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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 1582 by gezelter, Tue Jun 14 20:41:44 2011 UTC vs.
Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC

# Line 47 | Line 47 | namespace OpenMD {
47   using namespace std;
48   namespace OpenMD {
49  
50 +  ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
51 +
52 +    // In a parallel computation, row and colum scans must visit all
53 +    // surrounding cells (not just the 14 upper triangular blocks that
54 +    // are used when the processor can see all pairs)
55 + #ifdef IS_MPI
56 +    cellOffsets_.clear();
57 +    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
58 +    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
59 +    cellOffsets_.push_back( Vector3i( 1,-1,-1) );                          
60 +    cellOffsets_.push_back( Vector3i(-1, 0,-1) );
61 +    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
62 +    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
63 +    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
64 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );      
65 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
66 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
67 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
68 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
69 +    cellOffsets_.push_back( Vector3i(-1, 0, 0) );      
70 +    cellOffsets_.push_back( Vector3i( 0, 0, 0) );
71 +    cellOffsets_.push_back( Vector3i( 1, 0, 0) );
72 +    cellOffsets_.push_back( Vector3i(-1, 1, 0) );
73 +    cellOffsets_.push_back( Vector3i( 0, 1, 0) );
74 +    cellOffsets_.push_back( Vector3i( 1, 1, 0) );
75 +    cellOffsets_.push_back( Vector3i(-1,-1, 1) );
76 +    cellOffsets_.push_back( Vector3i( 0,-1, 1) );
77 +    cellOffsets_.push_back( Vector3i( 1,-1, 1) );
78 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
79 +    cellOffsets_.push_back( Vector3i( 0, 0, 1) );
80 +    cellOffsets_.push_back( Vector3i( 1, 0, 1) );
81 +    cellOffsets_.push_back( Vector3i(-1, 1, 1) );
82 +    cellOffsets_.push_back( Vector3i( 0, 1, 1) );
83 +    cellOffsets_.push_back( Vector3i( 1, 1, 1) );
84 + #endif    
85 +  }
86 +
87 +
88    /**
89     * distributeInitialData is essentially a copy of the older fortran
90     * SimulationSetup
91     */
54 –  
92    void ForceMatrixDecomposition::distributeInitialData() {
93      snap_ = sman_->getCurrentSnapshot();
94      storageLayout_ = sman_->getStorageLayout();
95      ff_ = info_->getForceField();
96      nLocal_ = snap_->getNumberOfAtoms();
97 <
97 >    
98      nGroups_ = info_->getNLocalCutoffGroups();
62 –    cerr << "in dId, nGroups = " << nGroups_ << "\n";
99      // gather the information for atomtype IDs (atids):
100 <    identsLocal = info_->getIdentArray();
100 >    idents = info_->getIdentArray();
101      AtomLocalToGlobal = info_->getGlobalAtomIndices();
102      cgLocalToGlobal = info_->getGlobalGroupIndices();
103      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
104 +
105      massFactors = info_->getMassFactors();
69 –    PairList excludes = info_->getExcludedInteractions();
70 –    PairList oneTwo = info_->getOneTwoInteractions();
71 –    PairList oneThree = info_->getOneThreeInteractions();
72 –    PairList oneFour = info_->getOneFourInteractions();
106  
107 +    PairList* excludes = info_->getExcludedInteractions();
108 +    PairList* oneTwo = info_->getOneTwoInteractions();
109 +    PairList* oneThree = info_->getOneThreeInteractions();
110 +    PairList* oneFour = info_->getOneFourInteractions();
111 +
112   #ifdef IS_MPI
113  
114 <    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
115 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
78 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
79 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
80 <    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
114 >    MPI::Intracomm row = rowComm.getComm();
115 >    MPI::Intracomm col = colComm.getComm();
116  
117 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
118 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
119 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
120 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
121 <    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
117 >    AtomPlanIntRow = new Plan<int>(row, nLocal_);
118 >    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
119 >    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
120 >    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
121 >    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
122  
123 <    cgCommIntRow = new Communicator<Row,int>(nGroups_);
124 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
125 <    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
126 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
123 >    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
124 >    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
125 >    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
126 >    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
127 >    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
128  
129 <    nAtomsInRow_ = AtomCommIntRow->getSize();
130 <    nAtomsInCol_ = AtomCommIntColumn->getSize();
131 <    nGroupsInRow_ = cgCommIntRow->getSize();
132 <    nGroupsInCol_ = cgCommIntColumn->getSize();
129 >    cgPlanIntRow = new Plan<int>(row, nGroups_);
130 >    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
131 >    cgPlanIntColumn = new Plan<int>(col, nGroups_);
132 >    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
133  
134 +    nAtomsInRow_ = AtomPlanIntRow->getSize();
135 +    nAtomsInCol_ = AtomPlanIntColumn->getSize();
136 +    nGroupsInRow_ = cgPlanIntRow->getSize();
137 +    nGroupsInCol_ = cgPlanIntColumn->getSize();
138 +
139      // Modify the data storage objects with the correct layouts and sizes:
140      atomRowData.resize(nAtomsInRow_);
141      atomRowData.setStorageLayout(storageLayout_);
# Line 108 | Line 149 | namespace OpenMD {
149      identsRow.resize(nAtomsInRow_);
150      identsCol.resize(nAtomsInCol_);
151      
152 <    AtomCommIntRow->gather(identsLocal, identsRow);
153 <    AtomCommIntColumn->gather(identsLocal, identsCol);
152 >    AtomPlanIntRow->gather(idents, identsRow);
153 >    AtomPlanIntColumn->gather(idents, identsCol);
154      
155 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
156 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
157 <    
117 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
118 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
155 >    // allocate memory for the parallel objects
156 >    atypesRow.resize(nAtomsInRow_);
157 >    atypesCol.resize(nAtomsInCol_);
158  
159 <    AtomCommRealRow->gather(massFactors, massFactorsRow);
160 <    AtomCommRealColumn->gather(massFactors, massFactorsCol);
159 >    for (int i = 0; i < nAtomsInRow_; i++)
160 >      atypesRow[i] = ff_->getAtomType(identsRow[i]);
161 >    for (int i = 0; i < nAtomsInCol_; i++)
162 >      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
163  
164 +    pot_row.resize(nAtomsInRow_);
165 +    pot_col.resize(nAtomsInCol_);
166 +
167 +    AtomRowToGlobal.resize(nAtomsInRow_);
168 +    AtomColToGlobal.resize(nAtomsInCol_);
169 +    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
170 +    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
171 +
172 +    cgRowToGlobal.resize(nGroupsInRow_);
173 +    cgColToGlobal.resize(nGroupsInCol_);
174 +    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175 +    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
176 +
177 +    massFactorsRow.resize(nAtomsInRow_);
178 +    massFactorsCol.resize(nAtomsInCol_);
179 +    AtomPlanRealRow->gather(massFactors, massFactorsRow);
180 +    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
181 +
182      groupListRow_.clear();
183      groupListRow_.resize(nGroupsInRow_);
184      for (int i = 0; i < nGroupsInRow_; i++) {
# Line 142 | Line 201 | namespace OpenMD {
201        }      
202      }
203  
204 <    skipsForAtom.clear();
205 <    skipsForAtom.resize(nAtomsInRow_);
204 >    excludesForAtom.clear();
205 >    excludesForAtom.resize(nAtomsInRow_);
206      toposForAtom.clear();
207      toposForAtom.resize(nAtomsInRow_);
208      topoDist.clear();
# Line 154 | Line 213 | namespace OpenMD {
213        for (int j = 0; j < nAtomsInCol_; j++) {
214          int jglob = AtomColToGlobal[j];
215  
216 <        if (excludes.hasPair(iglob, jglob))
217 <          skipsForAtom[i].push_back(j);      
216 >        if (excludes->hasPair(iglob, jglob))
217 >          excludesForAtom[i].push_back(j);      
218          
219 <        if (oneTwo.hasPair(iglob, jglob)) {
219 >        if (oneTwo->hasPair(iglob, jglob)) {
220            toposForAtom[i].push_back(j);
221            topoDist[i].push_back(1);
222          } else {
223 <          if (oneThree.hasPair(iglob, jglob)) {
223 >          if (oneThree->hasPair(iglob, jglob)) {
224              toposForAtom[i].push_back(j);
225              topoDist[i].push_back(2);
226            } else {
227 <            if (oneFour.hasPair(iglob, jglob)) {
227 >            if (oneFour->hasPair(iglob, jglob)) {
228                toposForAtom[i].push_back(j);
229                topoDist[i].push_back(3);
230              }
# Line 174 | Line 233 | namespace OpenMD {
233        }      
234      }
235  
236 < #endif
237 <
238 <    groupList_.clear();
180 <    groupList_.resize(nGroups_);
181 <    for (int i = 0; i < nGroups_; i++) {
182 <      int gid = cgLocalToGlobal[i];
183 <      for (int j = 0; j < nLocal_; j++) {
184 <        int aid = AtomLocalToGlobal[j];
185 <        if (globalGroupMembership[aid] == gid) {
186 <          groupList_[i].push_back(j);
187 <        }
188 <      }      
189 <    }
190 <
191 <    skipsForAtom.clear();
192 <    skipsForAtom.resize(nLocal_);
236 > #else
237 >    excludesForAtom.clear();
238 >    excludesForAtom.resize(nLocal_);
239      toposForAtom.clear();
240      toposForAtom.resize(nLocal_);
241      topoDist.clear();
# Line 201 | Line 247 | namespace OpenMD {
247        for (int j = 0; j < nLocal_; j++) {
248          int jglob = AtomLocalToGlobal[j];
249  
250 <        if (excludes.hasPair(iglob, jglob))
251 <          skipsForAtom[i].push_back(j);              
250 >        if (excludes->hasPair(iglob, jglob))          
251 >          excludesForAtom[i].push_back(j);              
252          
253 <        if (oneTwo.hasPair(iglob, jglob)) {
253 >        
254 >        if (oneTwo->hasPair(iglob, jglob)) {
255            toposForAtom[i].push_back(j);
256            topoDist[i].push_back(1);
257          } else {
258 <          if (oneThree.hasPair(iglob, jglob)) {
258 >          if (oneThree->hasPair(iglob, jglob)) {
259              toposForAtom[i].push_back(j);
260              topoDist[i].push_back(2);
261            } else {
262 <            if (oneFour.hasPair(iglob, jglob)) {
262 >            if (oneFour->hasPair(iglob, jglob)) {
263                toposForAtom[i].push_back(j);
264                topoDist[i].push_back(3);
265              }
# Line 220 | Line 267 | namespace OpenMD {
267          }
268        }      
269      }
270 <    
270 > #endif
271 >
272 >    // allocate memory for the parallel objects
273 >    atypesLocal.resize(nLocal_);
274 >
275 >    for (int i = 0; i < nLocal_; i++)
276 >      atypesLocal[i] = ff_->getAtomType(idents[i]);
277 >
278 >    groupList_.clear();
279 >    groupList_.resize(nGroups_);
280 >    for (int i = 0; i < nGroups_; i++) {
281 >      int gid = cgLocalToGlobal[i];
282 >      for (int j = 0; j < nLocal_; j++) {
283 >        int aid = AtomLocalToGlobal[j];
284 >        if (globalGroupMembership[aid] == gid) {
285 >          groupList_[i].push_back(j);
286 >        }
287 >      }      
288 >    }
289 >
290 >
291      createGtypeCutoffMap();
292 +
293    }
294    
295    void ForceMatrixDecomposition::createGtypeCutoffMap() {
296 <
296 >    
297      RealType tol = 1e-6;
298 +    largestRcut_ = 0.0;
299      RealType rc;
300      int atid;
301      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302 <    vector<RealType> atypeCutoff;
303 <    atypeCutoff.resize( atypes.size() );
304 <
302 >    
303 >    map<int, RealType> atypeCutoff;
304 >      
305      for (set<AtomType*>::iterator at = atypes.begin();
306           at != atypes.end(); ++at){
238 –      rc = interactionMan_->getSuggestedCutoffRadius(*at);
307        atid = (*at)->getIdent();
308 <      atypeCutoff[atid] = rc;
308 >      if (userChoseCutoff_)
309 >        atypeCutoff[atid] = userCutoff_;
310 >      else
311 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312      }
313 <
313 >    
314      vector<RealType> gTypeCutoffs;
244 –
315      // first we do a single loop over the cutoff groups to find the
316      // largest cutoff for any atypes present in this group.
317   #ifdef IS_MPI
# Line 299 | Line 369 | namespace OpenMD {
369  
370      vector<RealType> groupCutoff(nGroups_, 0.0);
371      groupToGtype.resize(nGroups_);
302 –
303 –    cerr << "nGroups = " << nGroups_ << "\n";
372      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305 –
373        groupCutoff[cg1] = 0.0;
374        vector<int> atomList = getAtomsInGroupRow(cg1);
308 –
375        for (vector<int>::iterator ia = atomList.begin();
376             ia != atomList.end(); ++ia) {            
377          int atom1 = (*ia);
378 <        atid = identsLocal[atom1];
379 <        if (atypeCutoff[atid] > groupCutoff[cg1]) {
378 >        atid = idents[atom1];
379 >        if (atypeCutoff[atid] > groupCutoff[cg1])
380            groupCutoff[cg1] = atypeCutoff[atid];
315 –        }
381        }
382 <
382 >      
383        bool gTypeFound = false;
384        for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
# Line 322 | Line 387 | namespace OpenMD {
387            gTypeFound = true;
388          }
389        }
390 <      if (!gTypeFound) {
390 >      if (!gTypeFound) {      
391          gTypeCutoffs.push_back( groupCutoff[cg1] );
392          groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393        }      
394      }
395   #endif
396  
332 –    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
397      // Now we find the maximum group cutoff value present in the simulation
398  
399 <    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
399 >    RealType groupMax = *max_element(gTypeCutoffs.begin(),
400 >                                     gTypeCutoffs.end());
401  
402   #ifdef IS_MPI
403 <    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
403 >    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
404 >                              MPI::MAX);
405   #endif
406      
407      RealType tradRcut = groupMax;
# Line 365 | Line 431 | namespace OpenMD {
431  
432          pair<int,int> key = make_pair(i,j);
433          gTypeCutoffMap[key].first = thisRcut;
368 –
434          if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
370 –
435          gTypeCutoffMap[key].second = thisRcut*thisRcut;
372 –        
436          gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
374 –
437          // sanity check
438          
439          if (userChoseCutoff_) {
440            if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
441              sprintf(painCave.errMsg,
442                      "ForceMatrixDecomposition::createGtypeCutoffMap "
443 <                    "user-specified rCut does not match computed group Cutoff\n");
443 >                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
444              painCave.severity = OPENMD_ERROR;
445              painCave.isFatal = 1;
446              simError();            
# Line 410 | Line 472 | namespace OpenMD {
472    }
473  
474    void ForceMatrixDecomposition::zeroWorkArrays() {
475 +    pairwisePot = 0.0;
476 +    embeddingPot = 0.0;
477  
414 –    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
415 –      longRangePot_[j] = 0.0;
416 –    }
417 –
478   #ifdef IS_MPI
479      if (storageLayout_ & DataStorage::dslForce) {
480        fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
# Line 430 | Line 490 | namespace OpenMD {
490           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
491  
492      fill(pot_col.begin(), pot_col.end(),
493 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434 <    
435 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
493 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
494  
495      if (storageLayout_ & DataStorage::dslParticlePot) {    
496 <      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
497 <      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
496 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
497 >           0.0);
498 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
499 >           0.0);
500      }
501  
502      if (storageLayout_ & DataStorage::dslDensity) {      
# Line 445 | Line 505 | namespace OpenMD {
505      }
506  
507      if (storageLayout_ & DataStorage::dslFunctional) {  
508 <      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
509 <      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
508 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
509 >           0.0);
510 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
511 >           0.0);
512      }
513  
514      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
# Line 456 | Line 518 | namespace OpenMD {
518             atomColData.functionalDerivative.end(), 0.0);
519      }
520  
521 < #else
522 <    
521 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
522 >      fill(atomRowData.skippedCharge.begin(),
523 >           atomRowData.skippedCharge.end(), 0.0);
524 >      fill(atomColData.skippedCharge.begin(),
525 >           atomColData.skippedCharge.end(), 0.0);
526 >    }
527 >
528 > #endif
529 >    // even in parallel, we need to zero out the local arrays:
530 >
531      if (storageLayout_ & DataStorage::dslParticlePot) {      
532        fill(snap_->atomData.particlePot.begin(),
533             snap_->atomData.particlePot.end(), 0.0);
# Line 475 | Line 545 | namespace OpenMD {
545        fill(snap_->atomData.functionalDerivative.begin(),
546             snap_->atomData.functionalDerivative.end(), 0.0);
547      }
548 < #endif
548 >    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
549 >      fill(snap_->atomData.skippedCharge.begin(),
550 >           snap_->atomData.skippedCharge.end(), 0.0);
551 >    }
552      
553    }
554  
# Line 486 | Line 559 | namespace OpenMD {
559   #ifdef IS_MPI
560      
561      // gather up the atomic positions
562 <    AtomCommVectorRow->gather(snap_->atomData.position,
562 >    AtomPlanVectorRow->gather(snap_->atomData.position,
563                                atomRowData.position);
564 <    AtomCommVectorColumn->gather(snap_->atomData.position,
564 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
565                                   atomColData.position);
566      
567      // gather up the cutoff group positions
568 <    cgCommVectorRow->gather(snap_->cgData.position,
568 >
569 >    cgPlanVectorRow->gather(snap_->cgData.position,
570                              cgRowData.position);
571 <    cgCommVectorColumn->gather(snap_->cgData.position,
571 >
572 >    cgPlanVectorColumn->gather(snap_->cgData.position,
573                                 cgColData.position);
574 +
575      
576      // if needed, gather the atomic rotation matrices
577      if (storageLayout_ & DataStorage::dslAmat) {
578 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
578 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
579                                  atomRowData.aMat);
580 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
580 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
581                                     atomColData.aMat);
582      }
583      
584      // if needed, gather the atomic eletrostatic frames
585      if (storageLayout_ & DataStorage::dslElectroFrame) {
586 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
586 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
587                                  atomRowData.electroFrame);
588 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
588 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
589                                     atomColData.electroFrame);
590      }
591 +
592   #endif      
593    }
594    
# Line 525 | Line 602 | namespace OpenMD {
602      
603      if (storageLayout_ & DataStorage::dslDensity) {
604        
605 <      AtomCommRealRow->scatter(atomRowData.density,
605 >      AtomPlanRealRow->scatter(atomRowData.density,
606                                 snap_->atomData.density);
607        
608        int n = snap_->atomData.density.size();
609        vector<RealType> rho_tmp(n, 0.0);
610 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
610 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
611        for (int i = 0; i < n; i++)
612          snap_->atomData.density[i] += rho_tmp[i];
613      }
# Line 546 | Line 623 | namespace OpenMD {
623      storageLayout_ = sman_->getStorageLayout();
624   #ifdef IS_MPI
625      if (storageLayout_ & DataStorage::dslFunctional) {
626 <      AtomCommRealRow->gather(snap_->atomData.functional,
626 >      AtomPlanRealRow->gather(snap_->atomData.functional,
627                                atomRowData.functional);
628 <      AtomCommRealColumn->gather(snap_->atomData.functional,
628 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
629                                   atomColData.functional);
630      }
631      
632      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
633 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
633 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
634                                atomRowData.functionalDerivative);
635 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
635 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
636                                   atomColData.functionalDerivative);
637      }
638   #endif
# Line 569 | Line 646 | namespace OpenMD {
646      int n = snap_->atomData.force.size();
647      vector<Vector3d> frc_tmp(n, V3Zero);
648      
649 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
649 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
650      for (int i = 0; i < n; i++) {
651        snap_->atomData.force[i] += frc_tmp[i];
652        frc_tmp[i] = 0.0;
653      }
654      
655 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
656 <    for (int i = 0; i < n; i++)
655 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
656 >    for (int i = 0; i < n; i++) {
657        snap_->atomData.force[i] += frc_tmp[i];
658 <    
659 <    
658 >    }
659 >        
660      if (storageLayout_ & DataStorage::dslTorque) {
661  
662 <      int nt = snap_->atomData.force.size();
662 >      int nt = snap_->atomData.torque.size();
663        vector<Vector3d> trq_tmp(nt, V3Zero);
664  
665 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
666 <      for (int i = 0; i < n; i++) {
665 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
666 >      for (int i = 0; i < nt; i++) {
667          snap_->atomData.torque[i] += trq_tmp[i];
668          trq_tmp[i] = 0.0;
669        }
670        
671 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
672 <      for (int i = 0; i < n; i++)
671 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
672 >      for (int i = 0; i < nt; i++)
673          snap_->atomData.torque[i] += trq_tmp[i];
674      }
675 +
676 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
677 +
678 +      int ns = snap_->atomData.skippedCharge.size();
679 +      vector<RealType> skch_tmp(ns, 0.0);
680 +
681 +      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
682 +      for (int i = 0; i < ns; i++) {
683 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
684 +        skch_tmp[i] = 0.0;
685 +      }
686 +      
687 +      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
688 +      for (int i = 0; i < ns; i++)
689 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
690 +            
691 +    }
692      
693      nLocal_ = snap_->getNumberOfAtoms();
694  
# Line 603 | Line 697 | namespace OpenMD {
697  
698      // scatter/gather pot_row into the members of my column
699            
700 <    AtomCommPotRow->scatter(pot_row, pot_temp);
700 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
701  
702      for (int ii = 0;  ii < pot_temp.size(); ii++ )
703 <      pot_local += pot_temp[ii];
703 >      pairwisePot += pot_temp[ii];
704      
705      fill(pot_temp.begin(), pot_temp.end(),
706           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
707        
708 <    AtomCommPotColumn->scatter(pot_col, pot_temp);    
708 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
709      
710      for (int ii = 0;  ii < pot_temp.size(); ii++ )
711 <      pot_local += pot_temp[ii];
711 >      pairwisePot += pot_temp[ii];    
712      
713 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
714 +      RealType ploc1 = pairwisePot[ii];
715 +      RealType ploc2 = 0.0;
716 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
717 +      pairwisePot[ii] = ploc2;
718 +    }
719 +
720 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
721 +      RealType ploc1 = embeddingPot[ii];
722 +      RealType ploc2 = 0.0;
723 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
724 +      embeddingPot[ii] = ploc2;
725 +    }
726 +
727   #endif
728 +
729    }
730  
731    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 717 | Line 826 | namespace OpenMD {
826      return d;    
827    }
828  
829 <  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
830 <    return skipsForAtom[atom1];
829 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
830 >    return excludesForAtom[atom1];
831    }
832  
833    /**
834 <   * There are a number of reasons to skip a pair or a
726 <   * particle. Mostly we do this to exclude atoms who are involved in
727 <   * short range interactions (bonds, bends, torsions), but we also
728 <   * need to exclude some overcounted interactions that result from
834 >   * We need to exclude some overcounted interactions that result from
835     * the parallel decomposition.
836     */
837    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
838      int unique_id_1, unique_id_2;
839 <
839 >    
840   #ifdef IS_MPI
841      // in MPI, we have to look up the unique IDs for each atom
842      unique_id_1 = AtomRowToGlobal[atom1];
# Line 745 | Line 851 | namespace OpenMD {
851      } else {
852        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
853      }
748 – #else
749 –    // in the normal loop, the atom numbers are unique
750 –    unique_id_1 = atom1;
751 –    unique_id_2 = atom2;
854   #endif
855 +    return false;
856 +  }
857 +
858 +  /**
859 +   * We need to handle the interactions for atoms who are involved in
860 +   * the same rigid body as well as some short range interactions
861 +   * (bonds, bends, torsions) differently from other interactions.
862 +   * We'll still visit the pairwise routines, but with a flag that
863 +   * tells those routines to exclude the pair from direct long range
864 +   * interactions.  Some indirect interactions (notably reaction
865 +   * field) must still be handled for these pairs.
866 +   */
867 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
868 +
869 +    // excludesForAtom was constructed to use row/column indices in the MPI
870 +    // version, and to use local IDs in the non-MPI version:
871      
872 <    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
873 <         i != skipsForAtom[atom1].end(); ++i) {
874 <      if ( (*i) == unique_id_2 ) return true;
875 <    }    
872 >    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
873 >         i != excludesForAtom[atom1].end(); ++i) {
874 >      if ( (*i) == atom2 )  return true;
875 >    }
876  
877 +    return false;
878    }
879  
880  
# Line 777 | Line 896 | namespace OpenMD {
896  
897      // filling interaction blocks with pointers
898    void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
899 <                                                     int atom1, int atom2) {    
899 >                                                     int atom1, int atom2) {
900 >
901 >    idat.excluded = excludeAtomPair(atom1, atom2);
902 >  
903   #ifdef IS_MPI
904 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
905 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
906 +    //                         ff_->getAtomType(identsCol[atom2]) );
907      
783 –    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
784 –                             ff_->getAtomType(identsCol[atom2]) );
785 –    
908      if (storageLayout_ & DataStorage::dslAmat) {
909        idat.A1 = &(atomRowData.aMat[atom1]);
910        idat.A2 = &(atomColData.aMat[atom2]);
# Line 818 | Line 940 | namespace OpenMD {
940        idat.particlePot2 = &(atomColData.particlePot[atom2]);
941      }
942  
943 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
944 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
945 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
946 +    }
947 +
948   #else
949  
950 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
951 <                             ff_->getAtomType(identsLocal[atom2]) );
950 >    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
951 >    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
952 >    //                         ff_->getAtomType(idents[atom2]) );
953  
954      if (storageLayout_ & DataStorage::dslAmat) {
955        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 838 | Line 966 | namespace OpenMD {
966        idat.t2 = &(snap_->atomData.torque[atom2]);
967      }
968  
969 <    if (storageLayout_ & DataStorage::dslDensity) {
969 >    if (storageLayout_ & DataStorage::dslDensity) {    
970        idat.rho1 = &(snap_->atomData.density[atom1]);
971        idat.rho2 = &(snap_->atomData.density[atom2]);
972      }
# Line 858 | Line 986 | namespace OpenMD {
986        idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
987      }
988  
989 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
990 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
991 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
992 +    }
993   #endif
994    }
995  
# Line 870 | Line 1002 | namespace OpenMD {
1002      atomRowData.force[atom1] += *(idat.f1);
1003      atomColData.force[atom2] -= *(idat.f1);
1004   #else
1005 <    longRangePot_ += *(idat.pot);
1006 <    
1005 >    pairwisePot += *(idat.pot);
1006 >
1007      snap_->atomData.force[atom1] += *(idat.f1);
1008      snap_->atomData.force[atom2] -= *(idat.f1);
1009   #endif
1010 <
1010 >    
1011    }
1012  
881 –
882 –  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
883 –                                              int atom1, int atom2) {
884 – #ifdef IS_MPI
885 –    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
886 –                             ff_->getAtomType(identsCol[atom2]) );
887 –
888 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
889 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
890 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
891 –    }
892 –    if (storageLayout_ & DataStorage::dslTorque) {
893 –      idat.t1 = &(atomRowData.torque[atom1]);
894 –      idat.t2 = &(atomColData.torque[atom2]);
895 –    }
896 – #else
897 –    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
898 –                             ff_->getAtomType(identsLocal[atom2]) );
899 –
900 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
901 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
902 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
903 –    }
904 –    if (storageLayout_ & DataStorage::dslTorque) {
905 –      idat.t1 = &(snap_->atomData.torque[atom1]);
906 –      idat.t2 = &(snap_->atomData.torque[atom2]);
907 –    }
908 – #endif    
909 –  }
910 –
1013    /*
1014     * buildNeighborList
1015     *
# Line 918 | Line 1020 | namespace OpenMD {
1020        
1021      vector<pair<int, int> > neighborList;
1022      groupCutoffs cuts;
1023 +    bool doAllPairs = false;
1024 +
1025   #ifdef IS_MPI
1026      cellListRow_.clear();
1027      cellListCol_.clear();
# Line 937 | Line 1041 | namespace OpenMD {
1041      nCells_.y() = (int) ( Hy.length() )/ rList_;
1042      nCells_.z() = (int) ( Hz.length() )/ rList_;
1043  
1044 +    // handle small boxes where the cell offsets can end up repeating cells
1045 +    
1046 +    if (nCells_.x() < 3) doAllPairs = true;
1047 +    if (nCells_.y() < 3) doAllPairs = true;
1048 +    if (nCells_.z() < 3) doAllPairs = true;
1049 +
1050      Mat3x3d invHmat = snap_->getInvHmat();
1051      Vector3d rs, scaled, dr;
1052      Vector3i whichCell;
# Line 950 | Line 1060 | namespace OpenMD {
1060      cellList_.resize(nCtot);
1061   #endif
1062  
1063 +    if (!doAllPairs) {
1064   #ifdef IS_MPI
954 –    for (int i = 0; i < nGroupsInRow_; i++) {
955 –      rs = cgRowData.position[i];
1065  
1066 <      // scaled positions relative to the box vectors
1067 <      scaled = invHmat * rs;
1068 <
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 <        scaled[j] += 0.5;
1066 >      for (int i = 0; i < nGroupsInRow_; i++) {
1067 >        rs = cgRowData.position[i];
1068 >        
1069 >        // scaled positions relative to the box vectors
1070 >        scaled = invHmat * rs;
1071 >        
1072 >        // wrap the vector back into the unit box by subtracting integer box
1073 >        // numbers
1074 >        for (int j = 0; j < 3; j++) {
1075 >          scaled[j] -= roundMe(scaled[j]);
1076 >          scaled[j] += 0.5;
1077 >        }
1078 >        
1079 >        // find xyz-indices of cell that cutoffGroup is in.
1080 >        whichCell.x() = nCells_.x() * scaled.x();
1081 >        whichCell.y() = nCells_.y() * scaled.y();
1082 >        whichCell.z() = nCells_.z() * scaled.z();
1083 >        
1084 >        // find single index of this cell:
1085 >        cellIndex = Vlinear(whichCell, nCells_);
1086 >        
1087 >        // add this cutoff group to the list of groups in this cell;
1088 >        cellListRow_[cellIndex].push_back(i);
1089        }
1090 <    
1091 <      // find xyz-indices of cell that cutoffGroup is in.
1092 <      whichCell.x() = nCells_.x() * scaled.x();
1093 <      whichCell.y() = nCells_.y() * scaled.y();
1094 <      whichCell.z() = nCells_.z() * scaled.z();
1095 <
1096 <      // find single index of this cell:
1097 <      cellIndex = Vlinear(whichCell, nCells_);
1098 <
1099 <      // add this cutoff group to the list of groups in this cell;
1100 <      cellListRow_[cellIndex].push_back(i);
1101 <    }
1102 <
1103 <    for (int i = 0; i < nGroupsInCol_; i++) {
1104 <      rs = cgColData.position[i];
1105 <
1106 <      // scaled positions relative to the box vectors
1107 <      scaled = invHmat * rs;
1108 <
1109 <      // wrap the vector back into the unit box by subtracting integer box
1110 <      // numbers
1111 <      for (int j = 0; j < 3; j++) {
1112 <        scaled[j] -= roundMe(scaled[j]);
989 <        scaled[j] += 0.5;
1090 >      for (int i = 0; i < nGroupsInCol_; i++) {
1091 >        rs = cgColData.position[i];
1092 >        
1093 >        // scaled positions relative to the box vectors
1094 >        scaled = invHmat * rs;
1095 >        
1096 >        // wrap the vector back into the unit box by subtracting integer box
1097 >        // numbers
1098 >        for (int j = 0; j < 3; j++) {
1099 >          scaled[j] -= roundMe(scaled[j]);
1100 >          scaled[j] += 0.5;
1101 >        }
1102 >        
1103 >        // find xyz-indices of cell that cutoffGroup is in.
1104 >        whichCell.x() = nCells_.x() * scaled.x();
1105 >        whichCell.y() = nCells_.y() * scaled.y();
1106 >        whichCell.z() = nCells_.z() * scaled.z();
1107 >        
1108 >        // find single index of this cell:
1109 >        cellIndex = Vlinear(whichCell, nCells_);
1110 >        
1111 >        // add this cutoff group to the list of groups in this cell;
1112 >        cellListCol_[cellIndex].push_back(i);
1113        }
1114 <
992 <      // find xyz-indices of cell that cutoffGroup is in.
993 <      whichCell.x() = nCells_.x() * scaled.x();
994 <      whichCell.y() = nCells_.y() * scaled.y();
995 <      whichCell.z() = nCells_.z() * scaled.z();
996 <
997 <      // find single index of this cell:
998 <      cellIndex = Vlinear(whichCell, nCells_);
999 <
1000 <      // add this cutoff group to the list of groups in this cell;
1001 <      cellListCol_[cellIndex].push_back(i);
1002 <    }
1114 >    
1115   #else
1116 <    for (int i = 0; i < nGroups_; i++) {
1117 <      rs = snap_->cgData.position[i];
1118 <
1119 <      // scaled positions relative to the box vectors
1120 <      scaled = invHmat * rs;
1121 <
1122 <      // wrap the vector back into the unit box by subtracting integer box
1123 <      // numbers
1124 <      for (int j = 0; j < 3; j++) {
1125 <        scaled[j] -= roundMe(scaled[j]);
1126 <        scaled[j] += 0.5;
1116 >      for (int i = 0; i < nGroups_; i++) {
1117 >        rs = snap_->cgData.position[i];
1118 >        
1119 >        // scaled positions relative to the box vectors
1120 >        scaled = invHmat * rs;
1121 >        
1122 >        // wrap the vector back into the unit box by subtracting integer box
1123 >        // numbers
1124 >        for (int j = 0; j < 3; j++) {
1125 >          scaled[j] -= roundMe(scaled[j]);
1126 >          scaled[j] += 0.5;
1127 >        }
1128 >        
1129 >        // find xyz-indices of cell that cutoffGroup is in.
1130 >        whichCell.x() = nCells_.x() * scaled.x();
1131 >        whichCell.y() = nCells_.y() * scaled.y();
1132 >        whichCell.z() = nCells_.z() * scaled.z();
1133 >        
1134 >        // find single index of this cell:
1135 >        cellIndex = Vlinear(whichCell, nCells_);
1136 >        
1137 >        // add this cutoff group to the list of groups in this cell;
1138 >        cellList_[cellIndex].push_back(i);
1139        }
1140  
1017 –      // find xyz-indices of cell that cutoffGroup is in.
1018 –      whichCell.x() = nCells_.x() * scaled.x();
1019 –      whichCell.y() = nCells_.y() * scaled.y();
1020 –      whichCell.z() = nCells_.z() * scaled.z();
1021 –
1022 –      // find single index of this cell:
1023 –      cellIndex = Vlinear(whichCell, nCells_);      
1024 –
1025 –      // add this cutoff group to the list of groups in this cell;
1026 –      cellList_[cellIndex].push_back(i);
1027 –    }
1141   #endif
1142  
1143 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1144 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1145 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1146 <          Vector3i m1v(m1x, m1y, m1z);
1147 <          int m1 = Vlinear(m1v, nCells_);
1035 <
1036 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1037 <               os != cellOffsets_.end(); ++os) {
1143 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1144 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1145 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1146 >            Vector3i m1v(m1x, m1y, m1z);
1147 >            int m1 = Vlinear(m1v, nCells_);
1148              
1149 <            Vector3i m2v = m1v + (*os);
1150 <            
1151 <            if (m2v.x() >= nCells_.x()) {
1152 <              m2v.x() = 0;          
1153 <            } else if (m2v.x() < 0) {
1044 <              m2v.x() = nCells_.x() - 1;
1045 <            }
1046 <            
1047 <            if (m2v.y() >= nCells_.y()) {
1048 <              m2v.y() = 0;          
1049 <            } else if (m2v.y() < 0) {
1050 <              m2v.y() = nCells_.y() - 1;
1051 <            }
1052 <            
1053 <            if (m2v.z() >= nCells_.z()) {
1054 <              m2v.z() = 0;          
1055 <            } else if (m2v.z() < 0) {
1056 <              m2v.z() = nCells_.z() - 1;
1057 <            }
1058 <            
1059 <            int m2 = Vlinear (m2v, nCells_);
1149 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1150 >                 os != cellOffsets_.end(); ++os) {
1151 >              
1152 >              Vector3i m2v = m1v + (*os);
1153 >            
1154  
1155 < #ifdef IS_MPI
1156 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1157 <                 j1 != cellListRow_[m1].end(); ++j1) {
1158 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1159 <                   j2 != cellListCol_[m2].end(); ++j2) {
1160 <                              
1161 <                // Always do this if we're in different cells or if
1162 <                // we're in the same cell and the global index of the
1163 <                // j2 cutoff group is less than the j1 cutoff group
1155 >              if (m2v.x() >= nCells_.x()) {
1156 >                m2v.x() = 0;          
1157 >              } else if (m2v.x() < 0) {
1158 >                m2v.x() = nCells_.x() - 1;
1159 >              }
1160 >              
1161 >              if (m2v.y() >= nCells_.y()) {
1162 >                m2v.y() = 0;          
1163 >              } else if (m2v.y() < 0) {
1164 >                m2v.y() = nCells_.y() - 1;
1165 >              }
1166 >              
1167 >              if (m2v.z() >= nCells_.z()) {
1168 >                m2v.z() = 0;          
1169 >              } else if (m2v.z() < 0) {
1170 >                m2v.z() = nCells_.z() - 1;
1171 >              }
1172  
1173 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1173 >              int m2 = Vlinear (m2v, nCells_);
1174 >              
1175 > #ifdef IS_MPI
1176 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1177 >                   j1 != cellListRow_[m1].end(); ++j1) {
1178 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1179 >                     j2 != cellListCol_[m2].end(); ++j2) {
1180 >                  
1181 >                  // In parallel, we need to visit *all* pairs of row
1182 >                  // & column indicies and will divide labor in the
1183 >                  // force evaluation later.
1184                    dr = cgColData.position[(*j2)] - cgRowData.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 <                  }
1189 >                  }                  
1190                  }
1191                }
1080 –            }
1192   #else
1193 <
1194 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1195 <                 j1 != cellList_[m1].end(); ++j1) {
1196 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1197 <                   j2 != cellList_[m2].end(); ++j2) {
1198 <
1199 <                // Always do this if we're in different cells or if
1200 <                // we're in the same cell and the global index of the
1201 <                // j2 cutoff group is less than the j1 cutoff group
1202 <
1203 <                if (m2 != m1 || (*j2) < (*j1)) {
1204 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1205 <                  snap_->wrapVector(dr);
1206 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1207 <                  if (dr.lengthSquare() < cuts.third) {
1208 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1193 >              
1194 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1195 >                   j1 != cellList_[m1].end(); ++j1) {
1196 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1197 >                     j2 != cellList_[m2].end(); ++j2) {
1198 >                  
1199 >                  // Always do this if we're in different cells or if
1200 >                  // we're in the same cell and the global index of the
1201 >                  // j2 cutoff group is less than the j1 cutoff group
1202 >                  
1203 >                  if (m2 != m1 || (*j2) < (*j1)) {
1204 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1205 >                    snap_->wrapVector(dr);
1206 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1207 >                    if (dr.lengthSquare() < cuts.third) {
1208 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1209 >                    }
1210                    }
1211                  }
1212                }
1101 –            }
1213   #endif
1214 +            }
1215            }
1216          }
1217        }
1218 +    } else {
1219 +      // branch to do all cutoff group pairs
1220 + #ifdef IS_MPI
1221 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1222 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1223 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1224 +          snap_->wrapVector(dr);
1225 +          cuts = getGroupCutoffs( j1, j2 );
1226 +          if (dr.lengthSquare() < cuts.third) {
1227 +            neighborList.push_back(make_pair(j1, j2));
1228 +          }
1229 +        }
1230 +      }
1231 + #else
1232 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1233 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1234 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1235 +          snap_->wrapVector(dr);
1236 +          cuts = getGroupCutoffs( j1, j2 );
1237 +          if (dr.lengthSquare() < cuts.third) {
1238 +            neighborList.push_back(make_pair(j1, j2));
1239 +          }
1240 +        }
1241 +      }        
1242 + #endif
1243      }
1244 <    
1244 >      
1245      // save the local cutoff group positions for the check that is
1246      // done on each loop:
1247      saved_CG_positions_.clear();

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