +      }
1059 + #else
1060 +      for (int i = 0; i < nGroups_; i++) {
1061 +        rs = snap_->cgData.position[i];
1062 +        
1063 +        // scaled positions relative to the box vectors
1064 +        scaled = invHmat * rs;
1065 +        
1066 +        // wrap the vector back into the unit box by subtracting integer box
1067 +        // numbers
1068 +        for (int j = 0; j < 3; j++) {
1069 +          scaled[j] -= roundMe(scaled[j]);
1070 +          scaled[j] += 0.5;
1071 +        }
1072 +        
1073 +        // find xyz-indices of cell that cutoffGroup is in.
1074 +        whichCell.x() = nCells_.x() * scaled.x();
1075 +        whichCell.y() = nCells_.y() * scaled.y();
1076 +        whichCell.z() = nCells_.z() * scaled.z();
1077 +        
1078 +        // find single index of this cell:
1079 +        cellIndex = Vlinear(whichCell, nCells_);      
1080 +        
1081 +        // add this cutoff group to the list of groups in this cell;
1082 +        cellList_[cellIndex].push_back(i);
1083 +      }
1084 + #endif
1085  
1086 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1087 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1088 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1089 <          Vector3i m1v(m1x, m1y, m1z);
1090 <          int m1 = Vlinear(m1v, nCells_);
738 <
739 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
740 <               os != cellOffsets_.end(); ++os) {
1086 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1087 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1088 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1089 >            Vector3i m1v(m1x, m1y, m1z);
1090 >            int m1 = Vlinear(m1v, nCells_);
1091              
1092 <            Vector3i m2v = m1v + (*os);
1093 <            
1094 <            if (m2v.x() >= nCells_.x()) {
1095 <              m2v.x() = 0;          
1096 <            } else if (m2v.x() < 0) {
1097 <              m2v.x() = nCells_.x() - 1;
1098 <            }
1099 <            
1100 <            if (m2v.y() >= nCells_.y()) {
1101 <              m2v.y() = 0;          
1102 <            } else if (m2v.y() < 0) {
1103 <              m2v.y() = nCells_.y() - 1;
1104 <            }
1105 <            
1106 <            if (m2v.z() >= nCells_.z()) {
1107 <              m2v.z() = 0;          
1108 <            } else if (m2v.z() < 0) {
1109 <              m2v.z() = nCells_.z() - 1;
1110 <            }
1111 <            
1112 <            int m2 = Vlinear (m2v, nCells_);
1113 <
1092 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1093 >                 os != cellOffsets_.end(); ++os) {
1094 >              
1095 >              Vector3i m2v = m1v + (*os);
1096 >              
1097 >              if (m2v.x() >= nCells_.x()) {
1098 >                m2v.x() = 0;          
1099 >              } else if (m2v.x() < 0) {
1100 >                m2v.x() = nCells_.x() - 1;
1101 >              }
1102 >              
1103 >              if (m2v.y() >= nCells_.y()) {
1104 >                m2v.y() = 0;          
1105 >              } else if (m2v.y() < 0) {
1106 >                m2v.y() = nCells_.y() - 1;
1107 >              }
1108 >              
1109 >              if (m2v.z() >= nCells_.z()) {
1110 >                m2v.z() = 0;          
1111 >              } else if (m2v.z() < 0) {
1112 >                m2v.z() = nCells_.z() - 1;
1113 >              }
1114 >              
1115 >              int m2 = Vlinear (m2v, nCells_);
1116 >              
1117   #ifdef IS_MPI
1118 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1119 <                 j1 != cellListRow_[m1].end(); ++j1) {
1120 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1121 <                   j2 != cellListCol_[m2].end(); ++j2) {
1122 <                              
1123 <                // Always do this if we're in different cells or if
1124 <                // we're in the same cell and the global index of the
1125 <                // j2 cutoff group is less than the j1 cutoff group
1126 <
1127 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1128 <                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1129 <                  snap_->wrapVector(dr);
1130 <                  if (dr.lengthSquare() < rl2) {
1131 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1118 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1119 >                   j1 != cellListRow_[m1].end(); ++j1) {
1120 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1121 >                     j2 != cellListCol_[m2].end(); ++j2) {
1122 >                  
1123 >                  // Always do this if we're in different cells or if
1124 >                  // we're in the same cell and the global index of the
1125 >                  // j2 cutoff group is less than the j1 cutoff group
1126 >                  
1127 >                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1128 >                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1129 >                    snap_->wrapVector(dr);
1130 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1131 >                    if (dr.lengthSquare() < cuts.third) {
1132 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1133 >                    }
1134                    }
1135                  }
1136                }
782 –            }
1137   #else
1138 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1139 <                 j1 != cellList_[m1].end(); ++j1) {
1140 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1141 <                   j2 != cellList_[m2].end(); ++j2) {
1142 <                              
1143 <                // Always do this if we're in different cells or if
1144 <                // we're in the same cell and the global index of the
1145 <                // j2 cutoff group is less than the j1 cutoff group
1146 <
1147 <                if (m2 != m1 || (*j2) < (*j1)) {
1148 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1149 <                  snap_->wrapVector(dr);
1150 <                  if (dr.lengthSquare() < rl2) {
1151 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1138 >              
1139 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1140 >                   j1 != cellList_[m1].end(); ++j1) {
1141 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1142 >                     j2 != cellList_[m2].end(); ++j2) {
1143 >                  
1144 >                  // Always do this if we're in different cells or if
1145 >                  // we're in the same cell and the global index of the
1146 >                  // j2 cutoff group is less than the j1 cutoff group
1147 >                  
1148 >                  if (m2 != m1 || (*j2) < (*j1)) {
1149 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1150 >                    snap_->wrapVector(dr);
1151 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1152 >                    if (dr.lengthSquare() < cuts.third) {
1153 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1154 >                    }
1155                    }
1156                  }
1157                }
801 –            }
1158   #endif
1159 +            }
1160            }
1161          }
1162        }
1163 +    } else {
1164 +      // branch to do all cutoff group pairs
1165 + #ifdef IS_MPI
1166 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1167 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1168 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1169 +          snap_->wrapVector(dr);
1170 +          cuts = getGroupCutoffs( j1, j2 );
1171 +          if (dr.lengthSquare() < cuts.third) {
1172 +            neighborList.push_back(make_pair(j1, j2));
1173 +          }
1174 +        }
1175 +      }
1176 + #else
1177 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1178 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1179 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1180 +          snap_->wrapVector(dr);
1181 +          cuts = getGroupCutoffs( j1, j2 );
1182 +          if (dr.lengthSquare() < cuts.third) {
1183 +            neighborList.push_back(make_pair(j1, j2));
1184 +          }
1185 +        }
1186 +      }        
1187 + #endif
1188      }
1189 <
1189 >      
1190      // save the local cutoff group positions for the check that is
1191      // done on each loop:
1192      saved_CG_positions_.clear();
1193      for (int i = 0; i < nGroups_; i++)
1194        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1195 <
1195 >    
1196      return neighborList;
1197    }
1198   } //end namespace OpenMD

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