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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 1567 by gezelter, Tue May 24 21:24:45 2011 UTC vs.
Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC

# Line 42 | Line 42
42   #include "math/SquareMatrix3.hpp"
43   #include "nonbonded/NonBondedInteraction.hpp"
44   #include "brains/SnapshotManager.hpp"
45 + #include "brains/PairList.hpp"
46  
47   using namespace std;
48   namespace OpenMD {
# Line 54 | Line 55 | namespace OpenMD {
55    void ForceMatrixDecomposition::distributeInitialData() {
56      snap_ = sman_->getCurrentSnapshot();
57      storageLayout_ = sman_->getStorageLayout();
58 +    ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
60 <    nGroups_ = snap_->getNumberOfCutoffGroups();
60 >    
61 >    nGroups_ = info_->getNLocalCutoffGroups();
62 >    // gather the information for atomtype IDs (atids):
63 >    idents = info_->getIdentArray();
64 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
65 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
66 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67  
68 +    massFactors = info_->getMassFactors();
69 +
70 +    PairList* excludes = info_->getExcludedInteractions();
71 +    PairList* oneTwo = info_->getOneTwoInteractions();
72 +    PairList* oneThree = info_->getOneThreeInteractions();
73 +    PairList* oneFour = info_->getOneFourInteractions();
74 +
75   #ifdef IS_MPI
76  
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 88 | 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));
94 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
95 <                                      vector<RealType> (nAtomsInCol_, 0.0));
96 <
97 <
98 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
100 –    // gather the information for atomtype IDs (atids):
101 –    vector<int> identsLocal = info_->getIdentArray();
102 –    identsRow.reserve(nAtomsInRow_);
103 –    identsCol.reserve(nAtomsInCol_);
104 –    
105 –    AtomCommIntRow->gather(identsLocal, identsRow);
106 –    AtomCommIntColumn->gather(identsLocal, identsCol);
107 –    
108 –    AtomLocalToGlobal = info_->getGlobalAtomIndices();
115      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
117      
112 –    cgLocalToGlobal = info_->getGlobalGroupIndices();
118      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120  
121 <    // still need:
122 <    // topoDist
123 <    // exclude
121 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
122 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
123 >
124 >    groupListRow_.clear();
125 >    groupListRow_.resize(nGroupsInRow_);
126 >    for (int i = 0; i < nGroupsInRow_; i++) {
127 >      int gid = cgRowToGlobal[i];
128 >      for (int j = 0; j < nAtomsInRow_; j++) {
129 >        int aid = AtomRowToGlobal[j];
130 >        if (globalGroupMembership[aid] == gid)
131 >          groupListRow_[i].push_back(j);
132 >      }      
133 >    }
134 >
135 >    groupListCol_.clear();
136 >    groupListCol_.resize(nGroupsInCol_);
137 >    for (int i = 0; i < nGroupsInCol_; i++) {
138 >      int gid = cgColToGlobal[i];
139 >      for (int j = 0; j < nAtomsInCol_; j++) {
140 >        int aid = AtomColToGlobal[j];
141 >        if (globalGroupMembership[aid] == gid)
142 >          groupListCol_[i].push_back(j);
143 >      }      
144 >    }
145 >
146 >    excludesForAtom.clear();
147 >    excludesForAtom.resize(nAtomsInRow_);
148 >    toposForAtom.clear();
149 >    toposForAtom.resize(nAtomsInRow_);
150 >    topoDist.clear();
151 >    topoDist.resize(nAtomsInRow_);
152 >    for (int i = 0; i < nAtomsInRow_; i++) {
153 >      int iglob = AtomRowToGlobal[i];
154 >
155 >      for (int j = 0; j < nAtomsInCol_; j++) {
156 >        int jglob = AtomColToGlobal[j];
157 >
158 >        if (excludes->hasPair(iglob, jglob))
159 >          excludesForAtom[i].push_back(j);      
160 >        
161 >        if (oneTwo->hasPair(iglob, jglob)) {
162 >          toposForAtom[i].push_back(j);
163 >          topoDist[i].push_back(1);
164 >        } else {
165 >          if (oneThree->hasPair(iglob, jglob)) {
166 >            toposForAtom[i].push_back(j);
167 >            topoDist[i].push_back(2);
168 >          } else {
169 >            if (oneFour->hasPair(iglob, jglob)) {
170 >              toposForAtom[i].push_back(j);
171 >              topoDist[i].push_back(3);
172 >            }
173 >          }
174 >        }
175 >      }      
176 >    }
177 >
178   #endif
179 +
180 +    groupList_.clear();
181 +    groupList_.resize(nGroups_);
182 +    for (int i = 0; i < nGroups_; i++) {
183 +      int gid = cgLocalToGlobal[i];
184 +      for (int j = 0; j < nLocal_; j++) {
185 +        int aid = AtomLocalToGlobal[j];
186 +        if (globalGroupMembership[aid] == gid) {
187 +          groupList_[i].push_back(j);
188 +        }
189 +      }      
190 +    }
191 +
192 +    excludesForAtom.clear();
193 +    excludesForAtom.resize(nLocal_);
194 +    toposForAtom.clear();
195 +    toposForAtom.resize(nLocal_);
196 +    topoDist.clear();
197 +    topoDist.resize(nLocal_);
198 +
199 +    for (int i = 0; i < nLocal_; i++) {
200 +      int iglob = AtomLocalToGlobal[i];
201 +
202 +      for (int j = 0; j < nLocal_; j++) {
203 +        int jglob = AtomLocalToGlobal[j];
204 +
205 +        if (excludes->hasPair(iglob, jglob))
206 +          excludesForAtom[i].push_back(j);              
207 +        
208 +        if (oneTwo->hasPair(iglob, jglob)) {
209 +          toposForAtom[i].push_back(j);
210 +          topoDist[i].push_back(1);
211 +        } else {
212 +          if (oneThree->hasPair(iglob, jglob)) {
213 +            toposForAtom[i].push_back(j);
214 +            topoDist[i].push_back(2);
215 +          } else {
216 +            if (oneFour->hasPair(iglob, jglob)) {
217 +              toposForAtom[i].push_back(j);
218 +              topoDist[i].push_back(3);
219 +            }
220 +          }
221 +        }
222 +      }      
223 +    }
224 +    
225 +    createGtypeCutoffMap();
226 +
227    }
228 +  
229 +  void ForceMatrixDecomposition::createGtypeCutoffMap() {
230      
231 +    RealType tol = 1e-6;
232 +    RealType rc;
233 +    int atid;
234 +    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
235 +    map<int, RealType> atypeCutoff;
236 +      
237 +    for (set<AtomType*>::iterator at = atypes.begin();
238 +         at != atypes.end(); ++at){
239 +      atid = (*at)->getIdent();
240 +      if (userChoseCutoff_)
241 +        atypeCutoff[atid] = userCutoff_;
242 +      else
243 +        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
244 +    }
245  
246 +    vector<RealType> gTypeCutoffs;
247 +    // first we do a single loop over the cutoff groups to find the
248 +    // largest cutoff for any atypes present in this group.
249 + #ifdef IS_MPI
250 +    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
251 +    groupRowToGtype.resize(nGroupsInRow_);
252 +    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
253 +      vector<int> atomListRow = getAtomsInGroupRow(cg1);
254 +      for (vector<int>::iterator ia = atomListRow.begin();
255 +           ia != atomListRow.end(); ++ia) {            
256 +        int atom1 = (*ia);
257 +        atid = identsRow[atom1];
258 +        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
259 +          groupCutoffRow[cg1] = atypeCutoff[atid];
260 +        }
261 +      }
262  
263 +      bool gTypeFound = false;
264 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
265 +        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
266 +          groupRowToGtype[cg1] = gt;
267 +          gTypeFound = true;
268 +        }
269 +      }
270 +      if (!gTypeFound) {
271 +        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
272 +        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
273 +      }
274 +      
275 +    }
276 +    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
277 +    groupColToGtype.resize(nGroupsInCol_);
278 +    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
279 +      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
280 +      for (vector<int>::iterator jb = atomListCol.begin();
281 +           jb != atomListCol.end(); ++jb) {            
282 +        int atom2 = (*jb);
283 +        atid = identsCol[atom2];
284 +        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
285 +          groupCutoffCol[cg2] = atypeCutoff[atid];
286 +        }
287 +      }
288 +      bool gTypeFound = false;
289 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
290 +        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
291 +          groupColToGtype[cg2] = gt;
292 +          gTypeFound = true;
293 +        }
294 +      }
295 +      if (!gTypeFound) {
296 +        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
297 +        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
298 +      }
299 +    }
300 + #else
301 +
302 +    vector<RealType> groupCutoff(nGroups_, 0.0);
303 +    groupToGtype.resize(nGroups_);
304 +    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305 +
306 +      groupCutoff[cg1] = 0.0;
307 +      vector<int> atomList = getAtomsInGroupRow(cg1);
308 +
309 +      for (vector<int>::iterator ia = atomList.begin();
310 +           ia != atomList.end(); ++ia) {            
311 +        int atom1 = (*ia);
312 +        atid = idents[atom1];
313 +        if (atypeCutoff[atid] > groupCutoff[cg1]) {
314 +          groupCutoff[cg1] = atypeCutoff[atid];
315 +        }
316 +      }
317 +
318 +      bool gTypeFound = false;
319 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
320 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
321 +          groupToGtype[cg1] = gt;
322 +          gTypeFound = true;
323 +        }
324 +      }
325 +      if (!gTypeFound) {
326 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
327 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
328 +      }      
329 +    }
330 + #endif
331 +
332 +    // Now we find the maximum group cutoff value present in the simulation
333 +
334 +    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
335 +
336 + #ifdef IS_MPI
337 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
338 + #endif
339 +    
340 +    RealType tradRcut = groupMax;
341 +
342 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
343 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
344 +        RealType thisRcut;
345 +        switch(cutoffPolicy_) {
346 +        case TRADITIONAL:
347 +          thisRcut = tradRcut;
348 +          break;
349 +        case MIX:
350 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
351 +          break;
352 +        case MAX:
353 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
354 +          break;
355 +        default:
356 +          sprintf(painCave.errMsg,
357 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
358 +                  "hit an unknown cutoff policy!\n");
359 +          painCave.severity = OPENMD_ERROR;
360 +          painCave.isFatal = 1;
361 +          simError();
362 +          break;
363 +        }
364 +
365 +        pair<int,int> key = make_pair(i,j);
366 +        gTypeCutoffMap[key].first = thisRcut;
367 +
368 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
369 +
370 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
371 +        
372 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
373 +
374 +        // sanity check
375 +        
376 +        if (userChoseCutoff_) {
377 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
378 +            sprintf(painCave.errMsg,
379 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
380 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
381 +            painCave.severity = OPENMD_ERROR;
382 +            painCave.isFatal = 1;
383 +            simError();            
384 +          }
385 +        }
386 +      }
387 +    }
388 +  }
389 +
390 +
391 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
392 +    int i, j;  
393 + #ifdef IS_MPI
394 +    i = groupRowToGtype[cg1];
395 +    j = groupColToGtype[cg2];
396 + #else
397 +    i = groupToGtype[cg1];
398 +    j = groupToGtype[cg2];
399 + #endif    
400 +    return gTypeCutoffMap[make_pair(i,j)];
401 +  }
402 +
403 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
404 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
405 +      if (toposForAtom[atom1][j] == atom2)
406 +        return topoDist[atom1][j];
407 +    }
408 +    return 0;
409 +  }
410 +
411 +  void ForceMatrixDecomposition::zeroWorkArrays() {
412 +    pairwisePot = 0.0;
413 +    embeddingPot = 0.0;
414 +
415 + #ifdef IS_MPI
416 +    if (storageLayout_ & DataStorage::dslForce) {
417 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
418 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
419 +    }
420 +
421 +    if (storageLayout_ & DataStorage::dslTorque) {
422 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
423 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
424 +    }
425 +    
426 +    fill(pot_row.begin(), pot_row.end(),
427 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
428 +
429 +    fill(pot_col.begin(), pot_col.end(),
430 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
431 +
432 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
433 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
434 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
435 +    }
436 +
437 +    if (storageLayout_ & DataStorage::dslDensity) {      
438 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
439 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
440 +    }
441 +
442 +    if (storageLayout_ & DataStorage::dslFunctional) {  
443 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
444 +      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
445 +    }
446 +
447 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
448 +      fill(atomRowData.functionalDerivative.begin(),
449 +           atomRowData.functionalDerivative.end(), 0.0);
450 +      fill(atomColData.functionalDerivative.begin(),
451 +           atomColData.functionalDerivative.end(), 0.0);
452 +    }
453 +
454 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
455 +      fill(atomRowData.skippedCharge.begin(),
456 +           atomRowData.skippedCharge.end(), 0.0);
457 +      fill(atomColData.skippedCharge.begin(),
458 +           atomColData.skippedCharge.end(), 0.0);
459 +    }
460 +
461 + #else
462 +    
463 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
464 +      fill(snap_->atomData.particlePot.begin(),
465 +           snap_->atomData.particlePot.end(), 0.0);
466 +    }
467 +    
468 +    if (storageLayout_ & DataStorage::dslDensity) {      
469 +      fill(snap_->atomData.density.begin(),
470 +           snap_->atomData.density.end(), 0.0);
471 +    }
472 +    if (storageLayout_ & DataStorage::dslFunctional) {
473 +      fill(snap_->atomData.functional.begin(),
474 +           snap_->atomData.functional.end(), 0.0);
475 +    }
476 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
477 +      fill(snap_->atomData.functionalDerivative.begin(),
478 +           snap_->atomData.functionalDerivative.end(), 0.0);
479 +    }
480 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
481 +      fill(snap_->atomData.skippedCharge.begin(),
482 +           snap_->atomData.skippedCharge.end(), 0.0);
483 +    }
484 + #endif
485 +    
486 +  }
487 +
488 +
489    void ForceMatrixDecomposition::distributeData()  {
490      snap_ = sman_->getCurrentSnapshot();
491      storageLayout_ = sman_->getStorageLayout();
# Line 156 | Line 521 | namespace OpenMD {
521   #endif      
522    }
523    
524 +  /* collects information obtained during the pre-pair loop onto local
525 +   * data structures.
526 +   */
527    void ForceMatrixDecomposition::collectIntermediateData() {
528      snap_ = sman_->getCurrentSnapshot();
529      storageLayout_ = sman_->getStorageLayout();
# Line 167 | Line 535 | namespace OpenMD {
535                                 snap_->atomData.density);
536        
537        int n = snap_->atomData.density.size();
538 <      std::vector<RealType> rho_tmp(n, 0.0);
538 >      vector<RealType> rho_tmp(n, 0.0);
539        AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
540        for (int i = 0; i < n; i++)
541          snap_->atomData.density[i] += rho_tmp[i];
542      }
543   #endif
544    }
545 <  
545 >
546 >  /*
547 >   * redistributes information obtained during the pre-pair loop out to
548 >   * row and column-indexed data structures
549 >   */
550    void ForceMatrixDecomposition::distributeIntermediateData() {
551      snap_ = sman_->getCurrentSnapshot();
552      storageLayout_ = sman_->getStorageLayout();
# Line 216 | Line 588 | namespace OpenMD {
588      
589      if (storageLayout_ & DataStorage::dslTorque) {
590  
591 <      int nt = snap_->atomData.force.size();
591 >      int nt = snap_->atomData.torque.size();
592        vector<Vector3d> trq_tmp(nt, V3Zero);
593  
594        AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
595 <      for (int i = 0; i < n; i++) {
595 >      for (int i = 0; i < nt; i++) {
596          snap_->atomData.torque[i] += trq_tmp[i];
597          trq_tmp[i] = 0.0;
598        }
599        
600        AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
601 <      for (int i = 0; i < n; i++)
601 >      for (int i = 0; i < nt; i++)
602          snap_->atomData.torque[i] += trq_tmp[i];
603      }
604 +
605 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
606 +
607 +      int ns = snap_->atomData.skippedCharge.size();
608 +      vector<RealType> skch_tmp(ns, 0.0);
609 +
610 +      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
611 +      for (int i = 0; i < ns; i++) {
612 +        snap_->atomData.skippedCharge[i] = skch_tmp[i];
613 +        skch_tmp[i] = 0.0;
614 +      }
615 +      
616 +      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
617 +      for (int i = 0; i < ns; i++)
618 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
619 +    }
620      
621      nLocal_ = snap_->getNumberOfAtoms();
622  
623 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
624 <                                       vector<RealType> (nLocal_, 0.0));
623 >    vector<potVec> pot_temp(nLocal_,
624 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
625 >
626 >    // scatter/gather pot_row into the members of my column
627 >          
628 >    AtomCommPotRow->scatter(pot_row, pot_temp);
629 >
630 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
631 >      pairwisePot += pot_temp[ii];
632      
633 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
634 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
635 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
636 <        pot_local[i] += pot_temp[i][ii];
637 <      }
638 <    }
633 >    fill(pot_temp.begin(), pot_temp.end(),
634 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
635 >      
636 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
637 >    
638 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
639 >      pairwisePot += pot_temp[ii];    
640   #endif
641 +
642    }
643  
644 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
645 + #ifdef IS_MPI
646 +    return nAtomsInRow_;
647 + #else
648 +    return nLocal_;
649 + #endif
650 +  }
651 +
652 +  /**
653 +   * returns the list of atoms belonging to this group.  
654 +   */
655 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
656 + #ifdef IS_MPI
657 +    return groupListRow_[cg1];
658 + #else
659 +    return groupList_[cg1];
660 + #endif
661 +  }
662 +
663 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
664 + #ifdef IS_MPI
665 +    return groupListCol_[cg2];
666 + #else
667 +    return groupList_[cg2];
668 + #endif
669 +  }
670    
671    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
672      Vector3d d;
# Line 285 | Line 708 | namespace OpenMD {
708      snap_->wrapVector(d);
709      return d;    
710    }
711 +
712 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
713 + #ifdef IS_MPI
714 +    return massFactorsRow[atom1];
715 + #else
716 +    return massFactors[atom1];
717 + #endif
718 +  }
719 +
720 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
721 + #ifdef IS_MPI
722 +    return massFactorsCol[atom2];
723 + #else
724 +    return massFactors[atom2];
725 + #endif
726 +
727 +  }
728      
729    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
730      Vector3d d;
# Line 297 | Line 737 | namespace OpenMD {
737  
738      snap_->wrapVector(d);
739      return d;    
740 +  }
741 +
742 +  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
743 +    return excludesForAtom[atom1];
744    }
745  
746 +  /**
747 +   * We need to exclude some overcounted interactions that result from
748 +   * the parallel decomposition.
749 +   */
750 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
751 +    int unique_id_1, unique_id_2;
752 +
753 + #ifdef IS_MPI
754 +    // in MPI, we have to look up the unique IDs for each atom
755 +    unique_id_1 = AtomRowToGlobal[atom1];
756 +    unique_id_2 = AtomColToGlobal[atom2];
757 +
758 +    // this situation should only arise in MPI simulations
759 +    if (unique_id_1 == unique_id_2) return true;
760 +    
761 +    // this prevents us from doing the pair on multiple processors
762 +    if (unique_id_1 < unique_id_2) {
763 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
764 +    } else {
765 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
766 +    }
767 + #endif
768 +    return false;
769 +  }
770 +
771 +  /**
772 +   * We need to handle the interactions for atoms who are involved in
773 +   * the same rigid body as well as some short range interactions
774 +   * (bonds, bends, torsions) differently from other interactions.
775 +   * We'll still visit the pairwise routines, but with a flag that
776 +   * tells those routines to exclude the pair from direct long range
777 +   * interactions.  Some indirect interactions (notably reaction
778 +   * field) must still be handled for these pairs.
779 +   */
780 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
781 +    int unique_id_2;
782 +    
783 + #ifdef IS_MPI
784 +    // in MPI, we have to look up the unique IDs for the row atom.
785 +    unique_id_2 = AtomColToGlobal[atom2];
786 + #else
787 +    // in the normal loop, the atom numbers are unique
788 +    unique_id_2 = atom2;
789 + #endif
790 +    
791 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
792 +         i != excludesForAtom[atom1].end(); ++i) {
793 +      if ( (*i) == unique_id_2 ) return true;
794 +    }
795 +
796 +    return false;
797 +  }
798 +
799 +
800    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
801   #ifdef IS_MPI
802      atomRowData.force[atom1] += fg;
# Line 316 | Line 814 | namespace OpenMD {
814    }
815  
816      // filling interaction blocks with pointers
817 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
818 <    InteractionData idat;
817 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
818 >                                                     int atom1, int atom2) {
819  
820 +    idat.excluded = excludeAtomPair(atom1, atom2);
821 +  
822   #ifdef IS_MPI
823 +    
824 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
825 +                             ff_->getAtomType(identsCol[atom2]) );
826 +    
827      if (storageLayout_ & DataStorage::dslAmat) {
828        idat.A1 = &(atomRowData.aMat[atom1]);
829        idat.A2 = &(atomColData.aMat[atom2]);
# Line 340 | Line 844 | namespace OpenMD {
844        idat.rho2 = &(atomColData.density[atom2]);
845      }
846  
847 +    if (storageLayout_ & DataStorage::dslFunctional) {
848 +      idat.frho1 = &(atomRowData.functional[atom1]);
849 +      idat.frho2 = &(atomColData.functional[atom2]);
850 +    }
851 +
852      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
853        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
854        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
855      }
856 +
857 +    if (storageLayout_ & DataStorage::dslParticlePot) {
858 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
859 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
860 +    }
861 +
862 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
863 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
864 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
865 +    }
866 +
867   #else
868 +
869 +    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
870 +                             ff_->getAtomType(idents[atom2]) );
871 +
872      if (storageLayout_ & DataStorage::dslAmat) {
873        idat.A1 = &(snap_->atomData.aMat[atom1]);
874        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 360 | Line 884 | namespace OpenMD {
884        idat.t2 = &(snap_->atomData.torque[atom2]);
885      }
886  
887 <    if (storageLayout_ & DataStorage::dslDensity) {
887 >    if (storageLayout_ & DataStorage::dslDensity) {    
888        idat.rho1 = &(snap_->atomData.density[atom1]);
889        idat.rho2 = &(snap_->atomData.density[atom2]);
890      }
891  
892 +    if (storageLayout_ & DataStorage::dslFunctional) {
893 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
894 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
895 +    }
896 +
897      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
898        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
899        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
900      }
901 +
902 +    if (storageLayout_ & DataStorage::dslParticlePot) {
903 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
904 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
905 +    }
906 +
907 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
908 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
909 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
910 +    }
911   #endif
373 –    return idat;
912    }
913  
914 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
915 <
378 <    InteractionData idat;
914 >  
915 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
916   #ifdef IS_MPI
917 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
918 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
919 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
920 <    }
921 <    if (storageLayout_ & DataStorage::dslTorque) {
385 <      idat.t1 = &(atomRowData.torque[atom1]);
386 <      idat.t2 = &(atomColData.torque[atom2]);
387 <    }
388 <    if (storageLayout_ & DataStorage::dslForce) {
389 <      idat.t1 = &(atomRowData.force[atom1]);
390 <      idat.t2 = &(atomColData.force[atom2]);
391 <    }
917 >    pot_row[atom1] += 0.5 *  *(idat.pot);
918 >    pot_col[atom2] += 0.5 *  *(idat.pot);
919 >
920 >    atomRowData.force[atom1] += *(idat.f1);
921 >    atomColData.force[atom2] -= *(idat.f1);
922   #else
923 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
924 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
925 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
926 <    }
397 <    if (storageLayout_ & DataStorage::dslTorque) {
398 <      idat.t1 = &(snap_->atomData.torque[atom1]);
399 <      idat.t2 = &(snap_->atomData.torque[atom2]);
400 <    }
401 <    if (storageLayout_ & DataStorage::dslForce) {
402 <      idat.t1 = &(snap_->atomData.force[atom1]);
403 <      idat.t2 = &(snap_->atomData.force[atom2]);
404 <    }
923 >    pairwisePot += *(idat.pot);
924 >
925 >    snap_->atomData.force[atom1] += *(idat.f1);
926 >    snap_->atomData.force[atom2] -= *(idat.f1);
927   #endif
928      
929    }
930  
409 –  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
410 –    SelfData sdat;
411 –    // Still Missing atype, skippedCharge, potVec pot,
412 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
413 –      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
414 –    }
415 –    
416 –    if (storageLayout_ & DataStorage::dslTorque) {
417 –      sdat.t = &(snap_->atomData.torque[atom1]);
418 –    }
419 –    
420 –    if (storageLayout_ & DataStorage::dslDensity) {
421 –      sdat.rho = &(snap_->atomData.density[atom1]);
422 –    }
423 –    
424 –    if (storageLayout_ & DataStorage::dslFunctional) {
425 –      sdat.frho = &(snap_->atomData.functional[atom1]);
426 –    }
427 –    
428 –    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
429 –      sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
430 –    }
431 –
432 –    return sdat;    
433 –  }
434 –
435 –
436 –
931    /*
932     * buildNeighborList
933     *
# Line 443 | Line 937 | namespace OpenMD {
937    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
938        
939      vector<pair<int, int> > neighborList;
940 +    groupCutoffs cuts;
941 +    bool doAllPairs = false;
942 +
943   #ifdef IS_MPI
944 <    CellListRow.clear();
945 <    CellListCol.clear();
944 >    cellListRow_.clear();
945 >    cellListCol_.clear();
946   #else
947 <    CellList.clear();
947 >    cellList_.clear();
948   #endif
949  
950 <    // dangerous to not do error checking.
454 <    RealType skinThickness_ = info_->getSimParams()->getSkinThickness();
455 <    RealType rCut_;
456 <
457 <    RealType rList_ = (rCut_ + skinThickness_);
950 >    RealType rList_ = (largestRcut_ + skinThickness_);
951      RealType rl2 = rList_ * rList_;
952      Snapshot* snap_ = sman_->getCurrentSnapshot();
953      Mat3x3d Hmat = snap_->getHmat();
954      Vector3d Hx = Hmat.getColumn(0);
955      Vector3d Hy = Hmat.getColumn(1);
956      Vector3d Hz = Hmat.getColumn(2);
464 –    Vector3i nCells;
957  
958 <    nCells.x() = (int) ( Hx.length() )/ rList_;
959 <    nCells.y() = (int) ( Hy.length() )/ rList_;
960 <    nCells.z() = (int) ( Hz.length() )/ rList_;
958 >    nCells_.x() = (int) ( Hx.length() )/ rList_;
959 >    nCells_.y() = (int) ( Hy.length() )/ rList_;
960 >    nCells_.z() = (int) ( Hz.length() )/ rList_;
961  
962 +    // handle small boxes where the cell offsets can end up repeating cells
963 +    
964 +    if (nCells_.x() < 3) doAllPairs = true;
965 +    if (nCells_.y() < 3) doAllPairs = true;
966 +    if (nCells_.z() < 3) doAllPairs = true;
967 +
968      Mat3x3d invHmat = snap_->getInvHmat();
969      Vector3d rs, scaled, dr;
970      Vector3i whichCell;
971      int cellIndex;
972 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
973  
974   #ifdef IS_MPI
975 <    for (int i = 0; i < nGroupsInRow_; i++) {
976 <      rs = cgRowData.position[i];
977 <      // scaled positions relative to the box vectors
978 <      scaled = invHmat * rs;
979 <      // wrap the vector back into the unit box by subtracting integer box
481 <      // numbers
482 <      for (int j = 0; j < 3; j++)
483 <        scaled[j] -= roundMe(scaled[j]);
484 <    
485 <      // find xyz-indices of cell that cutoffGroup is in.
486 <      whichCell.x() = nCells.x() * scaled.x();
487 <      whichCell.y() = nCells.y() * scaled.y();
488 <      whichCell.z() = nCells.z() * scaled.z();
975 >    cellListRow_.resize(nCtot);
976 >    cellListCol_.resize(nCtot);
977 > #else
978 >    cellList_.resize(nCtot);
979 > #endif
980  
981 <      // find single index of this cell:
982 <      cellIndex = Vlinear(whichCell, nCells);
492 <      // add this cutoff group to the list of groups in this cell;
493 <      CellListRow[cellIndex].push_back(i);
494 <    }
981 >    if (!doAllPairs) {
982 > #ifdef IS_MPI
983  
984 <    for (int i = 0; i < nGroupsInCol_; i++) {
985 <      rs = cgColData.position[i];
986 <      // scaled positions relative to the box vectors
987 <      scaled = invHmat * rs;
988 <      // wrap the vector back into the unit box by subtracting integer box
989 <      // numbers
990 <      for (int j = 0; j < 3; j++)
991 <        scaled[j] -= roundMe(scaled[j]);
992 <
993 <      // find xyz-indices of cell that cutoffGroup is in.
994 <      whichCell.x() = nCells.x() * scaled.x();
995 <      whichCell.y() = nCells.y() * scaled.y();
996 <      whichCell.z() = nCells.z() * scaled.z();
997 <
998 <      // find single index of this cell:
999 <      cellIndex = Vlinear(whichCell, nCells);
1000 <      // add this cutoff group to the list of groups in this cell;
1001 <      CellListCol[cellIndex].push_back(i);
1002 <    }
984 >      for (int i = 0; i < nGroupsInRow_; i++) {
985 >        rs = cgRowData.position[i];
986 >        
987 >        // scaled positions relative to the box vectors
988 >        scaled = invHmat * rs;
989 >        
990 >        // wrap the vector back into the unit box by subtracting integer box
991 >        // numbers
992 >        for (int j = 0; j < 3; j++) {
993 >          scaled[j] -= roundMe(scaled[j]);
994 >          scaled[j] += 0.5;
995 >        }
996 >        
997 >        // find xyz-indices of cell that cutoffGroup is in.
998 >        whichCell.x() = nCells_.x() * scaled.x();
999 >        whichCell.y() = nCells_.y() * scaled.y();
1000 >        whichCell.z() = nCells_.z() * scaled.z();
1001 >        
1002 >        // find single index of this cell:
1003 >        cellIndex = Vlinear(whichCell, nCells_);
1004 >        
1005 >        // add this cutoff group to the list of groups in this cell;
1006 >        cellListRow_[cellIndex].push_back(i);
1007 >      }
1008 >      
1009 >      for (int i = 0; i < nGroupsInCol_; i++) {
1010 >        rs = cgColData.position[i];
1011 >        
1012 >        // scaled positions relative to the box vectors
1013 >        scaled = invHmat * rs;
1014 >        
1015 >        // wrap the vector back into the unit box by subtracting integer box
1016 >        // numbers
1017 >        for (int j = 0; j < 3; j++) {
1018 >          scaled[j] -= roundMe(scaled[j]);
1019 >          scaled[j] += 0.5;
1020 >        }
1021 >        
1022 >        // find xyz-indices of cell that cutoffGroup is in.
1023 >        whichCell.x() = nCells_.x() * scaled.x();
1024 >        whichCell.y() = nCells_.y() * scaled.y();
1025 >        whichCell.z() = nCells_.z() * scaled.z();
1026 >        
1027 >        // find single index of this cell:
1028 >        cellIndex = Vlinear(whichCell, nCells_);
1029 >        
1030 >        // add this cutoff group to the list of groups in this cell;
1031 >        cellListCol_[cellIndex].push_back(i);
1032 >      }
1033   #else
1034 <    for (int i = 0; i < nGroups_; i++) {
1035 <      rs = snap_->cgData.position[i];
1036 <      // scaled positions relative to the box vectors
1037 <      scaled = invHmat * rs;
1038 <      // wrap the vector back into the unit box by subtracting integer box
1039 <      // numbers
1040 <      for (int j = 0; j < 3; j++)
1041 <        scaled[j] -= roundMe(scaled[j]);
1042 <
1043 <      // find xyz-indices of cell that cutoffGroup is in.
1044 <      whichCell.x() = nCells.x() * scaled.x();
1045 <      whichCell.y() = nCells.y() * scaled.y();
1046 <      whichCell.z() = nCells.z() * scaled.z();
1047 <
1048 <      // find single index of this cell:
1049 <      cellIndex = Vlinear(whichCell, nCells);
1050 <      // add this cutoff group to the list of groups in this cell;
1051 <      CellList[cellIndex].push_back(i);
1052 <    }
1034 >      for (int i = 0; i < nGroups_; i++) {
1035 >        rs = snap_->cgData.position[i];
1036 >        
1037 >        // scaled positions relative to the box vectors
1038 >        scaled = invHmat * rs;
1039 >        
1040 >        // wrap the vector back into the unit box by subtracting integer box
1041 >        // numbers
1042 >        for (int j = 0; j < 3; j++) {
1043 >          scaled[j] -= roundMe(scaled[j]);
1044 >          scaled[j] += 0.5;
1045 >        }
1046 >        
1047 >        // find xyz-indices of cell that cutoffGroup is in.
1048 >        whichCell.x() = nCells_.x() * scaled.x();
1049 >        whichCell.y() = nCells_.y() * scaled.y();
1050 >        whichCell.z() = nCells_.z() * scaled.z();
1051 >        
1052 >        // find single index of this cell:
1053 >        cellIndex = Vlinear(whichCell, nCells_);      
1054 >        
1055 >        // add this cutoff group to the list of groups in this cell;
1056 >        cellList_[cellIndex].push_back(i);
1057 >      }
1058   #endif
1059  
1060 <
1061 <
1062 <    for (int m1z = 0; m1z < nCells.z(); m1z++) {
1063 <      for (int m1y = 0; m1y < nCells.y(); m1y++) {
1064 <        for (int m1x = 0; m1x < nCells.x(); m1x++) {
1065 <          Vector3i m1v(m1x, m1y, m1z);
1066 <          int m1 = Vlinear(m1v, nCells);
1067 <          for (int offset = 0; offset < nOffset_; offset++) {
1068 <            Vector3i m2v = m1v + cellOffsets_[offset];
1069 <
1070 <            if (m2v.x() >= nCells.x()) {
1071 <              m2v.x() = 0;          
1072 <            } else if (m2v.x() < 0) {
1073 <              m2v.x() = nCells.x() - 1;
1074 <            }
1075 <
1076 <            if (m2v.y() >= nCells.y()) {
1077 <              m2v.y() = 0;          
1078 <            } else if (m2v.y() < 0) {
1079 <              m2v.y() = nCells.y() - 1;
1080 <            }
1081 <
1082 <            if (m2v.z() >= nCells.z()) {
1083 <              m2v.z() = 0;          
1084 <            } else if (m2v.z() < 0) {
1085 <              m2v.z() = nCells.z() - 1;
1086 <            }
1087 <
1088 <            int m2 = Vlinear (m2v, nCells);
1089 <
1060 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1061 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1062 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1063 >            Vector3i m1v(m1x, m1y, m1z);
1064 >            int m1 = Vlinear(m1v, nCells_);
1065 >            
1066 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1067 >                 os != cellOffsets_.end(); ++os) {
1068 >              
1069 >              Vector3i m2v = m1v + (*os);
1070 >              
1071 >              if (m2v.x() >= nCells_.x()) {
1072 >                m2v.x() = 0;          
1073 >              } else if (m2v.x() < 0) {
1074 >                m2v.x() = nCells_.x() - 1;
1075 >              }
1076 >              
1077 >              if (m2v.y() >= nCells_.y()) {
1078 >                m2v.y() = 0;          
1079 >              } else if (m2v.y() < 0) {
1080 >                m2v.y() = nCells_.y() - 1;
1081 >              }
1082 >              
1083 >              if (m2v.z() >= nCells_.z()) {
1084 >                m2v.z() = 0;          
1085 >              } else if (m2v.z() < 0) {
1086 >                m2v.z() = nCells_.z() - 1;
1087 >              }
1088 >              
1089 >              int m2 = Vlinear (m2v, nCells_);
1090 >              
1091   #ifdef IS_MPI
1092 <            for (vector<int>::iterator j1 = CellListRow[m1].begin();
1093 <                 j1 != CellListRow[m1].end(); ++j1) {
1094 <              for (vector<int>::iterator j2 = CellListCol[m2].begin();
1095 <                   j2 != CellListCol[m2].end(); ++j2) {
1096 <                              
1097 <                // Always do this if we're in different cells or if
1098 <                // we're in the same cell and the global index of the
1099 <                // j2 cutoff group is less than the j1 cutoff group
1100 <
1101 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1102 <                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1103 <                  snap_->wrapVector(dr);
1104 <                  if (dr.lengthSquare() < rl2) {
1105 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1092 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1093 >                   j1 != cellListRow_[m1].end(); ++j1) {
1094 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1095 >                     j2 != cellListCol_[m2].end(); ++j2) {
1096 >                  
1097 >                  // Always do this if we're in different cells or if
1098 >                  // we're in the same cell and the global index of the
1099 >                  // j2 cutoff group is less than the j1 cutoff group
1100 >                  
1101 >                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1102 >                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1103 >                    snap_->wrapVector(dr);
1104 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1105 >                    if (dr.lengthSquare() < cuts.third) {
1106 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1107 >                    }
1108                    }
1109                  }
1110                }
585 –            }
1111   #else
1112 <            for (vector<int>::iterator j1 = CellList[m1].begin();
1113 <                 j1 != CellList[m1].end(); ++j1) {
1114 <              for (vector<int>::iterator j2 = CellList[m2].begin();
1115 <                   j2 != CellList[m2].end(); ++j2) {
1116 <                              
1117 <                // Always do this if we're in different cells or if
1118 <                // we're in the same cell and the global index of the
1119 <                // j2 cutoff group is less than the j1 cutoff group
1120 <
1121 <                if (m2 != m1 || (*j2) < (*j1)) {
1122 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1123 <                  snap_->wrapVector(dr);
1124 <                  if (dr.lengthSquare() < rl2) {
1125 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1112 >              
1113 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1114 >                   j1 != cellList_[m1].end(); ++j1) {
1115 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1116 >                     j2 != cellList_[m2].end(); ++j2) {
1117 >                  
1118 >                  // Always do this if we're in different cells or if
1119 >                  // we're in the same cell and the global index of the
1120 >                  // j2 cutoff group is less than the j1 cutoff group
1121 >                  
1122 >                  if (m2 != m1 || (*j2) < (*j1)) {
1123 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1124 >                    snap_->wrapVector(dr);
1125 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1126 >                    if (dr.lengthSquare() < cuts.third) {
1127 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1128 >                    }
1129                    }
1130                  }
1131                }
604 –            }
1132   #endif
1133 +            }
1134            }
1135          }
1136        }
1137 +    } else {
1138 +      // branch to do all cutoff group pairs
1139 + #ifdef IS_MPI
1140 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1141 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1142 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1143 +          snap_->wrapVector(dr);
1144 +          cuts = getGroupCutoffs( j1, j2 );
1145 +          if (dr.lengthSquare() < cuts.third) {
1146 +            neighborList.push_back(make_pair(j1, j2));
1147 +          }
1148 +        }
1149 +      }
1150 + #else
1151 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1152 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1153 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1154 +          snap_->wrapVector(dr);
1155 +          cuts = getGroupCutoffs( j1, j2 );
1156 +          if (dr.lengthSquare() < cuts.third) {
1157 +            neighborList.push_back(make_pair(j1, j2));
1158 +          }
1159 +        }
1160 +      }        
1161 + #endif
1162      }
1163 +      
1164 +    // save the local cutoff group positions for the check that is
1165 +    // done on each loop:
1166 +    saved_CG_positions_.clear();
1167 +    for (int i = 0; i < nGroups_; i++)
1168 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1169 +    
1170      return neighborList;
1171    }
1172   } //end namespace OpenMD

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