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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 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1590 by gezelter, Mon Jul 11 01:39:49 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();
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_);
# Line 104 | Line 106 | namespace OpenMD {
106      cgColData.resize(nGroupsInCol_);
107      cgColData.setStorageLayout(DataStorage::dslPosition);
108          
109 <    identsRow.reserve(nAtomsInRow_);
110 <    identsCol.reserve(nAtomsInCol_);
109 >    identsRow.resize(nAtomsInRow_);
110 >    identsCol.resize(nAtomsInCol_);
111      
112 <    AtomCommIntRow->gather(identsLocal, identsRow);
113 <    AtomCommIntColumn->gather(identsLocal, identsCol);
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
115 +    // allocate memory for the parallel objects
116 +    AtomRowToGlobal.resize(nAtomsInRow_);
117 +    AtomColToGlobal.resize(nAtomsInCol_);
118 +    cgRowToGlobal.resize(nGroupsInRow_);
119 +    cgColToGlobal.resize(nGroupsInCol_);
120 +    massFactorsRow.resize(nAtomsInRow_);
121 +    massFactorsCol.resize(nAtomsInCol_);
122 +    pot_row.resize(nAtomsInRow_);
123 +    pot_col.resize(nAtomsInCol_);
124 +
125      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
126      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
127      
128      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
129      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
130  
131 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
132 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
131 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
132 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
133  
134      groupListRow_.clear();
135 <    groupListRow_.reserve(nGroupsInRow_);
135 >    groupListRow_.resize(nGroupsInRow_);
136      for (int i = 0; i < nGroupsInRow_; i++) {
137        int gid = cgRowToGlobal[i];
138        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 131 | Line 143 | namespace OpenMD {
143      }
144  
145      groupListCol_.clear();
146 <    groupListCol_.reserve(nGroupsInCol_);
146 >    groupListCol_.resize(nGroupsInCol_);
147      for (int i = 0; i < nGroupsInCol_; i++) {
148        int gid = cgColToGlobal[i];
149        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 141 | Line 153 | namespace OpenMD {
153        }      
154      }
155  
156 <    skipsForRowAtom.clear();
157 <    skipsForRowAtom.reserve(nAtomsInRow_);
156 >    excludesForAtom.clear();
157 >    excludesForAtom.resize(nAtomsInRow_);
158 >    toposForAtom.clear();
159 >    toposForAtom.resize(nAtomsInRow_);
160 >    topoDist.clear();
161 >    topoDist.resize(nAtomsInRow_);
162      for (int i = 0; i < nAtomsInRow_; i++) {
163        int iglob = AtomRowToGlobal[i];
148 –      for (int j = 0; j < nAtomsInCol_; j++) {
149 –        int jglob = AtomColToGlobal[j];        
150 –        if (excludes.hasPair(iglob, jglob))
151 –          skipsForRowAtom[i].push_back(j);      
152 –      }      
153 –    }
164  
155 –    toposForRowAtom.clear();
156 –    toposForRowAtom.reserve(nAtomsInRow_);
157 –    for (int i = 0; i < nAtomsInRow_; i++) {
158 –      int iglob = AtomRowToGlobal[i];
159 –      int nTopos = 0;
165        for (int j = 0; j < nAtomsInCol_; j++) {
166 <        int jglob = AtomColToGlobal[j];        
167 <        if (oneTwo.hasPair(iglob, jglob)) {
168 <          toposForRowAtom[i].push_back(j);
169 <          topoDistRow[i][nTopos] = 1;
170 <          nTopos++;
166 >        int jglob = AtomColToGlobal[j];
167 >
168 >        if (excludes->hasPair(iglob, jglob))
169 >          excludesForAtom[i].push_back(j);      
170 >        
171 >        if (oneTwo->hasPair(iglob, jglob)) {
172 >          toposForAtom[i].push_back(j);
173 >          topoDist[i].push_back(1);
174 >        } else {
175 >          if (oneThree->hasPair(iglob, jglob)) {
176 >            toposForAtom[i].push_back(j);
177 >            topoDist[i].push_back(2);
178 >          } else {
179 >            if (oneFour->hasPair(iglob, jglob)) {
180 >              toposForAtom[i].push_back(j);
181 >              topoDist[i].push_back(3);
182 >            }
183 >          }
184          }
167 –        if (oneThree.hasPair(iglob, jglob)) {
168 –          toposForRowAtom[i].push_back(j);
169 –          topoDistRow[i][nTopos] = 2;
170 –          nTopos++;
171 –        }
172 –        if (oneFour.hasPair(iglob, jglob)) {
173 –          toposForRowAtom[i].push_back(j);
174 –          topoDistRow[i][nTopos] = 3;
175 –          nTopos++;
176 –        }
185        }      
186      }
187  
188   #endif
189  
190      groupList_.clear();
191 <    groupList_.reserve(nGroups_);
191 >    groupList_.resize(nGroups_);
192      for (int i = 0; i < nGroups_; i++) {
193        int gid = cgLocalToGlobal[i];
194        for (int j = 0; j < nLocal_; j++) {
195          int aid = AtomLocalToGlobal[j];
196 <        if (globalGroupMembership[aid] == gid)
196 >        if (globalGroupMembership[aid] == gid) {
197            groupList_[i].push_back(j);
198 +        }
199        }      
200      }
201  
202 <    skipsForLocalAtom.clear();
203 <    skipsForLocalAtom.reserve(nLocal_);
202 >    excludesForAtom.clear();
203 >    excludesForAtom.resize(nLocal_);
204 >    toposForAtom.clear();
205 >    toposForAtom.resize(nLocal_);
206 >    topoDist.clear();
207 >    topoDist.resize(nLocal_);
208  
209      for (int i = 0; i < nLocal_; i++) {
210        int iglob = AtomLocalToGlobal[i];
211 +
212        for (int j = 0; j < nLocal_; j++) {
213 <        int jglob = AtomLocalToGlobal[j];        
214 <        if (excludes.hasPair(iglob, jglob))
215 <          skipsForLocalAtom[i].push_back(j);      
213 >        int jglob = AtomLocalToGlobal[j];
214 >
215 >        if (excludes->hasPair(iglob, jglob))
216 >          excludesForAtom[i].push_back(j);              
217 >        
218 >        if (oneTwo->hasPair(iglob, jglob)) {
219 >          toposForAtom[i].push_back(j);
220 >          topoDist[i].push_back(1);
221 >        } else {
222 >          if (oneThree->hasPair(iglob, jglob)) {
223 >            toposForAtom[i].push_back(j);
224 >            topoDist[i].push_back(2);
225 >          } else {
226 >            if (oneFour->hasPair(iglob, jglob)) {
227 >              toposForAtom[i].push_back(j);
228 >              topoDist[i].push_back(3);
229 >            }
230 >          }
231 >        }
232        }      
233      }
234 +    
235 +    createGtypeCutoffMap();
236  
237 <    toposForLocalAtom.clear();
238 <    toposForLocalAtom.reserve(nLocal_);
239 <    for (int i = 0; i < nLocal_; i++) {
240 <      int iglob = AtomLocalToGlobal[i];
241 <      int nTopos = 0;
242 <      for (int j = 0; j < nLocal_; j++) {
243 <        int jglob = AtomLocalToGlobal[j];        
244 <        if (oneTwo.hasPair(iglob, jglob)) {
245 <          toposForLocalAtom[i].push_back(j);
246 <          topoDistLocal[i][nTopos] = 1;
247 <          nTopos++;
237 >  }
238 >  
239 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
240 >    
241 >    RealType tol = 1e-6;
242 >    RealType rc;
243 >    int atid;
244 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
245 >    map<int, RealType> atypeCutoff;
246 >      
247 >    for (set<AtomType*>::iterator at = atypes.begin();
248 >         at != atypes.end(); ++at){
249 >      atid = (*at)->getIdent();
250 >      if (userChoseCutoff_)
251 >        atypeCutoff[atid] = userCutoff_;
252 >      else
253 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
254 >    }
255 >
256 >    vector<RealType> gTypeCutoffs;
257 >    // first we do a single loop over the cutoff groups to find the
258 >    // largest cutoff for any atypes present in this group.
259 > #ifdef IS_MPI
260 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
261 >    groupRowToGtype.resize(nGroupsInRow_);
262 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
263 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
264 >      for (vector<int>::iterator ia = atomListRow.begin();
265 >           ia != atomListRow.end(); ++ia) {            
266 >        int atom1 = (*ia);
267 >        atid = identsRow[atom1];
268 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
269 >          groupCutoffRow[cg1] = atypeCutoff[atid];
270          }
271 <        if (oneThree.hasPair(iglob, jglob)) {
272 <          toposForLocalAtom[i].push_back(j);
273 <          topoDistLocal[i][nTopos] = 2;
274 <          nTopos++;
271 >      }
272 >
273 >      bool gTypeFound = false;
274 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
275 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
276 >          groupRowToGtype[cg1] = gt;
277 >          gTypeFound = true;
278 >        }
279 >      }
280 >      if (!gTypeFound) {
281 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
282 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
283 >      }
284 >      
285 >    }
286 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
287 >    groupColToGtype.resize(nGroupsInCol_);
288 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
289 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
290 >      for (vector<int>::iterator jb = atomListCol.begin();
291 >           jb != atomListCol.end(); ++jb) {            
292 >        int atom2 = (*jb);
293 >        atid = identsCol[atom2];
294 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
295 >          groupCutoffCol[cg2] = atypeCutoff[atid];
296          }
297 <        if (oneFour.hasPair(iglob, jglob)) {
298 <          toposForLocalAtom[i].push_back(j);
299 <          topoDistLocal[i][nTopos] = 3;
300 <          nTopos++;
297 >      }
298 >      bool gTypeFound = false;
299 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
300 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
301 >          groupColToGtype[cg2] = gt;
302 >          gTypeFound = true;
303 >        }
304 >      }
305 >      if (!gTypeFound) {
306 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
307 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
308 >      }
309 >    }
310 > #else
311 >
312 >    vector<RealType> groupCutoff(nGroups_, 0.0);
313 >    groupToGtype.resize(nGroups_);
314 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
315 >
316 >      groupCutoff[cg1] = 0.0;
317 >      vector<int> atomList = getAtomsInGroupRow(cg1);
318 >
319 >      for (vector<int>::iterator ia = atomList.begin();
320 >           ia != atomList.end(); ++ia) {            
321 >        int atom1 = (*ia);
322 >        atid = idents[atom1];
323 >        if (atypeCutoff[atid] > groupCutoff[cg1]) {
324 >          groupCutoff[cg1] = atypeCutoff[atid];
325          }
326 +      }
327 +
328 +      bool gTypeFound = false;
329 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
330 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
331 +          groupToGtype[cg1] = gt;
332 +          gTypeFound = true;
333 +        }
334 +      }
335 +      if (!gTypeFound) {
336 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
337 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
338        }      
339      }
340 + #endif
341 +
342 +    // Now we find the maximum group cutoff value present in the simulation
343 +
344 +    RealType groupMax = *max_element(gTypeCutoffs.begin(),
345 +                                     gTypeCutoffs.end());
346 +
347 + #ifdef IS_MPI
348 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
349 +                              MPI::MAX);
350 + #endif
351 +    
352 +    RealType tradRcut = groupMax;
353 +
354 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
355 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
356 +        RealType thisRcut;
357 +        switch(cutoffPolicy_) {
358 +        case TRADITIONAL:
359 +          thisRcut = tradRcut;
360 +          break;
361 +        case MIX:
362 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
363 +          break;
364 +        case MAX:
365 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
366 +          break;
367 +        default:
368 +          sprintf(painCave.errMsg,
369 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
370 +                  "hit an unknown cutoff policy!\n");
371 +          painCave.severity = OPENMD_ERROR;
372 +          painCave.isFatal = 1;
373 +          simError();
374 +          break;
375 +        }
376 +
377 +        pair<int,int> key = make_pair(i,j);
378 +        gTypeCutoffMap[key].first = thisRcut;
379 +
380 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
381 +
382 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
383 +        
384 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
385 +
386 +        // sanity check
387 +        
388 +        if (userChoseCutoff_) {
389 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
390 +            sprintf(painCave.errMsg,
391 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
392 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
393 +            painCave.severity = OPENMD_ERROR;
394 +            painCave.isFatal = 1;
395 +            simError();            
396 +          }
397 +        }
398 +      }
399 +    }
400    }
230 –  
231 –  void ForceMatrixDecomposition::zeroWorkArrays() {
401  
402 <    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403 <      longRangePot_[j] = 0.0;
402 >
403 >  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
404 >    int i, j;  
405 > #ifdef IS_MPI
406 >    i = groupRowToGtype[cg1];
407 >    j = groupColToGtype[cg2];
408 > #else
409 >    i = groupToGtype[cg1];
410 >    j = groupToGtype[cg2];
411 > #endif    
412 >    return gTypeCutoffMap[make_pair(i,j)];
413 >  }
414 >
415 >  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
416 >    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
417 >      if (toposForAtom[atom1][j] == atom2)
418 >        return topoDist[atom1][j];
419      }
420 +    return 0;
421 +  }
422  
423 +  void ForceMatrixDecomposition::zeroWorkArrays() {
424 +    pairwisePot = 0.0;
425 +    embeddingPot = 0.0;
426 +
427   #ifdef IS_MPI
428      if (storageLayout_ & DataStorage::dslForce) {
429        fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
# Line 249 | Line 439 | namespace OpenMD {
439           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
440  
441      fill(pot_col.begin(), pot_col.end(),
442 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
253 <    
254 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
442 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
443  
444      if (storageLayout_ & DataStorage::dslParticlePot) {    
445 <      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
446 <      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
445 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
446 >           0.0);
447 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
448 >           0.0);
449      }
450  
451      if (storageLayout_ & DataStorage::dslDensity) {      
# Line 264 | Line 454 | namespace OpenMD {
454      }
455  
456      if (storageLayout_ & DataStorage::dslFunctional) {  
457 <      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
458 <      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
457 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
458 >           0.0);
459 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
460 >           0.0);
461      }
462  
463      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
# Line 275 | Line 467 | namespace OpenMD {
467             atomColData.functionalDerivative.end(), 0.0);
468      }
469  
470 < #else
471 <    
470 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
471 >      fill(atomRowData.skippedCharge.begin(),
472 >           atomRowData.skippedCharge.end(), 0.0);
473 >      fill(atomColData.skippedCharge.begin(),
474 >           atomColData.skippedCharge.end(), 0.0);
475 >    }
476 >
477 > #endif
478 >    // even in parallel, we need to zero out the local arrays:
479 >
480      if (storageLayout_ & DataStorage::dslParticlePot) {      
481        fill(snap_->atomData.particlePot.begin(),
482             snap_->atomData.particlePot.end(), 0.0);
# Line 294 | Line 494 | namespace OpenMD {
494        fill(snap_->atomData.functionalDerivative.begin(),
495             snap_->atomData.functionalDerivative.end(), 0.0);
496      }
497 < #endif
497 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
498 >      fill(snap_->atomData.skippedCharge.begin(),
499 >           snap_->atomData.skippedCharge.end(), 0.0);
500 >    }
501      
502    }
503  
# Line 331 | Line 534 | namespace OpenMD {
534        AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
535                                     atomColData.electroFrame);
536      }
537 +
538   #endif      
539    }
540    
# Line 397 | Line 601 | namespace OpenMD {
601      AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
602      for (int i = 0; i < n; i++)
603        snap_->atomData.force[i] += frc_tmp[i];
604 <    
401 <    
604 >        
605      if (storageLayout_ & DataStorage::dslTorque) {
606  
607 <      int nt = snap_->atomData.force.size();
607 >      int nt = snap_->atomData.torque.size();
608        vector<Vector3d> trq_tmp(nt, V3Zero);
609  
610        AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
611 <      for (int i = 0; i < n; i++) {
611 >      for (int i = 0; i < nt; i++) {
612          snap_->atomData.torque[i] += trq_tmp[i];
613          trq_tmp[i] = 0.0;
614        }
615        
616        AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
617 <      for (int i = 0; i < n; i++)
617 >      for (int i = 0; i < nt; i++)
618          snap_->atomData.torque[i] += trq_tmp[i];
619      }
620 +
621 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
622 +
623 +      int ns = snap_->atomData.skippedCharge.size();
624 +      vector<RealType> skch_tmp(ns, 0.0);
625 +
626 +      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
627 +      for (int i = 0; i < ns; i++) {
628 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
629 +        skch_tmp[i] = 0.0;
630 +      }
631 +      
632 +      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
633 +      for (int i = 0; i < ns; i++)
634 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
635 +    }
636      
637      nLocal_ = snap_->getNumberOfAtoms();
638  
# Line 425 | Line 644 | namespace OpenMD {
644      AtomCommPotRow->scatter(pot_row, pot_temp);
645  
646      for (int ii = 0;  ii < pot_temp.size(); ii++ )
647 <      pot_local += pot_temp[ii];
647 >      pairwisePot += pot_temp[ii];
648      
649      fill(pot_temp.begin(), pot_temp.end(),
650           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
# Line 433 | Line 652 | namespace OpenMD {
652      AtomCommPotColumn->scatter(pot_col, pot_temp);    
653      
654      for (int ii = 0;  ii < pot_temp.size(); ii++ )
655 <      pot_local += pot_temp[ii];
437 <    
655 >      pairwisePot += pot_temp[ii];    
656   #endif
657 +
658    }
659  
660    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 510 | Line 729 | namespace OpenMD {
729   #ifdef IS_MPI
730      return massFactorsRow[atom1];
731   #else
732 <    return massFactorsLocal[atom1];
732 >    return massFactors[atom1];
733   #endif
734    }
735  
# Line 518 | Line 737 | namespace OpenMD {
737   #ifdef IS_MPI
738      return massFactorsCol[atom2];
739   #else
740 <    return massFactorsLocal[atom2];
740 >    return massFactors[atom2];
741   #endif
742  
743    }
# Line 536 | Line 755 | namespace OpenMD {
755      return d;    
756    }
757  
758 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
759 < #ifdef IS_MPI
541 <    return skipsForRowAtom[atom1];
542 < #else
543 <    return skipsForLocalAtom[atom1];
544 < #endif
758 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
759 >    return excludesForAtom[atom1];
760    }
761  
762    /**
763 <   * There are a number of reasons to skip a pair or a
549 <   * particle. Mostly we do this to exclude atoms who are involved in
550 <   * short range interactions (bonds, bends, torsions), but we also
551 <   * need to exclude some overcounted interactions that result from
763 >   * We need to exclude some overcounted interactions that result from
764     * the parallel decomposition.
765     */
766    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
# Line 568 | Line 780 | namespace OpenMD {
780      } else {
781        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
782      }
783 + #endif
784 +    return false;
785 +  }
786 +
787 +  /**
788 +   * We need to handle the interactions for atoms who are involved in
789 +   * the same rigid body as well as some short range interactions
790 +   * (bonds, bends, torsions) differently from other interactions.
791 +   * We'll still visit the pairwise routines, but with a flag that
792 +   * tells those routines to exclude the pair from direct long range
793 +   * interactions.  Some indirect interactions (notably reaction
794 +   * field) must still be handled for these pairs.
795 +   */
796 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
797 +    int unique_id_2;
798 +    
799 + #ifdef IS_MPI
800 +    // in MPI, we have to look up the unique IDs for the row atom.
801 +    unique_id_2 = AtomColToGlobal[atom2];
802   #else
803      // in the normal loop, the atom numbers are unique
573 –    unique_id_1 = atom1;
804      unique_id_2 = atom2;
805   #endif
806      
807 < #ifdef IS_MPI
808 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
579 <         i != skipsForRowAtom[atom1].end(); ++i) {
807 >    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
808 >         i != excludesForAtom[atom1].end(); ++i) {
809        if ( (*i) == unique_id_2 ) return true;
581 –    }    
582 – #else
583 –    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
584 –         i != skipsForLocalAtom[atom1].end(); ++i) {
585 –      if ( (*i) == unique_id_2 ) return true;
586 –    }    
587 – #endif
588 –  }
589 –
590 –  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
591 –    
592 – #ifdef IS_MPI
593 –    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
594 –      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
810      }
596 – #else
597 –    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
598 –      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
599 –    }
600 – #endif
811  
812 <    // zero is default for unconnected (i.e. normal) pair interactions
603 <    return 0;
812 >    return false;
813    }
814  
815 +
816    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
817   #ifdef IS_MPI
818      atomRowData.force[atom1] += fg;
# Line 620 | Line 830 | namespace OpenMD {
830    }
831  
832      // filling interaction blocks with pointers
833 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
834 <    InteractionData idat;
833 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
834 >                                                     int atom1, int atom2) {
835  
836 +    idat.excluded = excludeAtomPair(atom1, atom2);
837 +  
838   #ifdef IS_MPI
839      
840      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
841                               ff_->getAtomType(identsCol[atom2]) );
630 –
842      
843      if (storageLayout_ & DataStorage::dslAmat) {
844        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 664 | Line 875 | namespace OpenMD {
875        idat.particlePot2 = &(atomColData.particlePot[atom2]);
876      }
877  
878 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
879 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
880 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
881 +    }
882 +
883   #else
884  
885 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
886 <                             ff_->getAtomType(identsLocal[atom2]) );
885 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
886 >                             ff_->getAtomType(idents[atom2]) );
887  
888      if (storageLayout_ & DataStorage::dslAmat) {
889        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 684 | Line 900 | namespace OpenMD {
900        idat.t2 = &(snap_->atomData.torque[atom2]);
901      }
902  
903 <    if (storageLayout_ & DataStorage::dslDensity) {
903 >    if (storageLayout_ & DataStorage::dslDensity) {    
904        idat.rho1 = &(snap_->atomData.density[atom1]);
905        idat.rho2 = &(snap_->atomData.density[atom2]);
906      }
# Line 704 | Line 920 | namespace OpenMD {
920        idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
921      }
922  
923 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
924 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
925 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
926 +    }
927   #endif
708 –    return idat;
928    }
929  
930    
931 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
931 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
932   #ifdef IS_MPI
933      pot_row[atom1] += 0.5 *  *(idat.pot);
934      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 717 | Line 936 | namespace OpenMD {
936      atomRowData.force[atom1] += *(idat.f1);
937      atomColData.force[atom2] -= *(idat.f1);
938   #else
939 <    longRangePot_ += *(idat.pot);
940 <    
939 >    pairwisePot += *(idat.pot);
940 >
941      snap_->atomData.force[atom1] += *(idat.f1);
942      snap_->atomData.force[atom2] -= *(idat.f1);
943   #endif
944 <
944 >    
945    }
946  
728 –
729 –  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
730 –
731 –    InteractionData idat;
732 – #ifdef IS_MPI
733 –    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
734 –                             ff_->getAtomType(identsCol[atom2]) );
735 –
736 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
737 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
738 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
739 –    }
740 –    if (storageLayout_ & DataStorage::dslTorque) {
741 –      idat.t1 = &(atomRowData.torque[atom1]);
742 –      idat.t2 = &(atomColData.torque[atom2]);
743 –    }
744 – #else
745 –    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
746 –                             ff_->getAtomType(identsLocal[atom2]) );
747 –
748 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
749 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
750 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
751 –    }
752 –    if (storageLayout_ & DataStorage::dslTorque) {
753 –      idat.t1 = &(snap_->atomData.torque[atom1]);
754 –      idat.t2 = &(snap_->atomData.torque[atom2]);
755 –    }
756 – #endif    
757 –  }
758 –
947    /*
948     * buildNeighborList
949     *
# Line 765 | Line 953 | namespace OpenMD {
953    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
954        
955      vector<pair<int, int> > neighborList;
956 +    groupCutoffs cuts;
957 +    bool doAllPairs = false;
958 +
959   #ifdef IS_MPI
960      cellListRow_.clear();
961      cellListCol_.clear();
# Line 772 | Line 963 | namespace OpenMD {
963      cellList_.clear();
964   #endif
965  
966 <    // dangerous to not do error checking.
776 <    RealType rCut_;
777 <
778 <    RealType rList_ = (rCut_ + skinThickness_);
966 >    RealType rList_ = (largestRcut_ + skinThickness_);
967      RealType rl2 = rList_ * rList_;
968      Snapshot* snap_ = sman_->getCurrentSnapshot();
969      Mat3x3d Hmat = snap_->getHmat();
# Line 787 | Line 975 | namespace OpenMD {
975      nCells_.y() = (int) ( Hy.length() )/ rList_;
976      nCells_.z() = (int) ( Hz.length() )/ rList_;
977  
978 +    // handle small boxes where the cell offsets can end up repeating cells
979 +    
980 +    if (nCells_.x() < 3) doAllPairs = true;
981 +    if (nCells_.y() < 3) doAllPairs = true;
982 +    if (nCells_.z() < 3) doAllPairs = true;
983 +
984      Mat3x3d invHmat = snap_->getInvHmat();
985      Vector3d rs, scaled, dr;
986      Vector3i whichCell;
987      int cellIndex;
988 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
989  
990   #ifdef IS_MPI
991 <    for (int i = 0; i < nGroupsInRow_; i++) {
992 <      rs = cgRowData.position[i];
798 <      // scaled positions relative to the box vectors
799 <      scaled = invHmat * rs;
800 <      // wrap the vector back into the unit box by subtracting integer box
801 <      // numbers
802 <      for (int j = 0; j < 3; j++)
803 <        scaled[j] -= roundMe(scaled[j]);
804 <    
805 <      // find xyz-indices of cell that cutoffGroup is in.
806 <      whichCell.x() = nCells_.x() * scaled.x();
807 <      whichCell.y() = nCells_.y() * scaled.y();
808 <      whichCell.z() = nCells_.z() * scaled.z();
809 <
810 <      // find single index of this cell:
811 <      cellIndex = Vlinear(whichCell, nCells_);
812 <      // add this cutoff group to the list of groups in this cell;
813 <      cellListRow_[cellIndex].push_back(i);
814 <    }
815 <
816 <    for (int i = 0; i < nGroupsInCol_; i++) {
817 <      rs = cgColData.position[i];
818 <      // scaled positions relative to the box vectors
819 <      scaled = invHmat * rs;
820 <      // wrap the vector back into the unit box by subtracting integer box
821 <      // numbers
822 <      for (int j = 0; j < 3; j++)
823 <        scaled[j] -= roundMe(scaled[j]);
824 <
825 <      // find xyz-indices of cell that cutoffGroup is in.
826 <      whichCell.x() = nCells_.x() * scaled.x();
827 <      whichCell.y() = nCells_.y() * scaled.y();
828 <      whichCell.z() = nCells_.z() * scaled.z();
829 <
830 <      // find single index of this cell:
831 <      cellIndex = Vlinear(whichCell, nCells_);
832 <      // add this cutoff group to the list of groups in this cell;
833 <      cellListCol_[cellIndex].push_back(i);
834 <    }
991 >    cellListRow_.resize(nCtot);
992 >    cellListCol_.resize(nCtot);
993   #else
994 <    for (int i = 0; i < nGroups_; i++) {
837 <      rs = snap_->cgData.position[i];
838 <      // scaled positions relative to the box vectors
839 <      scaled = invHmat * rs;
840 <      // wrap the vector back into the unit box by subtracting integer box
841 <      // numbers
842 <      for (int j = 0; j < 3; j++)
843 <        scaled[j] -= roundMe(scaled[j]);
844 <
845 <      // find xyz-indices of cell that cutoffGroup is in.
846 <      whichCell.x() = nCells_.x() * scaled.x();
847 <      whichCell.y() = nCells_.y() * scaled.y();
848 <      whichCell.z() = nCells_.z() * scaled.z();
849 <
850 <      // find single index of this cell:
851 <      cellIndex = Vlinear(whichCell, nCells_);
852 <      // add this cutoff group to the list of groups in this cell;
853 <      cellList_[cellIndex].push_back(i);
854 <    }
994 >    cellList_.resize(nCtot);
995   #endif
996  
997 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
858 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
859 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
860 <          Vector3i m1v(m1x, m1y, m1z);
861 <          int m1 = Vlinear(m1v, nCells_);
862 <
863 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
864 <               os != cellOffsets_.end(); ++os) {
865 <            
866 <            Vector3i m2v = m1v + (*os);
867 <            
868 <            if (m2v.x() >= nCells_.x()) {
869 <              m2v.x() = 0;          
870 <            } else if (m2v.x() < 0) {
871 <              m2v.x() = nCells_.x() - 1;
872 <            }
873 <            
874 <            if (m2v.y() >= nCells_.y()) {
875 <              m2v.y() = 0;          
876 <            } else if (m2v.y() < 0) {
877 <              m2v.y() = nCells_.y() - 1;
878 <            }
879 <            
880 <            if (m2v.z() >= nCells_.z()) {
881 <              m2v.z() = 0;          
882 <            } else if (m2v.z() < 0) {
883 <              m2v.z() = nCells_.z() - 1;
884 <            }
885 <            
886 <            int m2 = Vlinear (m2v, nCells_);
887 <
997 >    if (!doAllPairs) {
998   #ifdef IS_MPI
889 –            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
890 –                 j1 != cellListRow_[m1].end(); ++j1) {
891 –              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
892 –                   j2 != cellListCol_[m2].end(); ++j2) {
893 –                              
894 –                // Always do this if we're in different cells or if
895 –                // we're in the same cell and the global index of the
896 –                // j2 cutoff group is less than the j1 cutoff group
999  
1000 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1001 <                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1002 <                  snap_->wrapVector(dr);
1003 <                  if (dr.lengthSquare() < rl2) {
1004 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1000 >      for (int i = 0; i < nGroupsInRow_; i++) {
1001 >        rs = cgRowData.position[i];
1002 >        
1003 >        // scaled positions relative to the box vectors
1004 >        scaled = invHmat * rs;
1005 >        
1006 >        // wrap the vector back into the unit box by subtracting integer box
1007 >        // numbers
1008 >        for (int j = 0; j < 3; j++) {
1009 >          scaled[j] -= roundMe(scaled[j]);
1010 >          scaled[j] += 0.5;
1011 >        }
1012 >        
1013 >        // find xyz-indices of cell that cutoffGroup is in.
1014 >        whichCell.x() = nCells_.x() * scaled.x();
1015 >        whichCell.y() = nCells_.y() * scaled.y();
1016 >        whichCell.z() = nCells_.z() * scaled.z();
1017 >        
1018 >        // find single index of this cell:
1019 >        cellIndex = Vlinear(whichCell, nCells_);
1020 >        
1021 >        // add this cutoff group to the list of groups in this cell;
1022 >        cellListRow_[cellIndex].push_back(i);
1023 >      }
1024 >      
1025 >      for (int i = 0; i < nGroupsInCol_; i++) {
1026 >        rs = cgColData.position[i];
1027 >        
1028 >        // scaled positions relative to the box vectors
1029 >        scaled = invHmat * rs;
1030 >        
1031 >        // wrap the vector back into the unit box by subtracting integer box
1032 >        // numbers
1033 >        for (int j = 0; j < 3; j++) {
1034 >          scaled[j] -= roundMe(scaled[j]);
1035 >          scaled[j] += 0.5;
1036 >        }
1037 >        
1038 >        // find xyz-indices of cell that cutoffGroup is in.
1039 >        whichCell.x() = nCells_.x() * scaled.x();
1040 >        whichCell.y() = nCells_.y() * scaled.y();
1041 >        whichCell.z() = nCells_.z() * scaled.z();
1042 >        
1043 >        // find single index of this cell:
1044 >        cellIndex = Vlinear(whichCell, nCells_);
1045 >        
1046 >        // add this cutoff group to the list of groups in this cell;
1047 >        cellListCol_[cellIndex].push_back(i);
1048 >      }
1049 > #else
1050 >      for (int i = 0; i < nGroups_; i++) {
1051 >        rs = snap_->cgData.position[i];
1052 >        
1053 >        // scaled positions relative to the box vectors
1054 >        scaled = invHmat * rs;
1055 >        
1056 >        // wrap the vector back into the unit box by subtracting integer box
1057 >        // numbers
1058 >        for (int j = 0; j < 3; j++) {
1059 >          scaled[j] -= roundMe(scaled[j]);
1060 >          scaled[j] += 0.5;
1061 >        }
1062 >        
1063 >        // find xyz-indices of cell that cutoffGroup is in.
1064 >        whichCell.x() = nCells_.x() * scaled.x();
1065 >        whichCell.y() = nCells_.y() * scaled.y();
1066 >        whichCell.z() = nCells_.z() * scaled.z();
1067 >        
1068 >        // find single index of this cell:
1069 >        cellIndex = Vlinear(whichCell, nCells_);      
1070 >        
1071 >        // add this cutoff group to the list of groups in this cell;
1072 >        cellList_[cellIndex].push_back(i);
1073 >      }
1074 > #endif
1075 >
1076 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1077 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1078 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1079 >            Vector3i m1v(m1x, m1y, m1z);
1080 >            int m1 = Vlinear(m1v, nCells_);
1081 >            
1082 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1083 >                 os != cellOffsets_.end(); ++os) {
1084 >              
1085 >              Vector3i m2v = m1v + (*os);
1086 >              
1087 >              if (m2v.x() >= nCells_.x()) {
1088 >                m2v.x() = 0;          
1089 >              } else if (m2v.x() < 0) {
1090 >                m2v.x() = nCells_.x() - 1;
1091 >              }
1092 >              
1093 >              if (m2v.y() >= nCells_.y()) {
1094 >                m2v.y() = 0;          
1095 >              } else if (m2v.y() < 0) {
1096 >                m2v.y() = nCells_.y() - 1;
1097 >              }
1098 >              
1099 >              if (m2v.z() >= nCells_.z()) {
1100 >                m2v.z() = 0;          
1101 >              } else if (m2v.z() < 0) {
1102 >                m2v.z() = nCells_.z() - 1;
1103 >              }
1104 >              
1105 >              int m2 = Vlinear (m2v, nCells_);
1106 >              
1107 > #ifdef IS_MPI
1108 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1109 >                   j1 != cellListRow_[m1].end(); ++j1) {
1110 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1111 >                     j2 != cellListCol_[m2].end(); ++j2) {
1112 >                  
1113 >                  // Always do this if we're in different cells or if
1114 >                  // we're in the same cell and the global index of the
1115 >                  // j2 cutoff group is less than the j1 cutoff group
1116 >                  
1117 >                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1118 >                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1119 >                    snap_->wrapVector(dr);
1120 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1121 >                    if (dr.lengthSquare() < cuts.third) {
1122 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1123 >                    }
1124                    }
1125                  }
1126                }
906 –            }
1127   #else
1128 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1129 <                 j1 != cellList_[m1].end(); ++j1) {
1130 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1131 <                   j2 != cellList_[m2].end(); ++j2) {
1132 <                              
1133 <                // Always do this if we're in different cells or if
1134 <                // we're in the same cell and the global index of the
1135 <                // j2 cutoff group is less than the j1 cutoff group
1136 <
1137 <                if (m2 != m1 || (*j2) < (*j1)) {
1138 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1139 <                  snap_->wrapVector(dr);
1140 <                  if (dr.lengthSquare() < rl2) {
1141 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1128 >              
1129 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1130 >                   j1 != cellList_[m1].end(); ++j1) {
1131 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1132 >                     j2 != cellList_[m2].end(); ++j2) {
1133 >                  
1134 >                  // Always do this if we're in different cells or if
1135 >                  // we're in the same cell and the global index of the
1136 >                  // j2 cutoff group is less than the j1 cutoff group
1137 >                  
1138 >                  if (m2 != m1 || (*j2) < (*j1)) {
1139 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1140 >                    snap_->wrapVector(dr);
1141 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1142 >                    if (dr.lengthSquare() < cuts.third) {
1143 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1144 >                    }
1145                    }
1146                  }
1147                }
925 –            }
1148   #endif
1149 +            }
1150            }
1151          }
1152        }
1153 +    } else {
1154 +      // branch to do all cutoff group pairs
1155 + #ifdef IS_MPI
1156 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1157 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1158 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1159 +          snap_->wrapVector(dr);
1160 +          cuts = getGroupCutoffs( j1, j2 );
1161 +          if (dr.lengthSquare() < cuts.third) {
1162 +            neighborList.push_back(make_pair(j1, j2));
1163 +          }
1164 +        }
1165 +      }
1166 + #else
1167 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1168 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1169 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1170 +          snap_->wrapVector(dr);
1171 +          cuts = getGroupCutoffs( j1, j2 );
1172 +          if (dr.lengthSquare() < cuts.third) {
1173 +            neighborList.push_back(make_pair(j1, j2));
1174 +          }
1175 +        }
1176 +      }        
1177 + #endif
1178      }
1179 <
1179 >      
1180      // save the local cutoff group positions for the check that is
1181      // done on each loop:
1182      saved_CG_positions_.clear();
1183      for (int i = 0; i < nGroups_; i++)
1184        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1185 <
1185 >    
1186      return neighborList;
1187    }
1188   } //end namespace OpenMD

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