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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1567 by gezelter, Tue May 24 21:24:45 2011 UTC vs.
Revision 1612 by gezelter, Fri Aug 12 19:59:56 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 {
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     */
53 –  
92    void ForceMatrixDecomposition::distributeInitialData() {
93      snap_ = sman_->getCurrentSnapshot();
94      storageLayout_ = sman_->getStorageLayout();
95 +    ff_ = info_->getForceField();
96      nLocal_ = snap_->getNumberOfAtoms();
97 <    nGroups_ = snap_->getNumberOfCutoffGroups();
97 >    
98 >    nGroups_ = info_->getNLocalCutoffGroups();
99 >    // gather the information for atomtype IDs (atids):
100 >    idents = info_->getIdentArray();
101 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
102 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
103 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
104  
105 +    massFactors = info_->getMassFactors();
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_);
64 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
65 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(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_);
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 88 | Line 145 | namespace OpenMD {
145      cgRowData.setStorageLayout(DataStorage::dslPosition);
146      cgColData.resize(nGroupsInCol_);
147      cgColData.setStorageLayout(DataStorage::dslPosition);
148 +        
149 +    identsRow.resize(nAtomsInRow_);
150 +    identsCol.resize(nAtomsInCol_);
151      
152 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
153 <                                      vector<RealType> (nAtomsInRow_, 0.0));
154 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
155 <                                      vector<RealType> (nAtomsInCol_, 0.0));
152 >    AtomPlanIntRow->gather(idents, identsRow);
153 >    AtomPlanIntColumn->gather(idents, identsCol);
154 >    
155 >    // allocate memory for the parallel objects
156 >    atypesRow.resize(nAtomsInRow_);
157 >    atypesCol.resize(nAtomsInCol_);
158  
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 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
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++) {
185 >      int gid = cgRowToGlobal[i];
186 >      for (int j = 0; j < nAtomsInRow_; j++) {
187 >        int aid = AtomRowToGlobal[j];
188 >        if (globalGroupMembership[aid] == gid)
189 >          groupListRow_[i].push_back(j);
190 >      }      
191 >    }
192 >
193 >    groupListCol_.clear();
194 >    groupListCol_.resize(nGroupsInCol_);
195 >    for (int i = 0; i < nGroupsInCol_; i++) {
196 >      int gid = cgColToGlobal[i];
197 >      for (int j = 0; j < nAtomsInCol_; j++) {
198 >        int aid = AtomColToGlobal[j];
199 >        if (globalGroupMembership[aid] == gid)
200 >          groupListCol_[i].push_back(j);
201 >      }      
202 >    }
203 >
204 >    excludesForAtom.clear();
205 >    excludesForAtom.resize(nAtomsInRow_);
206 >    toposForAtom.clear();
207 >    toposForAtom.resize(nAtomsInRow_);
208 >    topoDist.clear();
209 >    topoDist.resize(nAtomsInRow_);
210 >    for (int i = 0; i < nAtomsInRow_; i++) {
211 >      int iglob = AtomRowToGlobal[i];
212 >
213 >      for (int j = 0; j < nAtomsInCol_; j++) {
214 >        int jglob = AtomColToGlobal[j];
215 >
216 >        if (excludes->hasPair(iglob, jglob))
217 >          excludesForAtom[i].push_back(j);      
218 >        
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)) {
224 >            toposForAtom[i].push_back(j);
225 >            topoDist[i].push_back(2);
226 >          } else {
227 >            if (oneFour->hasPair(iglob, jglob)) {
228 >              toposForAtom[i].push_back(j);
229 >              topoDist[i].push_back(3);
230 >            }
231 >          }
232 >        }
233 >      }      
234 >    }
235 >
236 > #endif
237 >
238 >    // allocate memory for the parallel objects
239 >    atypesLocal.resize(nLocal_);
240 >
241 >    for (int i = 0; i < nLocal_; i++)
242 >      atypesLocal[i] = ff_->getAtomType(idents[i]);
243 >
244 >    groupList_.clear();
245 >    groupList_.resize(nGroups_);
246 >    for (int i = 0; i < nGroups_; i++) {
247 >      int gid = cgLocalToGlobal[i];
248 >      for (int j = 0; j < nLocal_; j++) {
249 >        int aid = AtomLocalToGlobal[j];
250 >        if (globalGroupMembership[aid] == gid) {
251 >          groupList_[i].push_back(j);
252 >        }
253 >      }      
254 >    }
255 >
256 >    excludesForAtom.clear();
257 >    excludesForAtom.resize(nLocal_);
258 >    toposForAtom.clear();
259 >    toposForAtom.resize(nLocal_);
260 >    topoDist.clear();
261 >    topoDist.resize(nLocal_);
262 >
263 >    for (int i = 0; i < nLocal_; i++) {
264 >      int iglob = AtomLocalToGlobal[i];
265 >
266 >      for (int j = 0; j < nLocal_; j++) {
267 >        int jglob = AtomLocalToGlobal[j];
268 >
269 >        if (excludes->hasPair(iglob, jglob))
270 >          excludesForAtom[i].push_back(j);              
271 >        
272 >        if (oneTwo->hasPair(iglob, jglob)) {
273 >          toposForAtom[i].push_back(j);
274 >          topoDist[i].push_back(1);
275 >        } else {
276 >          if (oneThree->hasPair(iglob, jglob)) {
277 >            toposForAtom[i].push_back(j);
278 >            topoDist[i].push_back(2);
279 >          } else {
280 >            if (oneFour->hasPair(iglob, jglob)) {
281 >              toposForAtom[i].push_back(j);
282 >              topoDist[i].push_back(3);
283 >            }
284 >          }
285 >        }
286 >      }      
287 >    }
288      
289 <    // gather the information for atomtype IDs (atids):
290 <    vector<int> identsLocal = info_->getIdentArray();
291 <    identsRow.reserve(nAtomsInRow_);
292 <    identsCol.reserve(nAtomsInCol_);
289 >    createGtypeCutoffMap();
290 >
291 >  }
292 >  
293 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
294      
295 <    AtomCommIntRow->gather(identsLocal, identsRow);
296 <    AtomCommIntColumn->gather(identsLocal, identsCol);
295 >    RealType tol = 1e-6;
296 >    largestRcut_ = 0.0;
297 >    RealType rc;
298 >    int atid;
299 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
300      
301 <    AtomLocalToGlobal = info_->getGlobalAtomIndices();
302 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
303 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
301 >    map<int, RealType> atypeCutoff;
302 >      
303 >    for (set<AtomType*>::iterator at = atypes.begin();
304 >         at != atypes.end(); ++at){
305 >      atid = (*at)->getIdent();
306 >      if (userChoseCutoff_)
307 >        atypeCutoff[atid] = userCutoff_;
308 >      else
309 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
310 >    }
311      
312 <    cgLocalToGlobal = info_->getGlobalGroupIndices();
313 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
314 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
312 >    vector<RealType> gTypeCutoffs;
313 >    // first we do a single loop over the cutoff groups to find the
314 >    // largest cutoff for any atypes present in this group.
315 > #ifdef IS_MPI
316 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
317 >    groupRowToGtype.resize(nGroupsInRow_);
318 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
319 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
320 >      for (vector<int>::iterator ia = atomListRow.begin();
321 >           ia != atomListRow.end(); ++ia) {            
322 >        int atom1 = (*ia);
323 >        atid = identsRow[atom1];
324 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
325 >          groupCutoffRow[cg1] = atypeCutoff[atid];
326 >        }
327 >      }
328  
329 <    // still need:
330 <    // topoDist
331 <    // exclude
329 >      bool gTypeFound = false;
330 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
331 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
332 >          groupRowToGtype[cg1] = gt;
333 >          gTypeFound = true;
334 >        }
335 >      }
336 >      if (!gTypeFound) {
337 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
338 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
339 >      }
340 >      
341 >    }
342 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
343 >    groupColToGtype.resize(nGroupsInCol_);
344 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
345 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
346 >      for (vector<int>::iterator jb = atomListCol.begin();
347 >           jb != atomListCol.end(); ++jb) {            
348 >        int atom2 = (*jb);
349 >        atid = identsCol[atom2];
350 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
351 >          groupCutoffCol[cg2] = atypeCutoff[atid];
352 >        }
353 >      }
354 >      bool gTypeFound = false;
355 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
356 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
357 >          groupColToGtype[cg2] = gt;
358 >          gTypeFound = true;
359 >        }
360 >      }
361 >      if (!gTypeFound) {
362 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
363 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
364 >      }
365 >    }
366 > #else
367 >
368 >    vector<RealType> groupCutoff(nGroups_, 0.0);
369 >    groupToGtype.resize(nGroups_);
370 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
371 >      groupCutoff[cg1] = 0.0;
372 >      vector<int> atomList = getAtomsInGroupRow(cg1);
373 >      for (vector<int>::iterator ia = atomList.begin();
374 >           ia != atomList.end(); ++ia) {            
375 >        int atom1 = (*ia);
376 >        atid = idents[atom1];
377 >        if (atypeCutoff[atid] > groupCutoff[cg1])
378 >          groupCutoff[cg1] = atypeCutoff[atid];
379 >      }
380 >      
381 >      bool gTypeFound = false;
382 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
383 >        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
384 >          groupToGtype[cg1] = gt;
385 >          gTypeFound = true;
386 >        }
387 >      }
388 >      if (!gTypeFound) {      
389 >        gTypeCutoffs.push_back( groupCutoff[cg1] );
390 >        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
391 >      }      
392 >    }
393   #endif
394 +
395 +    // Now we find the maximum group cutoff value present in the simulation
396 +
397 +    RealType groupMax = *max_element(gTypeCutoffs.begin(),
398 +                                     gTypeCutoffs.end());
399 +
400 + #ifdef IS_MPI
401 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
402 +                              MPI::MAX);
403 + #endif
404 +    
405 +    RealType tradRcut = groupMax;
406 +
407 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
408 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
409 +        RealType thisRcut;
410 +        switch(cutoffPolicy_) {
411 +        case TRADITIONAL:
412 +          thisRcut = tradRcut;
413 +          break;
414 +        case MIX:
415 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
416 +          break;
417 +        case MAX:
418 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
419 +          break;
420 +        default:
421 +          sprintf(painCave.errMsg,
422 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
423 +                  "hit an unknown cutoff policy!\n");
424 +          painCave.severity = OPENMD_ERROR;
425 +          painCave.isFatal = 1;
426 +          simError();
427 +          break;
428 +        }
429 +
430 +        pair<int,int> key = make_pair(i,j);
431 +        gTypeCutoffMap[key].first = thisRcut;
432 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
433 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
434 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
435 +        // sanity check
436 +        
437 +        if (userChoseCutoff_) {
438 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
439 +            sprintf(painCave.errMsg,
440 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
441 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
442 +            painCave.severity = OPENMD_ERROR;
443 +            painCave.isFatal = 1;
444 +            simError();            
445 +          }
446 +        }
447 +      }
448 +    }
449    }
450 +
451 +
452 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
453 +    int i, j;  
454 + #ifdef IS_MPI
455 +    i = groupRowToGtype[cg1];
456 +    j = groupColToGtype[cg2];
457 + #else
458 +    i = groupToGtype[cg1];
459 +    j = groupToGtype[cg2];
460 + #endif    
461 +    return gTypeCutoffMap[make_pair(i,j)];
462 +  }
463 +
464 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
465 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
466 +      if (toposForAtom[atom1][j] == atom2)
467 +        return topoDist[atom1][j];
468 +    }
469 +    return 0;
470 +  }
471 +
472 +  void ForceMatrixDecomposition::zeroWorkArrays() {
473 +    pairwisePot = 0.0;
474 +    embeddingPot = 0.0;
475 +
476 + #ifdef IS_MPI
477 +    if (storageLayout_ & DataStorage::dslForce) {
478 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
479 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
480 +    }
481 +
482 +    if (storageLayout_ & DataStorage::dslTorque) {
483 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
484 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
485 +    }
486      
487 +    fill(pot_row.begin(), pot_row.end(),
488 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
489  
490 +    fill(pot_col.begin(), pot_col.end(),
491 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
492  
493 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
494 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
495 +           0.0);
496 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
497 +           0.0);
498 +    }
499 +
500 +    if (storageLayout_ & DataStorage::dslDensity) {      
501 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
502 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
503 +    }
504 +
505 +    if (storageLayout_ & DataStorage::dslFunctional) {  
506 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
507 +           0.0);
508 +      fill(atomColData.functional.begin(), atomColData.functional.end(),
509 +           0.0);
510 +    }
511 +
512 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
513 +      fill(atomRowData.functionalDerivative.begin(),
514 +           atomRowData.functionalDerivative.end(), 0.0);
515 +      fill(atomColData.functionalDerivative.begin(),
516 +           atomColData.functionalDerivative.end(), 0.0);
517 +    }
518 +
519 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
520 +      fill(atomRowData.skippedCharge.begin(),
521 +           atomRowData.skippedCharge.end(), 0.0);
522 +      fill(atomColData.skippedCharge.begin(),
523 +           atomColData.skippedCharge.end(), 0.0);
524 +    }
525 +
526 + #endif
527 +    // even in parallel, we need to zero out the local arrays:
528 +
529 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
530 +      fill(snap_->atomData.particlePot.begin(),
531 +           snap_->atomData.particlePot.end(), 0.0);
532 +    }
533 +    
534 +    if (storageLayout_ & DataStorage::dslDensity) {      
535 +      fill(snap_->atomData.density.begin(),
536 +           snap_->atomData.density.end(), 0.0);
537 +    }
538 +    if (storageLayout_ & DataStorage::dslFunctional) {
539 +      fill(snap_->atomData.functional.begin(),
540 +           snap_->atomData.functional.end(), 0.0);
541 +    }
542 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
543 +      fill(snap_->atomData.functionalDerivative.begin(),
544 +           snap_->atomData.functionalDerivative.end(), 0.0);
545 +    }
546 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
547 +      fill(snap_->atomData.skippedCharge.begin(),
548 +           snap_->atomData.skippedCharge.end(), 0.0);
549 +    }
550 +    
551 +  }
552 +
553 +
554    void ForceMatrixDecomposition::distributeData()  {
555      snap_ = sman_->getCurrentSnapshot();
556      storageLayout_ = sman_->getStorageLayout();
557   #ifdef IS_MPI
558      
559      // gather up the atomic positions
560 <    AtomCommVectorRow->gather(snap_->atomData.position,
560 >    AtomPlanVectorRow->gather(snap_->atomData.position,
561                                atomRowData.position);
562 <    AtomCommVectorColumn->gather(snap_->atomData.position,
562 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
563                                   atomColData.position);
564      
565      // gather up the cutoff group positions
566 <    cgCommVectorRow->gather(snap_->cgData.position,
566 >
567 >    cgPlanVectorRow->gather(snap_->cgData.position,
568                              cgRowData.position);
569 <    cgCommVectorColumn->gather(snap_->cgData.position,
569 >
570 >    cgPlanVectorColumn->gather(snap_->cgData.position,
571                                 cgColData.position);
572 +
573      
574      // if needed, gather the atomic rotation matrices
575      if (storageLayout_ & DataStorage::dslAmat) {
576 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
576 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
577                                  atomRowData.aMat);
578 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
578 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
579                                     atomColData.aMat);
580      }
581      
582      // if needed, gather the atomic eletrostatic frames
583      if (storageLayout_ & DataStorage::dslElectroFrame) {
584 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
584 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
585                                  atomRowData.electroFrame);
586 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
586 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
587                                     atomColData.electroFrame);
588      }
589 +
590   #endif      
591    }
592    
593 +  /* collects information obtained during the pre-pair loop onto local
594 +   * data structures.
595 +   */
596    void ForceMatrixDecomposition::collectIntermediateData() {
597      snap_ = sman_->getCurrentSnapshot();
598      storageLayout_ = sman_->getStorageLayout();
# Line 163 | Line 600 | namespace OpenMD {
600      
601      if (storageLayout_ & DataStorage::dslDensity) {
602        
603 <      AtomCommRealRow->scatter(atomRowData.density,
603 >      AtomPlanRealRow->scatter(atomRowData.density,
604                                 snap_->atomData.density);
605        
606        int n = snap_->atomData.density.size();
607 <      std::vector<RealType> rho_tmp(n, 0.0);
608 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
607 >      vector<RealType> rho_tmp(n, 0.0);
608 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
609        for (int i = 0; i < n; i++)
610          snap_->atomData.density[i] += rho_tmp[i];
611      }
612   #endif
613    }
614 <  
614 >
615 >  /*
616 >   * redistributes information obtained during the pre-pair loop out to
617 >   * row and column-indexed data structures
618 >   */
619    void ForceMatrixDecomposition::distributeIntermediateData() {
620      snap_ = sman_->getCurrentSnapshot();
621      storageLayout_ = sman_->getStorageLayout();
622   #ifdef IS_MPI
623      if (storageLayout_ & DataStorage::dslFunctional) {
624 <      AtomCommRealRow->gather(snap_->atomData.functional,
624 >      AtomPlanRealRow->gather(snap_->atomData.functional,
625                                atomRowData.functional);
626 <      AtomCommRealColumn->gather(snap_->atomData.functional,
626 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
627                                   atomColData.functional);
628      }
629      
630      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
631 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
631 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
632                                atomRowData.functionalDerivative);
633 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
633 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
634                                   atomColData.functionalDerivative);
635      }
636   #endif
# Line 203 | Line 644 | namespace OpenMD {
644      int n = snap_->atomData.force.size();
645      vector<Vector3d> frc_tmp(n, V3Zero);
646      
647 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
647 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
648      for (int i = 0; i < n; i++) {
649        snap_->atomData.force[i] += frc_tmp[i];
650        frc_tmp[i] = 0.0;
651      }
652      
653 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
654 <    for (int i = 0; i < n; i++)
653 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
654 >    for (int i = 0; i < n; i++) {
655        snap_->atomData.force[i] += frc_tmp[i];
656 <    
657 <    
656 >    }
657 >        
658      if (storageLayout_ & DataStorage::dslTorque) {
659  
660 <      int nt = snap_->atomData.force.size();
660 >      int nt = snap_->atomData.torque.size();
661        vector<Vector3d> trq_tmp(nt, V3Zero);
662  
663 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
664 <      for (int i = 0; i < n; i++) {
663 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
664 >      for (int i = 0; i < nt; i++) {
665          snap_->atomData.torque[i] += trq_tmp[i];
666          trq_tmp[i] = 0.0;
667        }
668        
669 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
670 <      for (int i = 0; i < n; i++)
669 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
670 >      for (int i = 0; i < nt; i++)
671          snap_->atomData.torque[i] += trq_tmp[i];
672 +    }
673 +
674 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
675 +
676 +      int ns = snap_->atomData.skippedCharge.size();
677 +      vector<RealType> skch_tmp(ns, 0.0);
678 +
679 +      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
680 +      for (int i = 0; i < ns; i++) {
681 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
682 +        skch_tmp[i] = 0.0;
683 +      }
684 +      
685 +      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
686 +      for (int i = 0; i < ns; i++)
687 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
688      }
689      
690      nLocal_ = snap_->getNumberOfAtoms();
691  
692 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
693 <                                       vector<RealType> (nLocal_, 0.0));
692 >    vector<potVec> pot_temp(nLocal_,
693 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
694 >
695 >    // scatter/gather pot_row into the members of my column
696 >          
697 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
698 >
699 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
700 >      pairwisePot += pot_temp[ii];
701      
702 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
703 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
704 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
705 <        pot_local[i] += pot_temp[i][ii];
706 <      }
702 >    fill(pot_temp.begin(), pot_temp.end(),
703 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
704 >      
705 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
706 >    
707 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
708 >      pairwisePot += pot_temp[ii];    
709 >    
710 >    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
711 >      RealType ploc1 = pairwisePot[ii];
712 >      RealType ploc2 = 0.0;
713 >      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
714 >      pairwisePot[ii] = ploc2;
715      }
716 +
717   #endif
718 +
719    }
720  
721 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
722 + #ifdef IS_MPI
723 +    return nAtomsInRow_;
724 + #else
725 +    return nLocal_;
726 + #endif
727 +  }
728 +
729 +  /**
730 +   * returns the list of atoms belonging to this group.  
731 +   */
732 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
733 + #ifdef IS_MPI
734 +    return groupListRow_[cg1];
735 + #else
736 +    return groupList_[cg1];
737 + #endif
738 +  }
739 +
740 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
741 + #ifdef IS_MPI
742 +    return groupListCol_[cg2];
743 + #else
744 +    return groupList_[cg2];
745 + #endif
746 +  }
747    
748    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
749      Vector3d d;
# Line 285 | Line 785 | namespace OpenMD {
785      snap_->wrapVector(d);
786      return d;    
787    }
788 +
789 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
790 + #ifdef IS_MPI
791 +    return massFactorsRow[atom1];
792 + #else
793 +    return massFactors[atom1];
794 + #endif
795 +  }
796 +
797 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
798 + #ifdef IS_MPI
799 +    return massFactorsCol[atom2];
800 + #else
801 +    return massFactors[atom2];
802 + #endif
803 +
804 +  }
805      
806    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
807      Vector3d d;
# Line 299 | Line 816 | namespace OpenMD {
816      return d;    
817    }
818  
819 +  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
820 +    return excludesForAtom[atom1];
821 +  }
822 +
823 +  /**
824 +   * We need to exclude some overcounted interactions that result from
825 +   * the parallel decomposition.
826 +   */
827 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
828 +    int unique_id_1, unique_id_2;
829 +    
830 + #ifdef IS_MPI
831 +    // in MPI, we have to look up the unique IDs for each atom
832 +    unique_id_1 = AtomRowToGlobal[atom1];
833 +    unique_id_2 = AtomColToGlobal[atom2];
834 +
835 +    // this situation should only arise in MPI simulations
836 +    if (unique_id_1 == unique_id_2) return true;
837 +    
838 +    // this prevents us from doing the pair on multiple processors
839 +    if (unique_id_1 < unique_id_2) {
840 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
841 +    } else {
842 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
843 +    }
844 + #endif
845 +    return false;
846 +  }
847 +
848 +  /**
849 +   * We need to handle the interactions for atoms who are involved in
850 +   * the same rigid body as well as some short range interactions
851 +   * (bonds, bends, torsions) differently from other interactions.
852 +   * We'll still visit the pairwise routines, but with a flag that
853 +   * tells those routines to exclude the pair from direct long range
854 +   * interactions.  Some indirect interactions (notably reaction
855 +   * field) must still be handled for these pairs.
856 +   */
857 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
858 +    int unique_id_2;
859 + #ifdef IS_MPI
860 +    // in MPI, we have to look up the unique IDs for the row atom.
861 +    unique_id_2 = AtomColToGlobal[atom2];
862 + #else
863 +    // in the normal loop, the atom numbers are unique
864 +    unique_id_2 = atom2;
865 + #endif
866 +    
867 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
868 +         i != excludesForAtom[atom1].end(); ++i) {
869 +      if ( (*i) == unique_id_2 ) return true;
870 +    }
871 +
872 +    return false;
873 +  }
874 +
875 +
876    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
877   #ifdef IS_MPI
878      atomRowData.force[atom1] += fg;
# Line 316 | Line 890 | namespace OpenMD {
890    }
891  
892      // filling interaction blocks with pointers
893 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
894 <    InteractionData idat;
893 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
894 >                                                     int atom1, int atom2) {
895  
896 +    idat.excluded = excludeAtomPair(atom1, atom2);
897 +  
898   #ifdef IS_MPI
899 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
900 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
901 +    //                         ff_->getAtomType(identsCol[atom2]) );
902 +    
903      if (storageLayout_ & DataStorage::dslAmat) {
904        idat.A1 = &(atomRowData.aMat[atom1]);
905        idat.A2 = &(atomColData.aMat[atom2]);
# Line 340 | Line 920 | namespace OpenMD {
920        idat.rho2 = &(atomColData.density[atom2]);
921      }
922  
923 +    if (storageLayout_ & DataStorage::dslFunctional) {
924 +      idat.frho1 = &(atomRowData.functional[atom1]);
925 +      idat.frho2 = &(atomColData.functional[atom2]);
926 +    }
927 +
928      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
929        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
930        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
931      }
932 +
933 +    if (storageLayout_ & DataStorage::dslParticlePot) {
934 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
935 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
936 +    }
937 +
938 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
939 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
940 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
941 +    }
942 +
943   #else
944 +
945 +    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
946 +    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
947 +    //                         ff_->getAtomType(idents[atom2]) );
948 +
949      if (storageLayout_ & DataStorage::dslAmat) {
950        idat.A1 = &(snap_->atomData.aMat[atom1]);
951        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 360 | Line 961 | namespace OpenMD {
961        idat.t2 = &(snap_->atomData.torque[atom2]);
962      }
963  
964 <    if (storageLayout_ & DataStorage::dslDensity) {
964 >    if (storageLayout_ & DataStorage::dslDensity) {    
965        idat.rho1 = &(snap_->atomData.density[atom1]);
966        idat.rho2 = &(snap_->atomData.density[atom2]);
967      }
968  
969 +    if (storageLayout_ & DataStorage::dslFunctional) {
970 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
971 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
972 +    }
973 +
974      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
975        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
976        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
977      }
978 +
979 +    if (storageLayout_ & DataStorage::dslParticlePot) {
980 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
981 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
982 +    }
983 +
984 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
985 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
986 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
987 +    }
988   #endif
373 –    return idat;
989    }
990  
991 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
992 <
378 <    InteractionData idat;
991 >  
992 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
993   #ifdef IS_MPI
994 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
995 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
996 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
997 <    }
998 <    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 <    }
994 >    pot_row[atom1] += 0.5 *  *(idat.pot);
995 >    pot_col[atom2] += 0.5 *  *(idat.pot);
996 >
997 >    atomRowData.force[atom1] += *(idat.f1);
998 >    atomColData.force[atom2] -= *(idat.f1);
999   #else
1000 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
1001 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1002 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1003 <    }
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 <    }
1000 >    pairwisePot += *(idat.pot);
1001 >
1002 >    snap_->atomData.force[atom1] += *(idat.f1);
1003 >    snap_->atomData.force[atom2] -= *(idat.f1);
1004   #endif
1005      
1006    }
1007  
409 –  SelfData ForceMatrixDecomposition::fillSelfData(int atom1) {
410 –    SelfData sdat;
411 –    // Still Missing atype, skippedCharge, potVec pot,
412 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
413 –      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
414 –    }
415 –    
416 –    if (storageLayout_ & DataStorage::dslTorque) {
417 –      sdat.t = &(snap_->atomData.torque[atom1]);
418 –    }
419 –    
420 –    if (storageLayout_ & DataStorage::dslDensity) {
421 –      sdat.rho = &(snap_->atomData.density[atom1]);
422 –    }
423 –    
424 –    if (storageLayout_ & DataStorage::dslFunctional) {
425 –      sdat.frho = &(snap_->atomData.functional[atom1]);
426 –    }
427 –    
428 –    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
429 –      sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
430 –    }
431 –
432 –    return sdat;    
433 –  }
434 –
435 –
436 –
1008    /*
1009     * buildNeighborList
1010     *
# Line 443 | Line 1014 | namespace OpenMD {
1014    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1015        
1016      vector<pair<int, int> > neighborList;
1017 +    groupCutoffs cuts;
1018 +    bool doAllPairs = false;
1019 +
1020   #ifdef IS_MPI
1021 <    CellListRow.clear();
1022 <    CellListCol.clear();
1021 >    cellListRow_.clear();
1022 >    cellListCol_.clear();
1023   #else
1024 <    CellList.clear();
1024 >    cellList_.clear();
1025   #endif
1026  
1027 <    // dangerous to not do error checking.
454 <    RealType skinThickness_ = info_->getSimParams()->getSkinThickness();
455 <    RealType rCut_;
456 <
457 <    RealType rList_ = (rCut_ + skinThickness_);
1027 >    RealType rList_ = (largestRcut_ + skinThickness_);
1028      RealType rl2 = rList_ * rList_;
1029      Snapshot* snap_ = sman_->getCurrentSnapshot();
1030      Mat3x3d Hmat = snap_->getHmat();
1031      Vector3d Hx = Hmat.getColumn(0);
1032      Vector3d Hy = Hmat.getColumn(1);
1033      Vector3d Hz = Hmat.getColumn(2);
464 –    Vector3i nCells;
1034  
1035 <    nCells.x() = (int) ( Hx.length() )/ rList_;
1036 <    nCells.y() = (int) ( Hy.length() )/ rList_;
1037 <    nCells.z() = (int) ( Hz.length() )/ rList_;
1035 >    nCells_.x() = (int) ( Hx.length() )/ rList_;
1036 >    nCells_.y() = (int) ( Hy.length() )/ rList_;
1037 >    nCells_.z() = (int) ( Hz.length() )/ rList_;
1038  
1039 +    // handle small boxes where the cell offsets can end up repeating cells
1040 +    
1041 +    if (nCells_.x() < 3) doAllPairs = true;
1042 +    if (nCells_.y() < 3) doAllPairs = true;
1043 +    if (nCells_.z() < 3) doAllPairs = true;
1044 +
1045      Mat3x3d invHmat = snap_->getInvHmat();
1046      Vector3d rs, scaled, dr;
1047      Vector3i whichCell;
1048      int cellIndex;
1049 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1050  
1051   #ifdef IS_MPI
1052 <    for (int i = 0; i < nGroupsInRow_; i++) {
1053 <      rs = cgRowData.position[i];
1054 <      // scaled positions relative to the box vectors
1055 <      scaled = invHmat * rs;
1056 <      // wrap the vector back into the unit box by subtracting integer box
481 <      // numbers
482 <      for (int j = 0; j < 3; j++)
483 <        scaled[j] -= roundMe(scaled[j]);
484 <    
485 <      // find xyz-indices of cell that cutoffGroup is in.
486 <      whichCell.x() = nCells.x() * scaled.x();
487 <      whichCell.y() = nCells.y() * scaled.y();
488 <      whichCell.z() = nCells.z() * scaled.z();
1052 >    cellListRow_.resize(nCtot);
1053 >    cellListCol_.resize(nCtot);
1054 > #else
1055 >    cellList_.resize(nCtot);
1056 > #endif
1057  
1058 <      // find single index of this cell:
1059 <      cellIndex = Vlinear(whichCell, nCells);
492 <      // add this cutoff group to the list of groups in this cell;
493 <      CellListRow[cellIndex].push_back(i);
494 <    }
1058 >    if (!doAllPairs) {
1059 > #ifdef IS_MPI
1060  
1061 <    for (int i = 0; i < nGroupsInCol_; i++) {
1062 <      rs = cgColData.position[i];
1063 <      // scaled positions relative to the box vectors
1064 <      scaled = invHmat * rs;
1065 <      // wrap the vector back into the unit box by subtracting integer box
1066 <      // numbers
1067 <      for (int j = 0; j < 3; j++)
1068 <        scaled[j] -= roundMe(scaled[j]);
1069 <
1070 <      // find xyz-indices of cell that cutoffGroup is in.
1071 <      whichCell.x() = nCells.x() * scaled.x();
1072 <      whichCell.y() = nCells.y() * scaled.y();
1073 <      whichCell.z() = nCells.z() * scaled.z();
1074 <
1075 <      // find single index of this cell:
1076 <      cellIndex = Vlinear(whichCell, nCells);
1077 <      // add this cutoff group to the list of groups in this cell;
1078 <      CellListCol[cellIndex].push_back(i);
1079 <    }
1061 >      for (int i = 0; i < nGroupsInRow_; i++) {
1062 >        rs = cgRowData.position[i];
1063 >        
1064 >        // scaled positions relative to the box vectors
1065 >        scaled = invHmat * rs;
1066 >        
1067 >        // wrap the vector back into the unit box by subtracting integer box
1068 >        // numbers
1069 >        for (int j = 0; j < 3; j++) {
1070 >          scaled[j] -= roundMe(scaled[j]);
1071 >          scaled[j] += 0.5;
1072 >        }
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 >        
1082 >        // add this cutoff group to the list of groups in this cell;
1083 >        cellListRow_[cellIndex].push_back(i);
1084 >      }
1085 >      for (int i = 0; i < nGroupsInCol_; i++) {
1086 >        rs = cgColData.position[i];
1087 >        
1088 >        // scaled positions relative to the box vectors
1089 >        scaled = invHmat * rs;
1090 >        
1091 >        // wrap the vector back into the unit box by subtracting integer box
1092 >        // numbers
1093 >        for (int j = 0; j < 3; j++) {
1094 >          scaled[j] -= roundMe(scaled[j]);
1095 >          scaled[j] += 0.5;
1096 >        }
1097 >        
1098 >        // find xyz-indices of cell that cutoffGroup is in.
1099 >        whichCell.x() = nCells_.x() * scaled.x();
1100 >        whichCell.y() = nCells_.y() * scaled.y();
1101 >        whichCell.z() = nCells_.z() * scaled.z();
1102 >        
1103 >        // find single index of this cell:
1104 >        cellIndex = Vlinear(whichCell, nCells_);
1105 >        
1106 >        // add this cutoff group to the list of groups in this cell;
1107 >        cellListCol_[cellIndex].push_back(i);
1108 >      }
1109 >    
1110   #else
1111 <    for (int i = 0; i < nGroups_; i++) {
1112 <      rs = snap_->cgData.position[i];
1113 <      // scaled positions relative to the box vectors
1114 <      scaled = invHmat * rs;
1115 <      // wrap the vector back into the unit box by subtracting integer box
1116 <      // numbers
1117 <      for (int j = 0; j < 3; j++)
1118 <        scaled[j] -= roundMe(scaled[j]);
1111 >      for (int i = 0; i < nGroups_; i++) {
1112 >        rs = snap_->cgData.position[i];
1113 >        
1114 >        // scaled positions relative to the box vectors
1115 >        scaled = invHmat * rs;
1116 >        
1117 >        // wrap the vector back into the unit box by subtracting integer box
1118 >        // numbers
1119 >        for (int j = 0; j < 3; j++) {
1120 >          scaled[j] -= roundMe(scaled[j]);
1121 >          scaled[j] += 0.5;
1122 >        }
1123 >        
1124 >        // find xyz-indices of cell that cutoffGroup is in.
1125 >        whichCell.x() = nCells_.x() * scaled.x();
1126 >        whichCell.y() = nCells_.y() * scaled.y();
1127 >        whichCell.z() = nCells_.z() * scaled.z();
1128 >        
1129 >        // find single index of this cell:
1130 >        cellIndex = Vlinear(whichCell, nCells_);
1131 >        
1132 >        // add this cutoff group to the list of groups in this cell;
1133 >        cellList_[cellIndex].push_back(i);
1134 >      }
1135  
525 –      // find xyz-indices of cell that cutoffGroup is in.
526 –      whichCell.x() = nCells.x() * scaled.x();
527 –      whichCell.y() = nCells.y() * scaled.y();
528 –      whichCell.z() = nCells.z() * scaled.z();
529 –
530 –      // find single index of this cell:
531 –      cellIndex = Vlinear(whichCell, nCells);
532 –      // add this cutoff group to the list of groups in this cell;
533 –      CellList[cellIndex].push_back(i);
534 –    }
1136   #endif
1137  
1138 +      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1139 +        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1140 +          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1141 +            Vector3i m1v(m1x, m1y, m1z);
1142 +            int m1 = Vlinear(m1v, nCells_);
1143 +            
1144 +            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1145 +                 os != cellOffsets_.end(); ++os) {
1146 +              
1147 +              Vector3i m2v = m1v + (*os);
1148 +            
1149  
1150 +              if (m2v.x() >= nCells_.x()) {
1151 +                m2v.x() = 0;          
1152 +              } else if (m2v.x() < 0) {
1153 +                m2v.x() = nCells_.x() - 1;
1154 +              }
1155 +              
1156 +              if (m2v.y() >= nCells_.y()) {
1157 +                m2v.y() = 0;          
1158 +              } else if (m2v.y() < 0) {
1159 +                m2v.y() = nCells_.y() - 1;
1160 +              }
1161 +              
1162 +              if (m2v.z() >= nCells_.z()) {
1163 +                m2v.z() = 0;          
1164 +              } else if (m2v.z() < 0) {
1165 +                m2v.z() = nCells_.z() - 1;
1166 +              }
1167  
1168 <    for (int m1z = 0; m1z < nCells.z(); m1z++) {
1169 <      for (int m1y = 0; m1y < nCells.y(); m1y++) {
541 <        for (int m1x = 0; m1x < nCells.x(); m1x++) {
542 <          Vector3i m1v(m1x, m1y, m1z);
543 <          int m1 = Vlinear(m1v, nCells);
544 <          for (int offset = 0; offset < nOffset_; offset++) {
545 <            Vector3i m2v = m1v + cellOffsets_[offset];
546 <
547 <            if (m2v.x() >= nCells.x()) {
548 <              m2v.x() = 0;          
549 <            } else if (m2v.x() < 0) {
550 <              m2v.x() = nCells.x() - 1;
551 <            }
552 <
553 <            if (m2v.y() >= nCells.y()) {
554 <              m2v.y() = 0;          
555 <            } else if (m2v.y() < 0) {
556 <              m2v.y() = nCells.y() - 1;
557 <            }
558 <
559 <            if (m2v.z() >= nCells.z()) {
560 <              m2v.z() = 0;          
561 <            } else if (m2v.z() < 0) {
562 <              m2v.z() = nCells.z() - 1;
563 <            }
564 <
565 <            int m2 = Vlinear (m2v, nCells);
566 <
1168 >              int m2 = Vlinear (m2v, nCells_);
1169 >              
1170   #ifdef IS_MPI
1171 <            for (vector<int>::iterator j1 = CellListRow[m1].begin();
1172 <                 j1 != CellListRow[m1].end(); ++j1) {
1173 <              for (vector<int>::iterator j2 = CellListCol[m2].begin();
1174 <                   j2 != CellListCol[m2].end(); ++j2) {
1175 <                              
1176 <                // Always do this if we're in different cells or if
1177 <                // we're in the same cell and the global index of the
1178 <                // j2 cutoff group is less than the j1 cutoff group
576 <
577 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1171 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1172 >                   j1 != cellListRow_[m1].end(); ++j1) {
1173 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1174 >                     j2 != cellListCol_[m2].end(); ++j2) {
1175 >                  
1176 >                  // In parallel, we need to visit *all* pairs of row
1177 >                  // & column indicies and will divide labor in the
1178 >                  // force evaluation later.
1179                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1180                    snap_->wrapVector(dr);
1181 <                  if (dr.lengthSquare() < rl2) {
1181 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1182 >                  if (dr.lengthSquare() < cuts.third) {
1183                      neighborList.push_back(make_pair((*j1), (*j2)));
1184 <                  }
1184 >                  }                  
1185                  }
1186                }
585 –            }
1187   #else
1188 <            for (vector<int>::iterator j1 = CellList[m1].begin();
1189 <                 j1 != CellList[m1].end(); ++j1) {
1190 <              for (vector<int>::iterator j2 = CellList[m2].begin();
1191 <                   j2 != CellList[m2].end(); ++j2) {
1192 <                              
1193 <                // Always do this if we're in different cells or if
1194 <                // we're in the same cell and the global index of the
1195 <                // j2 cutoff group is less than the j1 cutoff group
1196 <
1197 <                if (m2 != m1 || (*j2) < (*j1)) {
1198 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1199 <                  snap_->wrapVector(dr);
1200 <                  if (dr.lengthSquare() < rl2) {
1201 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1188 >              
1189 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1190 >                   j1 != cellList_[m1].end(); ++j1) {
1191 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1192 >                     j2 != cellList_[m2].end(); ++j2) {
1193 >                  
1194 >                  // Always do this if we're in different cells or if
1195 >                  // we're in the same cell and the global index of the
1196 >                  // j2 cutoff group is less than the j1 cutoff group
1197 >                  
1198 >                  if (m2 != m1 || (*j2) < (*j1)) {
1199 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1200 >                    snap_->wrapVector(dr);
1201 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1202 >                    if (dr.lengthSquare() < cuts.third) {
1203 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1204 >                    }
1205                    }
1206                  }
1207                }
604 –            }
1208   #endif
1209 +            }
1210            }
1211          }
1212        }
1213 +    } else {
1214 +      // branch to do all cutoff group pairs
1215 + #ifdef IS_MPI
1216 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1217 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1218 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1219 +          snap_->wrapVector(dr);
1220 +          cuts = getGroupCutoffs( j1, j2 );
1221 +          if (dr.lengthSquare() < cuts.third) {
1222 +            neighborList.push_back(make_pair(j1, j2));
1223 +          }
1224 +        }
1225 +      }
1226 + #else
1227 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1228 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1229 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1230 +          snap_->wrapVector(dr);
1231 +          cuts = getGroupCutoffs( j1, j2 );
1232 +          if (dr.lengthSquare() < cuts.third) {
1233 +            neighborList.push_back(make_pair(j1, j2));
1234 +          }
1235 +        }
1236 +      }        
1237 + #endif
1238      }
1239 +      
1240 +    // save the local cutoff group positions for the check that is
1241 +    // done on each loop:
1242 +    saved_CG_positions_.clear();
1243 +    for (int i = 0; i < nGroups_; i++)
1244 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1245 +    
1246      return neighborList;
1247    }
1248   } //end namespace OpenMD

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