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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 1568 by gezelter, Wed May 25 16:20:37 2011 UTC vs.
Revision 1591 by gezelter, Tue Jul 12 15:25:07 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));
114 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
115 <                                      vector<RealType> (nAtomsInCol_, 0.0));
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114 >    
115 >    // allocate memory for the parallel objects
116 >    atypesRow.resize(nAtomsInRow_);
117 >    atypesCol.resize(nAtomsInCol_);
118  
119 +    for (int i = 0; i < nAtomsInRow_; i++)
120 +      atypesRow[i] = ff_->getAtomType(identsRow[i]);
121 +    for (int i = 0; i < nAtomsInCol_; i++)
122 +      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
123  
124 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
125 <    
126 <    // gather the information for atomtype IDs (atids):
127 <    vector<int> identsLocal = info_->getIdentArray();
128 <    identsRow.reserve(nAtomsInRow_);
103 <    identsCol.reserve(nAtomsInCol_);
104 <    
105 <    AtomCommIntRow->gather(identsLocal, identsRow);
106 <    AtomCommIntColumn->gather(identsLocal, identsCol);
107 <    
108 <    AtomLocalToGlobal = info_->getGlobalAtomIndices();
124 >    pot_row.resize(nAtomsInRow_);
125 >    pot_col.resize(nAtomsInCol_);
126 >
127 >    AtomRowToGlobal.resize(nAtomsInRow_);
128 >    AtomColToGlobal.resize(nAtomsInCol_);
129      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
130      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
131      
132 <    cgLocalToGlobal = info_->getGlobalGroupIndices();
132 >    cgRowToGlobal.resize(nGroupsInRow_);
133 >    cgColToGlobal.resize(nGroupsInCol_);
134      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
135      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
136  
137 <    // still need:
138 <    // topoDist
139 <    // exclude
137 >    massFactorsRow.resize(nAtomsInRow_);
138 >    massFactorsCol.resize(nAtomsInCol_);
139 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
140 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
141 >
142 >    groupListRow_.clear();
143 >    groupListRow_.resize(nGroupsInRow_);
144 >    for (int i = 0; i < nGroupsInRow_; i++) {
145 >      int gid = cgRowToGlobal[i];
146 >      for (int j = 0; j < nAtomsInRow_; j++) {
147 >        int aid = AtomRowToGlobal[j];
148 >        if (globalGroupMembership[aid] == gid)
149 >          groupListRow_[i].push_back(j);
150 >      }      
151 >    }
152 >
153 >    groupListCol_.clear();
154 >    groupListCol_.resize(nGroupsInCol_);
155 >    for (int i = 0; i < nGroupsInCol_; i++) {
156 >      int gid = cgColToGlobal[i];
157 >      for (int j = 0; j < nAtomsInCol_; j++) {
158 >        int aid = AtomColToGlobal[j];
159 >        if (globalGroupMembership[aid] == gid)
160 >          groupListCol_[i].push_back(j);
161 >      }      
162 >    }
163 >
164 >    excludesForAtom.clear();
165 >    excludesForAtom.resize(nAtomsInRow_);
166 >    toposForAtom.clear();
167 >    toposForAtom.resize(nAtomsInRow_);
168 >    topoDist.clear();
169 >    topoDist.resize(nAtomsInRow_);
170 >    for (int i = 0; i < nAtomsInRow_; i++) {
171 >      int iglob = AtomRowToGlobal[i];
172 >
173 >      for (int j = 0; j < nAtomsInCol_; j++) {
174 >        int jglob = AtomColToGlobal[j];
175 >
176 >        if (excludes->hasPair(iglob, jglob))
177 >          excludesForAtom[i].push_back(j);      
178 >        
179 >        if (oneTwo->hasPair(iglob, jglob)) {
180 >          toposForAtom[i].push_back(j);
181 >          topoDist[i].push_back(1);
182 >        } else {
183 >          if (oneThree->hasPair(iglob, jglob)) {
184 >            toposForAtom[i].push_back(j);
185 >            topoDist[i].push_back(2);
186 >          } else {
187 >            if (oneFour->hasPair(iglob, jglob)) {
188 >              toposForAtom[i].push_back(j);
189 >              topoDist[i].push_back(3);
190 >            }
191 >          }
192 >        }
193 >      }      
194 >    }
195 >
196   #endif
197 +
198 +    // allocate memory for the parallel objects
199 +    atypesLocal.resize(nLocal_);
200 +
201 +    for (int i = 0; i < nLocal_; i++)
202 +      atypesLocal[i] = ff_->getAtomType(idents[i]);
203 +
204 +    groupList_.clear();
205 +    groupList_.resize(nGroups_);
206 +    for (int i = 0; i < nGroups_; i++) {
207 +      int gid = cgLocalToGlobal[i];
208 +      for (int j = 0; j < nLocal_; j++) {
209 +        int aid = AtomLocalToGlobal[j];
210 +        if (globalGroupMembership[aid] == gid) {
211 +          groupList_[i].push_back(j);
212 +        }
213 +      }      
214 +    }
215 +
216 +    excludesForAtom.clear();
217 +    excludesForAtom.resize(nLocal_);
218 +    toposForAtom.clear();
219 +    toposForAtom.resize(nLocal_);
220 +    topoDist.clear();
221 +    topoDist.resize(nLocal_);
222 +
223 +    for (int i = 0; i < nLocal_; i++) {
224 +      int iglob = AtomLocalToGlobal[i];
225 +
226 +      for (int j = 0; j < nLocal_; j++) {
227 +        int jglob = AtomLocalToGlobal[j];
228 +
229 +        if (excludes->hasPair(iglob, jglob))
230 +          excludesForAtom[i].push_back(j);              
231 +        
232 +        if (oneTwo->hasPair(iglob, jglob)) {
233 +          toposForAtom[i].push_back(j);
234 +          topoDist[i].push_back(1);
235 +        } else {
236 +          if (oneThree->hasPair(iglob, jglob)) {
237 +            toposForAtom[i].push_back(j);
238 +            topoDist[i].push_back(2);
239 +          } else {
240 +            if (oneFour->hasPair(iglob, jglob)) {
241 +              toposForAtom[i].push_back(j);
242 +              topoDist[i].push_back(3);
243 +            }
244 +          }
245 +        }
246 +      }      
247 +    }
248 +    
249 +    createGtypeCutoffMap();
250 +
251    }
252 +  
253 +  void ForceMatrixDecomposition::createGtypeCutoffMap() {
254      
255 +    RealType tol = 1e-6;
256 +    RealType rc;
257 +    int atid;
258 +    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
259 +    map<int, RealType> atypeCutoff;
260 +      
261 +    for (set<AtomType*>::iterator at = atypes.begin();
262 +         at != atypes.end(); ++at){
263 +      atid = (*at)->getIdent();
264 +      if (userChoseCutoff_)
265 +        atypeCutoff[atid] = userCutoff_;
266 +      else
267 +        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
268 +    }
269  
270 +    vector<RealType> gTypeCutoffs;
271 +    // first we do a single loop over the cutoff groups to find the
272 +    // largest cutoff for any atypes present in this group.
273 + #ifdef IS_MPI
274 +    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
275 +    groupRowToGtype.resize(nGroupsInRow_);
276 +    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
277 +      vector<int> atomListRow = getAtomsInGroupRow(cg1);
278 +      for (vector<int>::iterator ia = atomListRow.begin();
279 +           ia != atomListRow.end(); ++ia) {            
280 +        int atom1 = (*ia);
281 +        atid = identsRow[atom1];
282 +        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
283 +          groupCutoffRow[cg1] = atypeCutoff[atid];
284 +        }
285 +      }
286  
287 +      bool gTypeFound = false;
288 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
289 +        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
290 +          groupRowToGtype[cg1] = gt;
291 +          gTypeFound = true;
292 +        }
293 +      }
294 +      if (!gTypeFound) {
295 +        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
296 +        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
297 +      }
298 +      
299 +    }
300 +    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
301 +    groupColToGtype.resize(nGroupsInCol_);
302 +    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
303 +      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
304 +      for (vector<int>::iterator jb = atomListCol.begin();
305 +           jb != atomListCol.end(); ++jb) {            
306 +        int atom2 = (*jb);
307 +        atid = identsCol[atom2];
308 +        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
309 +          groupCutoffCol[cg2] = atypeCutoff[atid];
310 +        }
311 +      }
312 +      bool gTypeFound = false;
313 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
314 +        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
315 +          groupColToGtype[cg2] = gt;
316 +          gTypeFound = true;
317 +        }
318 +      }
319 +      if (!gTypeFound) {
320 +        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
321 +        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
322 +      }
323 +    }
324 + #else
325 +
326 +    vector<RealType> groupCutoff(nGroups_, 0.0);
327 +    groupToGtype.resize(nGroups_);
328 +    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
329 +
330 +      groupCutoff[cg1] = 0.0;
331 +      vector<int> atomList = getAtomsInGroupRow(cg1);
332 +
333 +      for (vector<int>::iterator ia = atomList.begin();
334 +           ia != atomList.end(); ++ia) {            
335 +        int atom1 = (*ia);
336 +        atid = idents[atom1];
337 +        if (atypeCutoff[atid] > groupCutoff[cg1]) {
338 +          groupCutoff[cg1] = atypeCutoff[atid];
339 +        }
340 +      }
341 +
342 +      bool gTypeFound = false;
343 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
344 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
345 +          groupToGtype[cg1] = gt;
346 +          gTypeFound = true;
347 +        }
348 +      }
349 +      if (!gTypeFound) {
350 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
351 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
352 +      }      
353 +    }
354 + #endif
355 +
356 +    // Now we find the maximum group cutoff value present in the simulation
357 +
358 +    RealType groupMax = *max_element(gTypeCutoffs.begin(),
359 +                                     gTypeCutoffs.end());
360 +
361 + #ifdef IS_MPI
362 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
363 +                              MPI::MAX);
364 + #endif
365 +    
366 +    RealType tradRcut = groupMax;
367 +
368 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
369 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
370 +        RealType thisRcut;
371 +        switch(cutoffPolicy_) {
372 +        case TRADITIONAL:
373 +          thisRcut = tradRcut;
374 +          break;
375 +        case MIX:
376 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
377 +          break;
378 +        case MAX:
379 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
380 +          break;
381 +        default:
382 +          sprintf(painCave.errMsg,
383 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
384 +                  "hit an unknown cutoff policy!\n");
385 +          painCave.severity = OPENMD_ERROR;
386 +          painCave.isFatal = 1;
387 +          simError();
388 +          break;
389 +        }
390 +
391 +        pair<int,int> key = make_pair(i,j);
392 +        gTypeCutoffMap[key].first = thisRcut;
393 +
394 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
395 +
396 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
397 +        
398 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
399 +
400 +        // sanity check
401 +        
402 +        if (userChoseCutoff_) {
403 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
404 +            sprintf(painCave.errMsg,
405 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
406 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
407 +            painCave.severity = OPENMD_ERROR;
408 +            painCave.isFatal = 1;
409 +            simError();            
410 +          }
411 +        }
412 +      }
413 +    }
414 +  }
415 +
416 +
417 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
418 +    int i, j;  
419 + #ifdef IS_MPI
420 +    i = groupRowToGtype[cg1];
421 +    j = groupColToGtype[cg2];
422 + #else
423 +    i = groupToGtype[cg1];
424 +    j = groupToGtype[cg2];
425 + #endif    
426 +    return gTypeCutoffMap[make_pair(i,j)];
427 +  }
428 +
429 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
430 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
431 +      if (toposForAtom[atom1][j] == atom2)
432 +        return topoDist[atom1][j];
433 +    }
434 +    return 0;
435 +  }
436 +
437 +  void ForceMatrixDecomposition::zeroWorkArrays() {
438 +    pairwisePot = 0.0;
439 +    embeddingPot = 0.0;
440 +
441 + #ifdef IS_MPI
442 +    if (storageLayout_ & DataStorage::dslForce) {
443 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
444 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
445 +    }
446 +
447 +    if (storageLayout_ & DataStorage::dslTorque) {
448 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
449 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
450 +    }
451 +    
452 +    fill(pot_row.begin(), pot_row.end(),
453 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
454 +
455 +    fill(pot_col.begin(), pot_col.end(),
456 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
457 +
458 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
459 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
460 +           0.0);
461 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
462 +           0.0);
463 +    }
464 +
465 +    if (storageLayout_ & DataStorage::dslDensity) {      
466 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
467 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
468 +    }
469 +
470 +    if (storageLayout_ & DataStorage::dslFunctional) {  
471 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
472 +           0.0);
473 +      fill(atomColData.functional.begin(), atomColData.functional.end(),
474 +           0.0);
475 +    }
476 +
477 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
478 +      fill(atomRowData.functionalDerivative.begin(),
479 +           atomRowData.functionalDerivative.end(), 0.0);
480 +      fill(atomColData.functionalDerivative.begin(),
481 +           atomColData.functionalDerivative.end(), 0.0);
482 +    }
483 +
484 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
485 +      fill(atomRowData.skippedCharge.begin(),
486 +           atomRowData.skippedCharge.end(), 0.0);
487 +      fill(atomColData.skippedCharge.begin(),
488 +           atomColData.skippedCharge.end(), 0.0);
489 +    }
490 +
491 + #endif
492 +    // even in parallel, we need to zero out the local arrays:
493 +
494 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
495 +      fill(snap_->atomData.particlePot.begin(),
496 +           snap_->atomData.particlePot.end(), 0.0);
497 +    }
498 +    
499 +    if (storageLayout_ & DataStorage::dslDensity) {      
500 +      fill(snap_->atomData.density.begin(),
501 +           snap_->atomData.density.end(), 0.0);
502 +    }
503 +    if (storageLayout_ & DataStorage::dslFunctional) {
504 +      fill(snap_->atomData.functional.begin(),
505 +           snap_->atomData.functional.end(), 0.0);
506 +    }
507 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
508 +      fill(snap_->atomData.functionalDerivative.begin(),
509 +           snap_->atomData.functionalDerivative.end(), 0.0);
510 +    }
511 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
512 +      fill(snap_->atomData.skippedCharge.begin(),
513 +           snap_->atomData.skippedCharge.end(), 0.0);
514 +    }
515 +    
516 +  }
517 +
518 +
519    void ForceMatrixDecomposition::distributeData()  {
520      snap_ = sman_->getCurrentSnapshot();
521      storageLayout_ = sman_->getStorageLayout();
# Line 153 | Line 548 | namespace OpenMD {
548        AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
549                                     atomColData.electroFrame);
550      }
551 +
552   #endif      
553    }
554    
555 +  /* collects information obtained during the pre-pair loop onto local
556 +   * data structures.
557 +   */
558    void ForceMatrixDecomposition::collectIntermediateData() {
559      snap_ = sman_->getCurrentSnapshot();
560      storageLayout_ = sman_->getStorageLayout();
# Line 167 | Line 566 | namespace OpenMD {
566                                 snap_->atomData.density);
567        
568        int n = snap_->atomData.density.size();
569 <      std::vector<RealType> rho_tmp(n, 0.0);
569 >      vector<RealType> rho_tmp(n, 0.0);
570        AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
571        for (int i = 0; i < n; i++)
572          snap_->atomData.density[i] += rho_tmp[i];
573      }
574   #endif
575    }
576 <  
576 >
577 >  /*
578 >   * redistributes information obtained during the pre-pair loop out to
579 >   * row and column-indexed data structures
580 >   */
581    void ForceMatrixDecomposition::distributeIntermediateData() {
582      snap_ = sman_->getCurrentSnapshot();
583      storageLayout_ = sman_->getStorageLayout();
# Line 212 | Line 615 | namespace OpenMD {
615      AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
616      for (int i = 0; i < n; i++)
617        snap_->atomData.force[i] += frc_tmp[i];
618 <    
216 <    
618 >        
619      if (storageLayout_ & DataStorage::dslTorque) {
620  
621 <      int nt = snap_->atomData.force.size();
621 >      int nt = snap_->atomData.torque.size();
622        vector<Vector3d> trq_tmp(nt, V3Zero);
623  
624        AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
625 <      for (int i = 0; i < n; i++) {
625 >      for (int i = 0; i < nt; i++) {
626          snap_->atomData.torque[i] += trq_tmp[i];
627          trq_tmp[i] = 0.0;
628        }
629        
630        AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
631 <      for (int i = 0; i < n; i++)
631 >      for (int i = 0; i < nt; i++)
632          snap_->atomData.torque[i] += trq_tmp[i];
633      }
634 +
635 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
636 +
637 +      int ns = snap_->atomData.skippedCharge.size();
638 +      vector<RealType> skch_tmp(ns, 0.0);
639 +
640 +      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
641 +      for (int i = 0; i < ns; i++) {
642 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
643 +        skch_tmp[i] = 0.0;
644 +      }
645 +      
646 +      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
647 +      for (int i = 0; i < ns; i++)
648 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
649 +    }
650      
651      nLocal_ = snap_->getNumberOfAtoms();
652  
653 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
654 <                                       vector<RealType> (nLocal_, 0.0));
653 >    vector<potVec> pot_temp(nLocal_,
654 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
655 >
656 >    // scatter/gather pot_row into the members of my column
657 >          
658 >    AtomCommPotRow->scatter(pot_row, pot_temp);
659 >
660 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
661 >      pairwisePot += pot_temp[ii];
662      
663 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
664 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
665 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
666 <        pot_local[i] += pot_temp[i][ii];
667 <      }
668 <    }
663 >    fill(pot_temp.begin(), pot_temp.end(),
664 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
665 >      
666 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
667 >    
668 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
669 >      pairwisePot += pot_temp[ii];    
670 > #endif
671 >
672 >  }
673 >
674 >  int ForceMatrixDecomposition::getNAtomsInRow() {  
675 > #ifdef IS_MPI
676 >    return nAtomsInRow_;
677 > #else
678 >    return nLocal_;
679 > #endif
680 >  }
681 >
682 >  /**
683 >   * returns the list of atoms belonging to this group.  
684 >   */
685 >  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
686 > #ifdef IS_MPI
687 >    return groupListRow_[cg1];
688 > #else
689 >    return groupList_[cg1];
690   #endif
691    }
692  
693 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
694 + #ifdef IS_MPI
695 +    return groupListCol_[cg2];
696 + #else
697 +    return groupList_[cg2];
698 + #endif
699 +  }
700    
701    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
702      Vector3d d;
# Line 285 | Line 738 | namespace OpenMD {
738      snap_->wrapVector(d);
739      return d;    
740    }
741 +
742 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
743 + #ifdef IS_MPI
744 +    return massFactorsRow[atom1];
745 + #else
746 +    return massFactors[atom1];
747 + #endif
748 +  }
749 +
750 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
751 + #ifdef IS_MPI
752 +    return massFactorsCol[atom2];
753 + #else
754 +    return massFactors[atom2];
755 + #endif
756 +
757 +  }
758      
759    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
760      Vector3d d;
# Line 299 | Line 769 | namespace OpenMD {
769      return d;    
770    }
771  
772 +  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
773 +    return excludesForAtom[atom1];
774 +  }
775 +
776 +  /**
777 +   * We need to exclude some overcounted interactions that result from
778 +   * the parallel decomposition.
779 +   */
780 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
781 +    int unique_id_1, unique_id_2;
782 +
783 + #ifdef IS_MPI
784 +    // in MPI, we have to look up the unique IDs for each atom
785 +    unique_id_1 = AtomRowToGlobal[atom1];
786 +    unique_id_2 = AtomColToGlobal[atom2];
787 +
788 +    // this situation should only arise in MPI simulations
789 +    if (unique_id_1 == unique_id_2) return true;
790 +    
791 +    // this prevents us from doing the pair on multiple processors
792 +    if (unique_id_1 < unique_id_2) {
793 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
794 +    } else {
795 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
796 +    }
797 + #endif
798 +    return false;
799 +  }
800 +
801 +  /**
802 +   * We need to handle the interactions for atoms who are involved in
803 +   * the same rigid body as well as some short range interactions
804 +   * (bonds, bends, torsions) differently from other interactions.
805 +   * We'll still visit the pairwise routines, but with a flag that
806 +   * tells those routines to exclude the pair from direct long range
807 +   * interactions.  Some indirect interactions (notably reaction
808 +   * field) must still be handled for these pairs.
809 +   */
810 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
811 +    int unique_id_2;
812 +    
813 + #ifdef IS_MPI
814 +    // in MPI, we have to look up the unique IDs for the row atom.
815 +    unique_id_2 = AtomColToGlobal[atom2];
816 + #else
817 +    // in the normal loop, the atom numbers are unique
818 +    unique_id_2 = atom2;
819 + #endif
820 +    
821 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
822 +         i != excludesForAtom[atom1].end(); ++i) {
823 +      if ( (*i) == unique_id_2 ) return true;
824 +    }
825 +
826 +    return false;
827 +  }
828 +
829 +
830    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
831   #ifdef IS_MPI
832      atomRowData.force[atom1] += fg;
# Line 316 | Line 844 | namespace OpenMD {
844    }
845  
846      // filling interaction blocks with pointers
847 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
848 <    InteractionData idat;
847 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
848 >                                                     int atom1, int atom2) {
849  
850 +    idat.excluded = excludeAtomPair(atom1, atom2);
851 +  
852   #ifdef IS_MPI
853 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
854 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
855 +    //                         ff_->getAtomType(identsCol[atom2]) );
856 +    
857      if (storageLayout_ & DataStorage::dslAmat) {
858        idat.A1 = &(atomRowData.aMat[atom1]);
859        idat.A2 = &(atomColData.aMat[atom2]);
# Line 340 | Line 874 | namespace OpenMD {
874        idat.rho2 = &(atomColData.density[atom2]);
875      }
876  
877 +    if (storageLayout_ & DataStorage::dslFunctional) {
878 +      idat.frho1 = &(atomRowData.functional[atom1]);
879 +      idat.frho2 = &(atomColData.functional[atom2]);
880 +    }
881 +
882      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
883        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
884        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
885      }
886 +
887 +    if (storageLayout_ & DataStorage::dslParticlePot) {
888 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
889 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
890 +    }
891 +
892 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
893 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
894 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
895 +    }
896 +
897   #else
898 +
899 +    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
900 +    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
901 +    //                         ff_->getAtomType(idents[atom2]) );
902 +
903      if (storageLayout_ & DataStorage::dslAmat) {
904        idat.A1 = &(snap_->atomData.aMat[atom1]);
905        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 360 | Line 915 | namespace OpenMD {
915        idat.t2 = &(snap_->atomData.torque[atom2]);
916      }
917  
918 <    if (storageLayout_ & DataStorage::dslDensity) {
918 >    if (storageLayout_ & DataStorage::dslDensity) {    
919        idat.rho1 = &(snap_->atomData.density[atom1]);
920        idat.rho2 = &(snap_->atomData.density[atom2]);
921      }
922  
923 +    if (storageLayout_ & DataStorage::dslFunctional) {
924 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
925 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
926 +    }
927 +
928      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
929        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
930        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
931      }
932 +
933 +    if (storageLayout_ & DataStorage::dslParticlePot) {
934 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
935 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
936 +    }
937 +
938 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
939 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
940 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
941 +    }
942   #endif
373 –    return idat;
943    }
944  
945 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
946 <
378 <    InteractionData idat;
945 >  
946 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
947   #ifdef IS_MPI
948 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
949 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
950 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
951 <    }
952 <    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 <    }
948 >    pot_row[atom1] += 0.5 *  *(idat.pot);
949 >    pot_col[atom2] += 0.5 *  *(idat.pot);
950 >
951 >    atomRowData.force[atom1] += *(idat.f1);
952 >    atomColData.force[atom2] -= *(idat.f1);
953   #else
954 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
955 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
956 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
957 <    }
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 <    }
954 >    pairwisePot += *(idat.pot);
955 >
956 >    snap_->atomData.force[atom1] += *(idat.f1);
957 >    snap_->atomData.force[atom2] -= *(idat.f1);
958   #endif
959      
960    }
961  
409 –
410 –
411 –
962    /*
963     * buildNeighborList
964     *
# Line 418 | Line 968 | namespace OpenMD {
968    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
969        
970      vector<pair<int, int> > neighborList;
971 +    groupCutoffs cuts;
972 +    bool doAllPairs = false;
973 +
974   #ifdef IS_MPI
975      cellListRow_.clear();
976      cellListCol_.clear();
# Line 425 | Line 978 | namespace OpenMD {
978      cellList_.clear();
979   #endif
980  
981 <    // dangerous to not do error checking.
429 <    RealType rCut_;
430 <
431 <    RealType rList_ = (rCut_ + skinThickness_);
981 >    RealType rList_ = (largestRcut_ + skinThickness_);
982      RealType rl2 = rList_ * rList_;
983      Snapshot* snap_ = sman_->getCurrentSnapshot();
984      Mat3x3d Hmat = snap_->getHmat();
# Line 440 | Line 990 | namespace OpenMD {
990      nCells_.y() = (int) ( Hy.length() )/ rList_;
991      nCells_.z() = (int) ( Hz.length() )/ rList_;
992  
993 +    // handle small boxes where the cell offsets can end up repeating cells
994 +    
995 +    if (nCells_.x() < 3) doAllPairs = true;
996 +    if (nCells_.y() < 3) doAllPairs = true;
997 +    if (nCells_.z() < 3) doAllPairs = true;
998 +
999      Mat3x3d invHmat = snap_->getInvHmat();
1000      Vector3d rs, scaled, dr;
1001      Vector3i whichCell;
1002      int cellIndex;
1003 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1004  
1005   #ifdef IS_MPI
1006 <    for (int i = 0; i < nGroupsInRow_; i++) {
1007 <      rs = cgRowData.position[i];
1008 <      // scaled positions relative to the box vectors
1009 <      scaled = invHmat * rs;
1010 <      // wrap the vector back into the unit box by subtracting integer box
454 <      // numbers
455 <      for (int j = 0; j < 3; j++)
456 <        scaled[j] -= roundMe(scaled[j]);
457 <    
458 <      // find xyz-indices of cell that cutoffGroup is in.
459 <      whichCell.x() = nCells_.x() * scaled.x();
460 <      whichCell.y() = nCells_.y() * scaled.y();
461 <      whichCell.z() = nCells_.z() * scaled.z();
1006 >    cellListRow_.resize(nCtot);
1007 >    cellListCol_.resize(nCtot);
1008 > #else
1009 >    cellList_.resize(nCtot);
1010 > #endif
1011  
1012 <      // find single index of this cell:
1013 <      cellIndex = Vlinear(whichCell, nCells_);
465 <      // add this cutoff group to the list of groups in this cell;
466 <      cellListRow_[cellIndex].push_back(i);
467 <    }
1012 >    if (!doAllPairs) {
1013 > #ifdef IS_MPI
1014  
1015 <    for (int i = 0; i < nGroupsInCol_; i++) {
1016 <      rs = cgColData.position[i];
1017 <      // scaled positions relative to the box vectors
1018 <      scaled = invHmat * rs;
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 <
1024 <      // find xyz-indices of cell that cutoffGroup is in.
1025 <      whichCell.x() = nCells_.x() * scaled.x();
1026 <      whichCell.y() = nCells_.y() * scaled.y();
1027 <      whichCell.z() = nCells_.z() * scaled.z();
1028 <
1029 <      // find single index of this cell:
1030 <      cellIndex = Vlinear(whichCell, nCells_);
1031 <      // add this cutoff group to the list of groups in this cell;
1032 <      cellListCol_[cellIndex].push_back(i);
1033 <    }
1015 >      for (int i = 0; i < nGroupsInRow_; i++) {
1016 >        rs = cgRowData.position[i];
1017 >        
1018 >        // scaled positions relative to the box vectors
1019 >        scaled = invHmat * rs;
1020 >        
1021 >        // wrap the vector back into the unit box by subtracting integer box
1022 >        // numbers
1023 >        for (int j = 0; j < 3; j++) {
1024 >          scaled[j] -= roundMe(scaled[j]);
1025 >          scaled[j] += 0.5;
1026 >        }
1027 >        
1028 >        // find xyz-indices of cell that cutoffGroup is in.
1029 >        whichCell.x() = nCells_.x() * scaled.x();
1030 >        whichCell.y() = nCells_.y() * scaled.y();
1031 >        whichCell.z() = nCells_.z() * scaled.z();
1032 >        
1033 >        // find single index of this cell:
1034 >        cellIndex = Vlinear(whichCell, nCells_);
1035 >        
1036 >        // add this cutoff group to the list of groups in this cell;
1037 >        cellListRow_[cellIndex].push_back(i);
1038 >      }
1039 >      
1040 >      for (int i = 0; i < nGroupsInCol_; i++) {
1041 >        rs = cgColData.position[i];
1042 >        
1043 >        // scaled positions relative to the box vectors
1044 >        scaled = invHmat * rs;
1045 >        
1046 >        // wrap the vector back into the unit box by subtracting integer box
1047 >        // numbers
1048 >        for (int j = 0; j < 3; j++) {
1049 >          scaled[j] -= roundMe(scaled[j]);
1050 >          scaled[j] += 0.5;
1051 >        }
1052 >        
1053 >        // find xyz-indices of cell that cutoffGroup is in.
1054 >        whichCell.x() = nCells_.x() * scaled.x();
1055 >        whichCell.y() = nCells_.y() * scaled.y();
1056 >        whichCell.z() = nCells_.z() * scaled.z();
1057 >        
1058 >        // find single index of this cell:
1059 >        cellIndex = Vlinear(whichCell, nCells_);
1060 >        
1061 >        // add this cutoff group to the list of groups in this cell;
1062 >        cellListCol_[cellIndex].push_back(i);
1063 >      }
1064   #else
1065 <    for (int i = 0; i < nGroups_; i++) {
1066 <      rs = snap_->cgData.position[i];
1067 <      // scaled positions relative to the box vectors
1068 <      scaled = invHmat * rs;
1069 <      // wrap the vector back into the unit box by subtracting integer box
1070 <      // numbers
1071 <      for (int j = 0; j < 3; j++)
1072 <        scaled[j] -= roundMe(scaled[j]);
1073 <
1074 <      // find xyz-indices of cell that cutoffGroup is in.
1075 <      whichCell.x() = nCells_.x() * scaled.x();
1076 <      whichCell.y() = nCells_.y() * scaled.y();
1077 <      whichCell.z() = nCells_.z() * scaled.z();
1078 <
1079 <      // find single index of this cell:
1080 <      cellIndex = Vlinear(whichCell, nCells_);
1081 <      // add this cutoff group to the list of groups in this cell;
1082 <      cellList_[cellIndex].push_back(i);
1083 <    }
1065 >      for (int i = 0; i < nGroups_; i++) {
1066 >        rs = snap_->cgData.position[i];
1067 >        
1068 >        // scaled positions relative to the box vectors
1069 >        scaled = invHmat * rs;
1070 >        
1071 >        // wrap the vector back into the unit box by subtracting integer box
1072 >        // numbers
1073 >        for (int j = 0; j < 3; j++) {
1074 >          scaled[j] -= roundMe(scaled[j]);
1075 >          scaled[j] += 0.5;
1076 >        }
1077 >        
1078 >        // find xyz-indices of cell that cutoffGroup is in.
1079 >        whichCell.x() = nCells_.x() * scaled.x();
1080 >        whichCell.y() = nCells_.y() * scaled.y();
1081 >        whichCell.z() = nCells_.z() * scaled.z();
1082 >        
1083 >        // find single index of this cell:
1084 >        cellIndex = Vlinear(whichCell, nCells_);      
1085 >        
1086 >        // add this cutoff group to the list of groups in this cell;
1087 >        cellList_[cellIndex].push_back(i);
1088 >      }
1089   #endif
1090  
1091 <
1092 <
1093 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1094 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1095 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
515 <          Vector3i m1v(m1x, m1y, m1z);
516 <          int m1 = Vlinear(m1v, nCells_);
517 <
518 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
519 <               os != cellOffsets_.end(); ++os) {
1091 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1092 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1093 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1094 >            Vector3i m1v(m1x, m1y, m1z);
1095 >            int m1 = Vlinear(m1v, nCells_);
1096              
1097 <            Vector3i m2v = m1v + (*os);
1098 <            
1099 <            if (m2v.x() >= nCells_.x()) {
1100 <              m2v.x() = 0;          
1101 <            } else if (m2v.x() < 0) {
1102 <              m2v.x() = nCells_.x() - 1;
1103 <            }
1104 <            
1105 <            if (m2v.y() >= nCells_.y()) {
1106 <              m2v.y() = 0;          
1107 <            } else if (m2v.y() < 0) {
1108 <              m2v.y() = nCells_.y() - 1;
1109 <            }
1110 <            
1111 <            if (m2v.z() >= nCells_.z()) {
1112 <              m2v.z() = 0;          
1113 <            } else if (m2v.z() < 0) {
1114 <              m2v.z() = nCells_.z() - 1;
1115 <            }
1116 <            
1117 <            int m2 = Vlinear (m2v, nCells_);
1118 <
1097 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1098 >                 os != cellOffsets_.end(); ++os) {
1099 >              
1100 >              Vector3i m2v = m1v + (*os);
1101 >              
1102 >              if (m2v.x() >= nCells_.x()) {
1103 >                m2v.x() = 0;          
1104 >              } else if (m2v.x() < 0) {
1105 >                m2v.x() = nCells_.x() - 1;
1106 >              }
1107 >              
1108 >              if (m2v.y() >= nCells_.y()) {
1109 >                m2v.y() = 0;          
1110 >              } else if (m2v.y() < 0) {
1111 >                m2v.y() = nCells_.y() - 1;
1112 >              }
1113 >              
1114 >              if (m2v.z() >= nCells_.z()) {
1115 >                m2v.z() = 0;          
1116 >              } else if (m2v.z() < 0) {
1117 >                m2v.z() = nCells_.z() - 1;
1118 >              }
1119 >              
1120 >              int m2 = Vlinear (m2v, nCells_);
1121 >              
1122   #ifdef IS_MPI
1123 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1124 <                 j1 != cellListRow_[m1].end(); ++j1) {
1125 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1126 <                   j2 != cellListCol_[m2].end(); ++j2) {
1127 <                              
1128 <                // Always do this if we're in different cells or if
1129 <                // we're in the same cell and the global index of the
1130 <                // j2 cutoff group is less than the j1 cutoff group
1131 <
1132 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1133 <                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1134 <                  snap_->wrapVector(dr);
1135 <                  if (dr.lengthSquare() < rl2) {
1136 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1123 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1124 >                   j1 != cellListRow_[m1].end(); ++j1) {
1125 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1126 >                     j2 != cellListCol_[m2].end(); ++j2) {
1127 >                  
1128 >                  // Always do this if we're in different cells or if
1129 >                  // we're in the same cell and the global index of the
1130 >                  // j2 cutoff group is less than the j1 cutoff group
1131 >                  
1132 >                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1133 >                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1134 >                    snap_->wrapVector(dr);
1135 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1136 >                    if (dr.lengthSquare() < cuts.third) {
1137 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1138 >                    }
1139                    }
1140                  }
1141                }
561 –            }
1142   #else
1143 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1144 <                 j1 != cellList_[m1].end(); ++j1) {
1145 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1146 <                   j2 != cellList_[m2].end(); ++j2) {
1147 <                              
1148 <                // Always do this if we're in different cells or if
1149 <                // we're in the same cell and the global index of the
1150 <                // j2 cutoff group is less than the j1 cutoff group
1151 <
1152 <                if (m2 != m1 || (*j2) < (*j1)) {
1153 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1154 <                  snap_->wrapVector(dr);
1155 <                  if (dr.lengthSquare() < rl2) {
1156 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1143 >              
1144 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1145 >                   j1 != cellList_[m1].end(); ++j1) {
1146 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1147 >                     j2 != cellList_[m2].end(); ++j2) {
1148 >                  
1149 >                  // Always do this if we're in different cells or if
1150 >                  // we're in the same cell and the global index of the
1151 >                  // j2 cutoff group is less than the j1 cutoff group
1152 >                  
1153 >                  if (m2 != m1 || (*j2) < (*j1)) {
1154 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1155 >                    snap_->wrapVector(dr);
1156 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1157 >                    if (dr.lengthSquare() < cuts.third) {
1158 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1159 >                    }
1160                    }
1161                  }
1162                }
580 –            }
1163   #endif
1164 +            }
1165            }
1166          }
1167        }
1168 +    } else {
1169 +      // branch to do all cutoff group pairs
1170 + #ifdef IS_MPI
1171 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1172 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1173 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1174 +          snap_->wrapVector(dr);
1175 +          cuts = getGroupCutoffs( j1, j2 );
1176 +          if (dr.lengthSquare() < cuts.third) {
1177 +            neighborList.push_back(make_pair(j1, j2));
1178 +          }
1179 +        }
1180 +      }
1181 + #else
1182 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1183 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1184 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1185 +          snap_->wrapVector(dr);
1186 +          cuts = getGroupCutoffs( j1, j2 );
1187 +          if (dr.lengthSquare() < cuts.third) {
1188 +            neighborList.push_back(make_pair(j1, j2));
1189 +          }
1190 +        }
1191 +      }        
1192 + #endif
1193      }
1194 <
1194 >      
1195      // save the local cutoff group positions for the check that is
1196      // done on each loop:
1197      saved_CG_positions_.clear();
1198      for (int i = 0; i < nGroups_; i++)
1199        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1200 <
1200 >    
1201      return neighborList;
1202    }
1203   } //end namespace OpenMD

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