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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 1571 by gezelter, Fri May 27 16:45:44 2011 UTC vs.
Revision 1588 by gezelter, Sat Jul 9 15:05:59 2011 UTC

# Line 57 | Line 57 | namespace OpenMD {
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 <    identsLocal = info_->getIdentArray();
63 >    idents = info_->getIdentArray();
64      AtomLocalToGlobal = info_->getGlobalAtomIndices();
65      cgLocalToGlobal = info_->getGlobalGroupIndices();
66      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67 –    vector<RealType> massFactorsLocal = info_->getMassFactors();
68 –    PairList excludes = info_->getExcludedInteractions();
69 –    PairList oneTwo = info_->getOneTwoInteractions();
70 –    PairList oneThree = info_->getOneThreeInteractions();
71 –    PairList oneFour = info_->getOneFourInteractions();
72 –    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 102 | 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));
108 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
109 <                                      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);
115 <    AtomCommIntColumn->gather(identsLocal, identsCol);
116 <    
115 >    vector<int>::iterator it;
116 >    for (it = AtomLocalToGlobal.begin(); it != AtomLocalToGlobal.end(); ++it) {
117 >      cerr << "my AtomLocalToGlobal = " << (*it) << "\n";
118 >    }
119      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
120      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
121      
122      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
123      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
124  
125 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
126 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
125 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
126 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
127  
128      groupListRow_.clear();
129 <    groupListRow_.reserve(nGroupsInRow_);
129 >    groupListRow_.resize(nGroupsInRow_);
130      for (int i = 0; i < nGroupsInRow_; i++) {
131        int gid = cgRowToGlobal[i];
132        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 135 | Line 137 | namespace OpenMD {
137      }
138  
139      groupListCol_.clear();
140 <    groupListCol_.reserve(nGroupsInCol_);
140 >    groupListCol_.resize(nGroupsInCol_);
141      for (int i = 0; i < nGroupsInCol_; i++) {
142        int gid = cgColToGlobal[i];
143        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 145 | Line 147 | namespace OpenMD {
147        }      
148      }
149  
150 <    skipsForRowAtom.clear();
151 <    skipsForRowAtom.reserve(nAtomsInRow_);
150 >    excludesForAtom.clear();
151 >    excludesForAtom.resize(nAtomsInRow_);
152 >    toposForAtom.clear();
153 >    toposForAtom.resize(nAtomsInRow_);
154 >    topoDist.clear();
155 >    topoDist.resize(nAtomsInRow_);
156      for (int i = 0; i < nAtomsInRow_; i++) {
157        int iglob = AtomRowToGlobal[i];
152 –      for (int j = 0; j < nAtomsInCol_; j++) {
153 –        int jglob = AtomColToGlobal[j];        
154 –        if (excludes.hasPair(iglob, jglob))
155 –          skipsForRowAtom[i].push_back(j);      
156 –      }      
157 –    }
158  
159 –    toposForRowAtom.clear();
160 –    toposForRowAtom.reserve(nAtomsInRow_);
161 –    for (int i = 0; i < nAtomsInRow_; i++) {
162 –      int iglob = AtomRowToGlobal[i];
163 –      int nTopos = 0;
159        for (int j = 0; j < nAtomsInCol_; j++) {
160 <        int jglob = AtomColToGlobal[j];        
161 <        if (oneTwo.hasPair(iglob, jglob)) {
162 <          toposForRowAtom[i].push_back(j);
163 <          topoDistRow[i][nTopos] = 1;
164 <          nTopos++;
160 >        int jglob = AtomColToGlobal[j];
161 >
162 >        if (excludes->hasPair(iglob, jglob))
163 >          excludesForAtom[i].push_back(j);      
164 >        
165 >        if (oneTwo->hasPair(iglob, jglob)) {
166 >          toposForAtom[i].push_back(j);
167 >          topoDist[i].push_back(1);
168 >        } else {
169 >          if (oneThree->hasPair(iglob, jglob)) {
170 >            toposForAtom[i].push_back(j);
171 >            topoDist[i].push_back(2);
172 >          } else {
173 >            if (oneFour->hasPair(iglob, jglob)) {
174 >              toposForAtom[i].push_back(j);
175 >              topoDist[i].push_back(3);
176 >            }
177 >          }
178          }
171 –        if (oneThree.hasPair(iglob, jglob)) {
172 –          toposForRowAtom[i].push_back(j);
173 –          topoDistRow[i][nTopos] = 2;
174 –          nTopos++;
175 –        }
176 –        if (oneFour.hasPair(iglob, jglob)) {
177 –          toposForRowAtom[i].push_back(j);
178 –          topoDistRow[i][nTopos] = 3;
179 –          nTopos++;
180 –        }
179        }      
180      }
181  
182   #endif
183  
184      groupList_.clear();
185 <    groupList_.reserve(nGroups_);
185 >    groupList_.resize(nGroups_);
186      for (int i = 0; i < nGroups_; i++) {
187        int gid = cgLocalToGlobal[i];
188        for (int j = 0; j < nLocal_; j++) {
189          int aid = AtomLocalToGlobal[j];
190 <        if (globalGroupMembership[aid] == gid)
190 >        if (globalGroupMembership[aid] == gid) {
191            groupList_[i].push_back(j);
192 +        }
193        }      
194      }
195  
196 <    skipsForLocalAtom.clear();
197 <    skipsForLocalAtom.reserve(nLocal_);
196 >    excludesForAtom.clear();
197 >    excludesForAtom.resize(nLocal_);
198 >    toposForAtom.clear();
199 >    toposForAtom.resize(nLocal_);
200 >    topoDist.clear();
201 >    topoDist.resize(nLocal_);
202  
203      for (int i = 0; i < nLocal_; i++) {
204        int iglob = AtomLocalToGlobal[i];
205 +
206        for (int j = 0; j < nLocal_; j++) {
207 <        int jglob = AtomLocalToGlobal[j];        
208 <        if (excludes.hasPair(iglob, jglob))
209 <          skipsForLocalAtom[i].push_back(j);      
207 >        int jglob = AtomLocalToGlobal[j];
208 >
209 >        if (excludes->hasPair(iglob, jglob))
210 >          excludesForAtom[i].push_back(j);              
211 >        
212 >        if (oneTwo->hasPair(iglob, jglob)) {
213 >          toposForAtom[i].push_back(j);
214 >          topoDist[i].push_back(1);
215 >        } else {
216 >          if (oneThree->hasPair(iglob, jglob)) {
217 >            toposForAtom[i].push_back(j);
218 >            topoDist[i].push_back(2);
219 >          } else {
220 >            if (oneFour->hasPair(iglob, jglob)) {
221 >              toposForAtom[i].push_back(j);
222 >              topoDist[i].push_back(3);
223 >            }
224 >          }
225 >        }
226        }      
227      }
228 +    
229 +    createGtypeCutoffMap();
230  
231 <    toposForLocalAtom.clear();
232 <    toposForLocalAtom.reserve(nLocal_);
233 <    for (int i = 0; i < nLocal_; i++) {
234 <      int iglob = AtomLocalToGlobal[i];
235 <      int nTopos = 0;
236 <      for (int j = 0; j < nLocal_; j++) {
237 <        int jglob = AtomLocalToGlobal[j];        
238 <        if (oneTwo.hasPair(iglob, jglob)) {
239 <          toposForLocalAtom[i].push_back(j);
240 <          topoDistLocal[i][nTopos] = 1;
241 <          nTopos++;
231 >  }
232 >  
233 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
234 >    
235 >    RealType tol = 1e-6;
236 >    RealType rc;
237 >    int atid;
238 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
239 >    map<int, RealType> atypeCutoff;
240 >      
241 >    for (set<AtomType*>::iterator at = atypes.begin();
242 >         at != atypes.end(); ++at){
243 >      atid = (*at)->getIdent();
244 >      if (userChoseCutoff_)
245 >        atypeCutoff[atid] = userCutoff_;
246 >      else
247 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
248 >    }
249 >
250 >    vector<RealType> gTypeCutoffs;
251 >    // first we do a single loop over the cutoff groups to find the
252 >    // largest cutoff for any atypes present in this group.
253 > #ifdef IS_MPI
254 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
255 >    groupRowToGtype.resize(nGroupsInRow_);
256 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
257 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
258 >      for (vector<int>::iterator ia = atomListRow.begin();
259 >           ia != atomListRow.end(); ++ia) {            
260 >        int atom1 = (*ia);
261 >        atid = identsRow[atom1];
262 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
263 >          groupCutoffRow[cg1] = atypeCutoff[atid];
264          }
265 <        if (oneThree.hasPair(iglob, jglob)) {
266 <          toposForLocalAtom[i].push_back(j);
267 <          topoDistLocal[i][nTopos] = 2;
268 <          nTopos++;
265 >      }
266 >
267 >      bool gTypeFound = false;
268 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
269 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
270 >          groupRowToGtype[cg1] = gt;
271 >          gTypeFound = true;
272 >        }
273 >      }
274 >      if (!gTypeFound) {
275 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
276 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
277 >      }
278 >      
279 >    }
280 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
281 >    groupColToGtype.resize(nGroupsInCol_);
282 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
283 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
284 >      for (vector<int>::iterator jb = atomListCol.begin();
285 >           jb != atomListCol.end(); ++jb) {            
286 >        int atom2 = (*jb);
287 >        atid = identsCol[atom2];
288 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
289 >          groupCutoffCol[cg2] = atypeCutoff[atid];
290          }
291 <        if (oneFour.hasPair(iglob, jglob)) {
292 <          toposForLocalAtom[i].push_back(j);
293 <          topoDistLocal[i][nTopos] = 3;
294 <          nTopos++;
291 >      }
292 >      bool gTypeFound = false;
293 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
294 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
295 >          groupColToGtype[cg2] = gt;
296 >          gTypeFound = true;
297 >        }
298 >      }
299 >      if (!gTypeFound) {
300 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
301 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
302 >      }
303 >    }
304 > #else
305 >
306 >    vector<RealType> groupCutoff(nGroups_, 0.0);
307 >    groupToGtype.resize(nGroups_);
308 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
309 >
310 >      groupCutoff[cg1] = 0.0;
311 >      vector<int> atomList = getAtomsInGroupRow(cg1);
312 >
313 >      for (vector<int>::iterator ia = atomList.begin();
314 >           ia != atomList.end(); ++ia) {            
315 >        int atom1 = (*ia);
316 >        atid = idents[atom1];
317 >        if (atypeCutoff[atid] > groupCutoff[cg1]) {
318 >          groupCutoff[cg1] = atypeCutoff[atid];
319          }
320 +      }
321 +
322 +      bool gTypeFound = false;
323 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
324 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
325 +          groupToGtype[cg1] = gt;
326 +          gTypeFound = true;
327 +        }
328 +      }
329 +      if (!gTypeFound) {
330 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
331 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
332        }      
333      }
334 + #endif
335 +
336 +    // Now we find the maximum group cutoff value present in the simulation
337 +
338 +    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
339 +
340 + #ifdef IS_MPI
341 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
342 + #endif
343 +    
344 +    RealType tradRcut = groupMax;
345 +
346 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
347 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
348 +        RealType thisRcut;
349 +        switch(cutoffPolicy_) {
350 +        case TRADITIONAL:
351 +          thisRcut = tradRcut;
352 +          break;
353 +        case MIX:
354 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
355 +          break;
356 +        case MAX:
357 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
358 +          break;
359 +        default:
360 +          sprintf(painCave.errMsg,
361 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
362 +                  "hit an unknown cutoff policy!\n");
363 +          painCave.severity = OPENMD_ERROR;
364 +          painCave.isFatal = 1;
365 +          simError();
366 +          break;
367 +        }
368 +
369 +        pair<int,int> key = make_pair(i,j);
370 +        gTypeCutoffMap[key].first = thisRcut;
371 +
372 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
373 +
374 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
375 +        
376 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
377 +
378 +        // sanity check
379 +        
380 +        if (userChoseCutoff_) {
381 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
382 +            sprintf(painCave.errMsg,
383 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
384 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
385 +            painCave.severity = OPENMD_ERROR;
386 +            painCave.isFatal = 1;
387 +            simError();            
388 +          }
389 +        }
390 +      }
391 +    }
392    }
393 <  
393 >
394 >
395 >  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
396 >    int i, j;  
397 > #ifdef IS_MPI
398 >    i = groupRowToGtype[cg1];
399 >    j = groupColToGtype[cg2];
400 > #else
401 >    i = groupToGtype[cg1];
402 >    j = groupToGtype[cg2];
403 > #endif    
404 >    return gTypeCutoffMap[make_pair(i,j)];
405 >  }
406 >
407 >  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
408 >    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
409 >      if (toposForAtom[atom1][j] == atom2)
410 >        return topoDist[atom1][j];
411 >    }
412 >    return 0;
413 >  }
414 >
415 >  void ForceMatrixDecomposition::zeroWorkArrays() {
416 >    pairwisePot = 0.0;
417 >    embeddingPot = 0.0;
418 >
419 > #ifdef IS_MPI
420 >    if (storageLayout_ & DataStorage::dslForce) {
421 >      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
422 >      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
423 >    }
424 >
425 >    if (storageLayout_ & DataStorage::dslTorque) {
426 >      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
427 >      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
428 >    }
429 >    
430 >    fill(pot_row.begin(), pot_row.end(),
431 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
432 >
433 >    fill(pot_col.begin(), pot_col.end(),
434 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
435 >
436 >    if (storageLayout_ & DataStorage::dslParticlePot) {    
437 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
438 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
439 >    }
440 >
441 >    if (storageLayout_ & DataStorage::dslDensity) {      
442 >      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
443 >      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
444 >    }
445 >
446 >    if (storageLayout_ & DataStorage::dslFunctional) {  
447 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
448 >      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
449 >    }
450 >
451 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
452 >      fill(atomRowData.functionalDerivative.begin(),
453 >           atomRowData.functionalDerivative.end(), 0.0);
454 >      fill(atomColData.functionalDerivative.begin(),
455 >           atomColData.functionalDerivative.end(), 0.0);
456 >    }
457 >
458 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
459 >      fill(atomRowData.skippedCharge.begin(),
460 >           atomRowData.skippedCharge.end(), 0.0);
461 >      fill(atomColData.skippedCharge.begin(),
462 >           atomColData.skippedCharge.end(), 0.0);
463 >    }
464 >
465 > #else
466 >    
467 >    if (storageLayout_ & DataStorage::dslParticlePot) {      
468 >      fill(snap_->atomData.particlePot.begin(),
469 >           snap_->atomData.particlePot.end(), 0.0);
470 >    }
471 >    
472 >    if (storageLayout_ & DataStorage::dslDensity) {      
473 >      fill(snap_->atomData.density.begin(),
474 >           snap_->atomData.density.end(), 0.0);
475 >    }
476 >    if (storageLayout_ & DataStorage::dslFunctional) {
477 >      fill(snap_->atomData.functional.begin(),
478 >           snap_->atomData.functional.end(), 0.0);
479 >    }
480 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
481 >      fill(snap_->atomData.functionalDerivative.begin(),
482 >           snap_->atomData.functionalDerivative.end(), 0.0);
483 >    }
484 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
485 >      fill(snap_->atomData.skippedCharge.begin(),
486 >           snap_->atomData.skippedCharge.end(), 0.0);
487 >    }
488 > #endif
489 >    
490 >  }
491 >
492 >
493    void ForceMatrixDecomposition::distributeData()  {
494      snap_ = sman_->getCurrentSnapshot();
495      storageLayout_ = sman_->getStorageLayout();
# Line 267 | Line 525 | namespace OpenMD {
525   #endif      
526    }
527    
528 +  /* collects information obtained during the pre-pair loop onto local
529 +   * data structures.
530 +   */
531    void ForceMatrixDecomposition::collectIntermediateData() {
532      snap_ = sman_->getCurrentSnapshot();
533      storageLayout_ = sman_->getStorageLayout();
# Line 278 | Line 539 | namespace OpenMD {
539                                 snap_->atomData.density);
540        
541        int n = snap_->atomData.density.size();
542 <      std::vector<RealType> rho_tmp(n, 0.0);
542 >      vector<RealType> rho_tmp(n, 0.0);
543        AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
544        for (int i = 0; i < n; i++)
545          snap_->atomData.density[i] += rho_tmp[i];
546      }
547   #endif
548    }
549 <  
549 >
550 >  /*
551 >   * redistributes information obtained during the pre-pair loop out to
552 >   * row and column-indexed data structures
553 >   */
554    void ForceMatrixDecomposition::distributeIntermediateData() {
555      snap_ = sman_->getCurrentSnapshot();
556      storageLayout_ = sman_->getStorageLayout();
# Line 327 | Line 592 | namespace OpenMD {
592      
593      if (storageLayout_ & DataStorage::dslTorque) {
594  
595 <      int nt = snap_->atomData.force.size();
595 >      int nt = snap_->atomData.torque.size();
596        vector<Vector3d> trq_tmp(nt, V3Zero);
597  
598        AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
599 <      for (int i = 0; i < n; i++) {
599 >      for (int i = 0; i < nt; i++) {
600          snap_->atomData.torque[i] += trq_tmp[i];
601          trq_tmp[i] = 0.0;
602        }
603        
604        AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
605 <      for (int i = 0; i < n; i++)
605 >      for (int i = 0; i < nt; i++)
606          snap_->atomData.torque[i] += trq_tmp[i];
607      }
608 +
609 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
610 +
611 +      int ns = snap_->atomData.skippedCharge.size();
612 +      vector<RealType> skch_tmp(ns, 0.0);
613 +
614 +      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
615 +      for (int i = 0; i < ns; i++) {
616 +        snap_->atomData.skippedCharge[i] = skch_tmp[i];
617 +        skch_tmp[i] = 0.0;
618 +      }
619 +      
620 +      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
621 +      for (int i = 0; i < ns; i++)
622 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
623 +    }
624      
625      nLocal_ = snap_->getNumberOfAtoms();
626  
627 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
628 <                                       vector<RealType> (nLocal_, 0.0));
627 >    vector<potVec> pot_temp(nLocal_,
628 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
629 >
630 >    // scatter/gather pot_row into the members of my column
631 >          
632 >    AtomCommPotRow->scatter(pot_row, pot_temp);
633 >
634 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
635 >      pairwisePot += pot_temp[ii];
636      
637 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
638 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
639 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
640 <        pot_local[i] += pot_temp[i][ii];
641 <      }
642 <    }
637 >    fill(pot_temp.begin(), pot_temp.end(),
638 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
639 >      
640 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
641 >    
642 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
643 >      pairwisePot += pot_temp[ii];    
644   #endif
645 +
646    }
647  
648    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 427 | Line 717 | namespace OpenMD {
717   #ifdef IS_MPI
718      return massFactorsRow[atom1];
719   #else
720 <    return massFactorsLocal[atom1];
720 >    return massFactors[atom1];
721   #endif
722    }
723  
# Line 435 | Line 725 | namespace OpenMD {
725   #ifdef IS_MPI
726      return massFactorsCol[atom2];
727   #else
728 <    return massFactorsLocal[atom2];
728 >    return massFactors[atom2];
729   #endif
730  
731    }
# Line 453 | Line 743 | namespace OpenMD {
743      return d;    
744    }
745  
746 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
747 < #ifdef IS_MPI
458 <    return skipsForRowAtom[atom1];
459 < #else
460 <    return skipsForLocalAtom[atom1];
461 < #endif
746 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
747 >    return excludesForAtom[atom1];
748    }
749  
750    /**
751 <   * there are a number of reasons to skip a pair or a particle mostly
752 <   * we do this to exclude atoms who are involved in short range
467 <   * interactions (bonds, bends, torsions), but we also need to
468 <   * exclude some overcounted interactions that result from the
469 <   * parallel decomposition.
751 >   * We need to exclude some overcounted interactions that result from
752 >   * the parallel decomposition.
753     */
754    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
755      int unique_id_1, unique_id_2;
# Line 485 | Line 768 | namespace OpenMD {
768      } else {
769        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
770      }
488 – #else
489 –    // in the normal loop, the atom numbers are unique
490 –    unique_id_1 = atom1;
491 –    unique_id_2 = atom2;
771   #endif
772 <    
494 < #ifdef IS_MPI
495 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
496 <         i != skipsForRowAtom[atom1].end(); ++i) {
497 <      if ( (*i) == unique_id_2 ) return true;
498 <    }    
499 < #else
500 <    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
501 <         i != skipsForLocalAtom[atom1].end(); ++i) {
502 <      if ( (*i) == unique_id_2 ) return true;
503 <    }    
504 < #endif
772 >    return false;
773    }
774  
775 <  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
775 >  /**
776 >   * We need to handle the interactions for atoms who are involved in
777 >   * the same rigid body as well as some short range interactions
778 >   * (bonds, bends, torsions) differently from other interactions.
779 >   * We'll still visit the pairwise routines, but with a flag that
780 >   * tells those routines to exclude the pair from direct long range
781 >   * interactions.  Some indirect interactions (notably reaction
782 >   * field) must still be handled for these pairs.
783 >   */
784 >  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
785 >    int unique_id_2;
786      
787   #ifdef IS_MPI
788 <    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
789 <      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
512 <    }
788 >    // in MPI, we have to look up the unique IDs for the row atom.
789 >    unique_id_2 = AtomColToGlobal[atom2];
790   #else
791 <    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
792 <      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
516 <    }
791 >    // in the normal loop, the atom numbers are unique
792 >    unique_id_2 = atom2;
793   #endif
794 +    
795 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
796 +         i != excludesForAtom[atom1].end(); ++i) {
797 +      if ( (*i) == unique_id_2 ) return true;
798 +    }
799  
800 <    // zero is default for unconnected (i.e. normal) pair interactions
520 <    return 0;
800 >    return false;
801    }
802  
803 +
804    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
805   #ifdef IS_MPI
806      atomRowData.force[atom1] += fg;
# Line 537 | Line 818 | namespace OpenMD {
818    }
819  
820      // filling interaction blocks with pointers
821 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
822 <    InteractionData idat;
821 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
822 >                                                     int atom1, int atom2) {
823  
824 +    idat.excluded = excludeAtomPair(atom1, atom2);
825 +  
826   #ifdef IS_MPI
827      
828      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
829                               ff_->getAtomType(identsCol[atom2]) );
830 <
830 >    
831      if (storageLayout_ & DataStorage::dslAmat) {
832        idat.A1 = &(atomRowData.aMat[atom1]);
833        idat.A2 = &(atomColData.aMat[atom2]);
# Line 565 | Line 848 | namespace OpenMD {
848        idat.rho2 = &(atomColData.density[atom2]);
849      }
850  
851 +    if (storageLayout_ & DataStorage::dslFunctional) {
852 +      idat.frho1 = &(atomRowData.functional[atom1]);
853 +      idat.frho2 = &(atomColData.functional[atom2]);
854 +    }
855 +
856      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
857        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
858        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
859      }
860  
861 +    if (storageLayout_ & DataStorage::dslParticlePot) {
862 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
863 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
864 +    }
865 +
866 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
867 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
868 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
869 +    }
870 +
871   #else
872  
873 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
874 <                             ff_->getAtomType(identsLocal[atom2]) );
873 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
874 >                             ff_->getAtomType(idents[atom2]) );
875  
876      if (storageLayout_ & DataStorage::dslAmat) {
877        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 590 | Line 888 | namespace OpenMD {
888        idat.t2 = &(snap_->atomData.torque[atom2]);
889      }
890  
891 <    if (storageLayout_ & DataStorage::dslDensity) {
891 >    if (storageLayout_ & DataStorage::dslDensity) {    
892        idat.rho1 = &(snap_->atomData.density[atom1]);
893        idat.rho2 = &(snap_->atomData.density[atom2]);
894      }
895  
896 +    if (storageLayout_ & DataStorage::dslFunctional) {
897 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
898 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
899 +    }
900 +
901      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
902        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
903        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
904      }
905 +
906 +    if (storageLayout_ & DataStorage::dslParticlePot) {
907 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
908 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
909 +    }
910 +
911 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
912 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
913 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
914 +    }
915   #endif
603 –    return idat;
916    }
917  
918 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
919 <
608 <    InteractionData idat;
918 >  
919 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
920   #ifdef IS_MPI
921 <    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
922 <                             ff_->getAtomType(identsCol[atom2]) );
921 >    pot_row[atom1] += 0.5 *  *(idat.pot);
922 >    pot_col[atom2] += 0.5 *  *(idat.pot);
923  
924 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
925 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
615 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
616 <    }
617 <    if (storageLayout_ & DataStorage::dslTorque) {
618 <      idat.t1 = &(atomRowData.torque[atom1]);
619 <      idat.t2 = &(atomColData.torque[atom2]);
620 <    }
621 <    if (storageLayout_ & DataStorage::dslForce) {
622 <      idat.t1 = &(atomRowData.force[atom1]);
623 <      idat.t2 = &(atomColData.force[atom2]);
624 <    }
924 >    atomRowData.force[atom1] += *(idat.f1);
925 >    atomColData.force[atom2] -= *(idat.f1);
926   #else
927 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
627 <                             ff_->getAtomType(identsLocal[atom2]) );
927 >    pairwisePot += *(idat.pot);
928  
929 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
930 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
931 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
932 <    }
633 <    if (storageLayout_ & DataStorage::dslTorque) {
634 <      idat.t1 = &(snap_->atomData.torque[atom1]);
635 <      idat.t2 = &(snap_->atomData.torque[atom2]);
636 <    }
637 <    if (storageLayout_ & DataStorage::dslForce) {
638 <      idat.t1 = &(snap_->atomData.force[atom1]);
639 <      idat.t2 = &(snap_->atomData.force[atom2]);
640 <    }
641 < #endif    
929 >    snap_->atomData.force[atom1] += *(idat.f1);
930 >    snap_->atomData.force[atom2] -= *(idat.f1);
931 > #endif
932 >    
933    }
934  
935    /*
# Line 650 | Line 941 | namespace OpenMD {
941    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
942        
943      vector<pair<int, int> > neighborList;
944 +    groupCutoffs cuts;
945 +    bool doAllPairs = false;
946 +
947   #ifdef IS_MPI
948      cellListRow_.clear();
949      cellListCol_.clear();
# Line 657 | Line 951 | namespace OpenMD {
951      cellList_.clear();
952   #endif
953  
954 <    // dangerous to not do error checking.
661 <    RealType rCut_;
662 <
663 <    RealType rList_ = (rCut_ + skinThickness_);
954 >    RealType rList_ = (largestRcut_ + skinThickness_);
955      RealType rl2 = rList_ * rList_;
956      Snapshot* snap_ = sman_->getCurrentSnapshot();
957      Mat3x3d Hmat = snap_->getHmat();
# Line 672 | Line 963 | namespace OpenMD {
963      nCells_.y() = (int) ( Hy.length() )/ rList_;
964      nCells_.z() = (int) ( Hz.length() )/ rList_;
965  
966 +    // handle small boxes where the cell offsets can end up repeating cells
967 +    
968 +    if (nCells_.x() < 3) doAllPairs = true;
969 +    if (nCells_.y() < 3) doAllPairs = true;
970 +    if (nCells_.z() < 3) doAllPairs = true;
971 +
972      Mat3x3d invHmat = snap_->getInvHmat();
973      Vector3d rs, scaled, dr;
974      Vector3i whichCell;
975      int cellIndex;
976 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
977  
978   #ifdef IS_MPI
979 <    for (int i = 0; i < nGroupsInRow_; i++) {
980 <      rs = cgRowData.position[i];
683 <      // scaled positions relative to the box vectors
684 <      scaled = invHmat * rs;
685 <      // wrap the vector back into the unit box by subtracting integer box
686 <      // numbers
687 <      for (int j = 0; j < 3; j++)
688 <        scaled[j] -= roundMe(scaled[j]);
689 <    
690 <      // find xyz-indices of cell that cutoffGroup is in.
691 <      whichCell.x() = nCells_.x() * scaled.x();
692 <      whichCell.y() = nCells_.y() * scaled.y();
693 <      whichCell.z() = nCells_.z() * scaled.z();
694 <
695 <      // find single index of this cell:
696 <      cellIndex = Vlinear(whichCell, nCells_);
697 <      // add this cutoff group to the list of groups in this cell;
698 <      cellListRow_[cellIndex].push_back(i);
699 <    }
700 <
701 <    for (int i = 0; i < nGroupsInCol_; i++) {
702 <      rs = cgColData.position[i];
703 <      // scaled positions relative to the box vectors
704 <      scaled = invHmat * rs;
705 <      // wrap the vector back into the unit box by subtracting integer box
706 <      // numbers
707 <      for (int j = 0; j < 3; j++)
708 <        scaled[j] -= roundMe(scaled[j]);
709 <
710 <      // find xyz-indices of cell that cutoffGroup is in.
711 <      whichCell.x() = nCells_.x() * scaled.x();
712 <      whichCell.y() = nCells_.y() * scaled.y();
713 <      whichCell.z() = nCells_.z() * scaled.z();
714 <
715 <      // find single index of this cell:
716 <      cellIndex = Vlinear(whichCell, nCells_);
717 <      // add this cutoff group to the list of groups in this cell;
718 <      cellListCol_[cellIndex].push_back(i);
719 <    }
979 >    cellListRow_.resize(nCtot);
980 >    cellListCol_.resize(nCtot);
981   #else
982 <    for (int i = 0; i < nGroups_; i++) {
722 <      rs = snap_->cgData.position[i];
723 <      // scaled positions relative to the box vectors
724 <      scaled = invHmat * rs;
725 <      // wrap the vector back into the unit box by subtracting integer box
726 <      // numbers
727 <      for (int j = 0; j < 3; j++)
728 <        scaled[j] -= roundMe(scaled[j]);
729 <
730 <      // find xyz-indices of cell that cutoffGroup is in.
731 <      whichCell.x() = nCells_.x() * scaled.x();
732 <      whichCell.y() = nCells_.y() * scaled.y();
733 <      whichCell.z() = nCells_.z() * scaled.z();
734 <
735 <      // find single index of this cell:
736 <      cellIndex = Vlinear(whichCell, nCells_);
737 <      // add this cutoff group to the list of groups in this cell;
738 <      cellList_[cellIndex].push_back(i);
739 <    }
982 >    cellList_.resize(nCtot);
983   #endif
984  
985 +    if (!doAllPairs) {
986 + #ifdef IS_MPI
987  
988 +      for (int i = 0; i < nGroupsInRow_; i++) {
989 +        rs = cgRowData.position[i];
990 +        
991 +        // scaled positions relative to the box vectors
992 +        scaled = invHmat * rs;
993 +        
994 +        // wrap the vector back into the unit box by subtracting integer box
995 +        // numbers
996 +        for (int j = 0; j < 3; j++) {
997 +          scaled[j] -= roundMe(scaled[j]);
998 +          scaled[j] += 0.5;
999 +        }
1000 +        
1001 +        // find xyz-indices of cell that cutoffGroup is in.
1002 +        whichCell.x() = nCells_.x() * scaled.x();
1003 +        whichCell.y() = nCells_.y() * scaled.y();
1004 +        whichCell.z() = nCells_.z() * scaled.z();
1005 +        
1006 +        // find single index of this cell:
1007 +        cellIndex = Vlinear(whichCell, nCells_);
1008 +        
1009 +        // add this cutoff group to the list of groups in this cell;
1010 +        cellListRow_[cellIndex].push_back(i);
1011 +      }
1012 +      
1013 +      for (int i = 0; i < nGroupsInCol_; i++) {
1014 +        rs = cgColData.position[i];
1015 +        
1016 +        // scaled positions relative to the box vectors
1017 +        scaled = invHmat * rs;
1018 +        
1019 +        // wrap the vector back into the unit box by subtracting integer box
1020 +        // numbers
1021 +        for (int j = 0; j < 3; j++) {
1022 +          scaled[j] -= roundMe(scaled[j]);
1023 +          scaled[j] += 0.5;
1024 +        }
1025 +        
1026 +        // find xyz-indices of cell that cutoffGroup is in.
1027 +        whichCell.x() = nCells_.x() * scaled.x();
1028 +        whichCell.y() = nCells_.y() * scaled.y();
1029 +        whichCell.z() = nCells_.z() * scaled.z();
1030 +        
1031 +        // find single index of this cell:
1032 +        cellIndex = Vlinear(whichCell, nCells_);
1033 +        
1034 +        // add this cutoff group to the list of groups in this cell;
1035 +        cellListCol_[cellIndex].push_back(i);
1036 +      }
1037 + #else
1038 +      for (int i = 0; i < nGroups_; i++) {
1039 +        rs = snap_->cgData.position[i];
1040 +        
1041 +        // scaled positions relative to the box vectors
1042 +        scaled = invHmat * rs;
1043 +        
1044 +        // wrap the vector back into the unit box by subtracting integer box
1045 +        // numbers
1046 +        for (int j = 0; j < 3; j++) {
1047 +          scaled[j] -= roundMe(scaled[j]);
1048 +          scaled[j] += 0.5;
1049 +        }
1050 +        
1051 +        // find xyz-indices of cell that cutoffGroup is in.
1052 +        whichCell.x() = nCells_.x() * scaled.x();
1053 +        whichCell.y() = nCells_.y() * scaled.y();
1054 +        whichCell.z() = nCells_.z() * scaled.z();
1055 +        
1056 +        // find single index of this cell:
1057 +        cellIndex = Vlinear(whichCell, nCells_);      
1058 +        
1059 +        // add this cutoff group to the list of groups in this cell;
1060 +        cellList_[cellIndex].push_back(i);
1061 +      }
1062 + #endif
1063  
1064 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1065 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1066 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1067 <          Vector3i m1v(m1x, m1y, m1z);
1068 <          int m1 = Vlinear(m1v, nCells_);
749 <
750 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
751 <               os != cellOffsets_.end(); ++os) {
1064 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1065 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1066 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1067 >            Vector3i m1v(m1x, m1y, m1z);
1068 >            int m1 = Vlinear(m1v, nCells_);
1069              
1070 <            Vector3i m2v = m1v + (*os);
1071 <            
1072 <            if (m2v.x() >= nCells_.x()) {
1073 <              m2v.x() = 0;          
1074 <            } else if (m2v.x() < 0) {
1075 <              m2v.x() = nCells_.x() - 1;
1076 <            }
1077 <            
1078 <            if (m2v.y() >= nCells_.y()) {
1079 <              m2v.y() = 0;          
1080 <            } else if (m2v.y() < 0) {
1081 <              m2v.y() = nCells_.y() - 1;
1082 <            }
1083 <            
1084 <            if (m2v.z() >= nCells_.z()) {
1085 <              m2v.z() = 0;          
1086 <            } else if (m2v.z() < 0) {
1087 <              m2v.z() = nCells_.z() - 1;
1088 <            }
1089 <            
1090 <            int m2 = Vlinear (m2v, nCells_);
1091 <
1070 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1071 >                 os != cellOffsets_.end(); ++os) {
1072 >              
1073 >              Vector3i m2v = m1v + (*os);
1074 >              
1075 >              if (m2v.x() >= nCells_.x()) {
1076 >                m2v.x() = 0;          
1077 >              } else if (m2v.x() < 0) {
1078 >                m2v.x() = nCells_.x() - 1;
1079 >              }
1080 >              
1081 >              if (m2v.y() >= nCells_.y()) {
1082 >                m2v.y() = 0;          
1083 >              } else if (m2v.y() < 0) {
1084 >                m2v.y() = nCells_.y() - 1;
1085 >              }
1086 >              
1087 >              if (m2v.z() >= nCells_.z()) {
1088 >                m2v.z() = 0;          
1089 >              } else if (m2v.z() < 0) {
1090 >                m2v.z() = nCells_.z() - 1;
1091 >              }
1092 >              
1093 >              int m2 = Vlinear (m2v, nCells_);
1094 >              
1095   #ifdef IS_MPI
1096 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1097 <                 j1 != cellListRow_[m1].end(); ++j1) {
1098 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1099 <                   j2 != cellListCol_[m2].end(); ++j2) {
1100 <                              
1101 <                // Always do this if we're in different cells or if
1102 <                // we're in the same cell and the global index of the
1103 <                // j2 cutoff group is less than the j1 cutoff group
1104 <
1105 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1106 <                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1107 <                  snap_->wrapVector(dr);
1108 <                  if (dr.lengthSquare() < rl2) {
1109 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1096 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1097 >                   j1 != cellListRow_[m1].end(); ++j1) {
1098 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1099 >                     j2 != cellListCol_[m2].end(); ++j2) {
1100 >                  
1101 >                  // Always do this if we're in different cells or if
1102 >                  // we're in the same cell and the global index of the
1103 >                  // j2 cutoff group is less than the j1 cutoff group
1104 >                  
1105 >                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1106 >                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1107 >                    snap_->wrapVector(dr);
1108 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1109 >                    if (dr.lengthSquare() < cuts.third) {
1110 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1111 >                    }
1112                    }
1113                  }
1114                }
793 –            }
1115   #else
1116 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1117 <                 j1 != cellList_[m1].end(); ++j1) {
1118 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1119 <                   j2 != cellList_[m2].end(); ++j2) {
1120 <                              
1121 <                // Always do this if we're in different cells or if
1122 <                // we're in the same cell and the global index of the
1123 <                // j2 cutoff group is less than the j1 cutoff group
1124 <
1125 <                if (m2 != m1 || (*j2) < (*j1)) {
1126 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1127 <                  snap_->wrapVector(dr);
1128 <                  if (dr.lengthSquare() < rl2) {
1129 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1116 >              
1117 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1118 >                   j1 != cellList_[m1].end(); ++j1) {
1119 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1120 >                     j2 != cellList_[m2].end(); ++j2) {
1121 >                  
1122 >                  // Always do this if we're in different cells or if
1123 >                  // we're in the same cell and the global index of the
1124 >                  // j2 cutoff group is less than the j1 cutoff group
1125 >                  
1126 >                  if (m2 != m1 || (*j2) < (*j1)) {
1127 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1128 >                    snap_->wrapVector(dr);
1129 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1130 >                    if (dr.lengthSquare() < cuts.third) {
1131 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1132 >                    }
1133                    }
1134                  }
1135                }
812 –            }
1136   #endif
1137 +            }
1138            }
1139          }
1140        }
1141 +    } else {
1142 +      // branch to do all cutoff group pairs
1143 + #ifdef IS_MPI
1144 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1145 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1146 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1147 +          snap_->wrapVector(dr);
1148 +          cuts = getGroupCutoffs( j1, j2 );
1149 +          if (dr.lengthSquare() < cuts.third) {
1150 +            neighborList.push_back(make_pair(j1, j2));
1151 +          }
1152 +        }
1153 +      }
1154 + #else
1155 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1156 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1157 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1158 +          snap_->wrapVector(dr);
1159 +          cuts = getGroupCutoffs( j1, j2 );
1160 +          if (dr.lengthSquare() < cuts.third) {
1161 +            neighborList.push_back(make_pair(j1, j2));
1162 +          }
1163 +        }
1164 +      }        
1165 + #endif
1166      }
1167 <
1167 >      
1168      // save the local cutoff group positions for the check that is
1169      // done on each loop:
1170      saved_CG_positions_.clear();
1171      for (int i = 0; i < nGroups_; i++)
1172        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1173 <
1173 >    
1174      return neighborList;
1175    }
1176   } //end namespace OpenMD

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