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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceDecomposition.cpp (file contents), Revision 1539 by gezelter, Fri Jan 14 22:31:31 2011 UTC vs.
branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC

# Line 38 | Line 38
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39   * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41 < #include "parallel/ForceDecomposition.hpp"
42 < #include "parallel/Communicator.hpp"
41 > #include "parallel/ForceMatrixDecomposition.hpp"
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 <  void ForceDecomposition::distributeInitialData() {
50 >  /**
51 >   * distributeInitialData is essentially a copy of the older fortran
52 >   * SimulationSetup
53 >   */
54 >  
55 >  void ForceMatrixDecomposition::distributeInitialData() {
56 >    snap_ = sman_->getCurrentSnapshot();
57 >    storageLayout_ = sman_->getStorageLayout();
58 >    ff_ = info_->getForceField();
59 >    nLocal_ = snap_->getNumberOfAtoms();
60 >
61 >    nGroups_ = info_->getNLocalCutoffGroups();
62 >    // gather the information for atomtype IDs (atids):
63 >    identsLocal = info_->getIdentArray();
64 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
65 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
66 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67 >    vector<RealType> massFactorsLocal = info_->getMassFactors();
68 >    PairList excludes = info_->getExcludedInteractions();
69 >    PairList oneTwo = info_->getOneTwoInteractions();
70 >    PairList oneThree = info_->getOneThreeInteractions();
71 >    PairList oneFour = info_->getOneFourInteractions();
72 >
73   #ifdef IS_MPI
74 +
75 +    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
76 +    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
77 +    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
78 +    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
79 +    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
80  
81 <    int nAtoms;
82 <    int nGroups;
81 >    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
82 >    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
83 >    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
84 >    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
85 >    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
86  
87 <    AtomCommRealI = new Comm<I,RealType>(nAtoms);
88 <    AtomCommVectorI = new Comm<I,Vector3d>(nAtoms);
89 <    AtomCommMatrixI = new Comm<I,Mat3x3d>(nAtoms);
87 >    cgCommIntRow = new Communicator<Row,int>(nGroups_);
88 >    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
89 >    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
90 >    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
91  
92 <    AtomCommRealJ = new Comm<J,RealType>(nAtoms);
93 <    AtomCommVectorJ = new Comm<J,Vector3d>(nAtoms);
94 <    AtomCommMatrixJ = new Comm<J,Mat3x3d>(nAtoms);
92 >    nAtomsInRow_ = AtomCommIntRow->getSize();
93 >    nAtomsInCol_ = AtomCommIntColumn->getSize();
94 >    nGroupsInRow_ = cgCommIntRow->getSize();
95 >    nGroupsInCol_ = cgCommIntColumn->getSize();
96  
97 <    cgCommVectorI = new Comm<I,Vector3d>(nGroups);
98 <    cgCommVectorJ = new Comm<J,Vector3d>(nGroups);
99 <    // more to come
97 >    // Modify the data storage objects with the correct layouts and sizes:
98 >    atomRowData.resize(nAtomsInRow_);
99 >    atomRowData.setStorageLayout(storageLayout_);
100 >    atomColData.resize(nAtomsInCol_);
101 >    atomColData.setStorageLayout(storageLayout_);
102 >    cgRowData.resize(nGroupsInRow_);
103 >    cgRowData.setStorageLayout(DataStorage::dslPosition);
104 >    cgColData.resize(nGroupsInCol_);
105 >    cgColData.setStorageLayout(DataStorage::dslPosition);
106 >        
107 >    identsRow.resize(nAtomsInRow_);
108 >    identsCol.resize(nAtomsInCol_);
109 >    
110 >    AtomCommIntRow->gather(identsLocal, identsRow);
111 >    AtomCommIntColumn->gather(identsLocal, identsCol);
112 >    
113 >    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
114 >    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
115 >    
116 >    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
117 >    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
118 >
119 >    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
120 >    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
121 >
122 >    groupListRow_.clear();
123 >    groupListRow_.resize(nGroupsInRow_);
124 >    for (int i = 0; i < nGroupsInRow_; i++) {
125 >      int gid = cgRowToGlobal[i];
126 >      for (int j = 0; j < nAtomsInRow_; j++) {
127 >        int aid = AtomRowToGlobal[j];
128 >        if (globalGroupMembership[aid] == gid)
129 >          groupListRow_[i].push_back(j);
130 >      }      
131 >    }
132 >
133 >    groupListCol_.clear();
134 >    groupListCol_.resize(nGroupsInCol_);
135 >    for (int i = 0; i < nGroupsInCol_; i++) {
136 >      int gid = cgColToGlobal[i];
137 >      for (int j = 0; j < nAtomsInCol_; j++) {
138 >        int aid = AtomColToGlobal[j];
139 >        if (globalGroupMembership[aid] == gid)
140 >          groupListCol_[i].push_back(j);
141 >      }      
142 >    }
143 >
144 >    skipsForRowAtom.clear();
145 >    skipsForRowAtom.resize(nAtomsInRow_);
146 >    for (int i = 0; i < nAtomsInRow_; i++) {
147 >      int iglob = AtomRowToGlobal[i];
148 >      for (int j = 0; j < nAtomsInCol_; j++) {
149 >        int jglob = AtomColToGlobal[j];        
150 >        if (excludes.hasPair(iglob, jglob))
151 >          skipsForRowAtom[i].push_back(j);      
152 >      }      
153 >    }
154 >
155 >    toposForRowAtom.clear();
156 >    toposForRowAtom.resize(nAtomsInRow_);
157 >    for (int i = 0; i < nAtomsInRow_; i++) {
158 >      int iglob = AtomRowToGlobal[i];
159 >      int nTopos = 0;
160 >      for (int j = 0; j < nAtomsInCol_; j++) {
161 >        int jglob = AtomColToGlobal[j];        
162 >        if (oneTwo.hasPair(iglob, jglob)) {
163 >          toposForRowAtom[i].push_back(j);
164 >          topoDistRow[i][nTopos] = 1;
165 >          nTopos++;
166 >        }
167 >        if (oneThree.hasPair(iglob, jglob)) {
168 >          toposForRowAtom[i].push_back(j);
169 >          topoDistRow[i][nTopos] = 2;
170 >          nTopos++;
171 >        }
172 >        if (oneFour.hasPair(iglob, jglob)) {
173 >          toposForRowAtom[i].push_back(j);
174 >          topoDistRow[i][nTopos] = 3;
175 >          nTopos++;
176 >        }
177 >      }      
178 >    }
179 >
180   #endif
181 +    groupList_.clear();
182 +    groupList_.resize(nGroups_);
183 +    for (int i = 0; i < nGroups_; i++) {
184 +      int gid = cgLocalToGlobal[i];
185 +      for (int j = 0; j < nLocal_; j++) {
186 +        int aid = AtomLocalToGlobal[j];
187 +        if (globalGroupMembership[aid] == gid) {
188 +          groupList_[i].push_back(j);
189 +
190 +        }
191 +      }      
192 +    }
193 +
194 +    skipsForLocalAtom.clear();
195 +    skipsForLocalAtom.resize(nLocal_);
196 +
197 +    for (int i = 0; i < nLocal_; i++) {
198 +      int iglob = AtomLocalToGlobal[i];
199 +      for (int j = 0; j < nLocal_; j++) {
200 +        int jglob = AtomLocalToGlobal[j];        
201 +        if (excludes.hasPair(iglob, jglob))
202 +          skipsForLocalAtom[i].push_back(j);      
203 +      }      
204 +    }
205 +    toposForLocalAtom.clear();
206 +    toposForLocalAtom.resize(nLocal_);
207 +    for (int i = 0; i < nLocal_; i++) {
208 +      int iglob = AtomLocalToGlobal[i];
209 +      int nTopos = 0;
210 +      for (int j = 0; j < nLocal_; j++) {
211 +        int jglob = AtomLocalToGlobal[j];        
212 +        if (oneTwo.hasPair(iglob, jglob)) {
213 +          toposForLocalAtom[i].push_back(j);
214 +          topoDistLocal[i][nTopos] = 1;
215 +          nTopos++;
216 +        }
217 +        if (oneThree.hasPair(iglob, jglob)) {
218 +          toposForLocalAtom[i].push_back(j);
219 +          topoDistLocal[i][nTopos] = 2;
220 +          nTopos++;
221 +        }
222 +        if (oneFour.hasPair(iglob, jglob)) {
223 +          toposForLocalAtom[i].push_back(j);
224 +          topoDistLocal[i][nTopos] = 3;
225 +          nTopos++;
226 +        }
227 +      }      
228 +    }    
229 +
230    }
231 <    
231 >  
232 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
233  
234 +    RealType tol = 1e-6;
235 +    RealType rc;
236 +    int atid;
237 +    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
238 +    vector<RealType> atypeCutoff;
239 +    atypeCutoff.resize( atypes.size() );
240  
241 <  void ForceDecomposition::distributeData()  {
241 >    for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
242 >      rc = interactionMan_->getSuggestedCutoffRadius(*at);
243 >      atid = (*at)->getIdent();
244 >      atypeCutoff[atid] = rc;
245 >    }
246 >
247 >    vector<RealType> gTypeCutoffs;
248 >
249 >    // first we do a single loop over the cutoff groups to find the
250 >    // largest cutoff for any atypes present in this group.
251   #ifdef IS_MPI
252 <    Snapshot* snap = sman_->getCurrentSnapshot();
252 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
253 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
254 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
255 >      for (vector<int>::iterator ia = atomListRow.begin();
256 >           ia != atomListRow.end(); ++ia) {            
257 >        int atom1 = (*ia);
258 >        atid = identsRow[atom1];
259 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
260 >          groupCutoffRow[cg1] = atypeCutoff[atid];
261 >        }
262 >      }
263 >
264 >      bool gTypeFound = false;
265 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
266 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
267 >          groupRowToGtype[cg1] = gt;
268 >          gTypeFound = true;
269 >        }
270 >      }
271 >      if (!gTypeFound) {
272 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
273 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
274 >      }
275 >      
276 >    }
277 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
278 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
279 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
280 >      for (vector<int>::iterator jb = atomListCol.begin();
281 >           jb != atomListCol.end(); ++jb) {            
282 >        int atom2 = (*jb);
283 >        atid = identsCol[atom2];
284 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
285 >          groupCutoffCol[cg2] = atypeCutoff[atid];
286 >        }
287 >      }
288 >      bool gTypeFound = false;
289 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
290 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
291 >          groupColToGtype[cg2] = gt;
292 >          gTypeFound = true;
293 >        }
294 >      }
295 >      if (!gTypeFound) {
296 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
297 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
298 >      }
299 >    }
300 > #else
301 >    vector<RealType> groupCutoff(nGroups_, 0.0);
302 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
303 >      groupCutoff[cg1] = 0.0;
304 >      vector<int> atomList = getAtomsInGroupRow(cg1);
305 >      for (vector<int>::iterator ia = atomList.begin();
306 >           ia != atomList.end(); ++ia) {            
307 >        int atom1 = (*ia);
308 >        atid = identsLocal[atom1];
309 >        if (atypeCutoff[atid] > groupCutoff[cg1]) {
310 >          groupCutoff[cg1] = atypeCutoff[atid];
311 >        }
312 >      }
313 >
314 >      bool gTypeFound = false;
315 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
316 >        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
317 >          groupToGtype[cg1] = gt;
318 >          gTypeFound = true;
319 >        }
320 >      }
321 >      if (!gTypeFound) {
322 >        gTypeCutoffs.push_back( groupCutoff[cg1] );
323 >        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
324 >      }      
325 >    }
326 > #endif
327  
328 +    // Now we find the maximum group cutoff value present in the simulation
329 +
330 +    vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
331 +    RealType groupMax = *groupMaxLoc;
332 +
333 + #ifdef IS_MPI
334 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
335 + #endif
336 +    
337 +    RealType tradRcut = groupMax;
338 +
339 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
340 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {
341 +        
342 +        RealType thisRcut;
343 +        switch(cutoffPolicy_) {
344 +        case TRADITIONAL:
345 +          thisRcut = tradRcut;
346 +        case MIX:
347 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
348 +        case MAX:
349 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
350 +        default:
351 +          sprintf(painCave.errMsg,
352 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
353 +                  "hit an unknown cutoff policy!\n");
354 +          painCave.severity = OPENMD_ERROR;
355 +          painCave.isFatal = 1;
356 +          simError();              
357 +        }
358 +
359 +        pair<int,int> key = make_pair(i,j);
360 +        gTypeCutoffMap[key].first = thisRcut;
361 +
362 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
363 +
364 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
365 +        
366 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
367 +
368 +        // sanity check
369 +        
370 +        if (userChoseCutoff_) {
371 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
372 +            sprintf(painCave.errMsg,
373 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
374 +                    "user-specified rCut does not match computed group Cutoff\n");
375 +            painCave.severity = OPENMD_ERROR;
376 +            painCave.isFatal = 1;
377 +            simError();            
378 +          }
379 +        }
380 +      }
381 +    }
382 +  }
383 +
384 +
385 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
386 +    int i, j;
387 +
388 + #ifdef IS_MPI
389 +    i = groupRowToGtype[cg1];
390 +    j = groupColToGtype[cg2];
391 + #else
392 +    i = groupToGtype[cg1];
393 +    j = groupToGtype[cg2];
394 + #endif
395 +    
396 +    return gTypeCutoffMap[make_pair(i,j)];
397 +  }
398 +
399 +
400 +  void ForceMatrixDecomposition::zeroWorkArrays() {
401 +
402 +    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403 +      longRangePot_[j] = 0.0;
404 +    }
405 +
406 + #ifdef IS_MPI
407 +    if (storageLayout_ & DataStorage::dslForce) {
408 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
409 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
410 +    }
411 +
412 +    if (storageLayout_ & DataStorage::dslTorque) {
413 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
414 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
415 +    }
416 +    
417 +    fill(pot_row.begin(), pot_row.end(),
418 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
419 +
420 +    fill(pot_col.begin(), pot_col.end(),
421 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422 +    
423 +    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
424 +
425 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
426 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
427 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
428 +    }
429 +
430 +    if (storageLayout_ & DataStorage::dslDensity) {      
431 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
432 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
433 +    }
434 +
435 +    if (storageLayout_ & DataStorage::dslFunctional) {  
436 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
437 +      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
438 +    }
439 +
440 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
441 +      fill(atomRowData.functionalDerivative.begin(),
442 +           atomRowData.functionalDerivative.end(), 0.0);
443 +      fill(atomColData.functionalDerivative.begin(),
444 +           atomColData.functionalDerivative.end(), 0.0);
445 +    }
446 +
447 + #else
448 +    
449 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
450 +      fill(snap_->atomData.particlePot.begin(),
451 +           snap_->atomData.particlePot.end(), 0.0);
452 +    }
453 +    
454 +    if (storageLayout_ & DataStorage::dslDensity) {      
455 +      fill(snap_->atomData.density.begin(),
456 +           snap_->atomData.density.end(), 0.0);
457 +    }
458 +    if (storageLayout_ & DataStorage::dslFunctional) {
459 +      fill(snap_->atomData.functional.begin(),
460 +           snap_->atomData.functional.end(), 0.0);
461 +    }
462 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
463 +      fill(snap_->atomData.functionalDerivative.begin(),
464 +           snap_->atomData.functionalDerivative.end(), 0.0);
465 +    }
466 + #endif
467 +    
468 +  }
469 +
470 +
471 +  void ForceMatrixDecomposition::distributeData()  {
472 +    snap_ = sman_->getCurrentSnapshot();
473 +    storageLayout_ = sman_->getStorageLayout();
474 + #ifdef IS_MPI
475 +    
476      // gather up the atomic positions
477 <    AtomCommVectorI->gather(snap->atomData.position,
478 <                            snap->atomIData.position);
479 <    AtomCommVectorJ->gather(snap->atomData.position,
480 <                           snap->atomJData.position);
477 >    AtomCommVectorRow->gather(snap_->atomData.position,
478 >                              atomRowData.position);
479 >    AtomCommVectorColumn->gather(snap_->atomData.position,
480 >                                 atomColData.position);
481      
482      // gather up the cutoff group positions
483 <    cgCommVectorI->gather(snap->cgData.position,
484 <                         snap->cgIData.position);
485 <    cgCommVectorJ->gather(snap->cgData.position,
486 <                         snap->cgJData.position);
483 >    cgCommVectorRow->gather(snap_->cgData.position,
484 >                            cgRowData.position);
485 >    cgCommVectorColumn->gather(snap_->cgData.position,
486 >                               cgColData.position);
487      
488      // if needed, gather the atomic rotation matrices
489 <    if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
490 <      AtomCommMatrixI->gather(snap->atomData.aMat,
491 <                             snap->atomIData.aMat);
492 <      AtomCommMatrixJ->gather(snap->atomData.aMat,
493 <                             snap->atomJData.aMat);
489 >    if (storageLayout_ & DataStorage::dslAmat) {
490 >      AtomCommMatrixRow->gather(snap_->atomData.aMat,
491 >                                atomRowData.aMat);
492 >      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
493 >                                   atomColData.aMat);
494      }
495      
496      // if needed, gather the atomic eletrostatic frames
497 <    if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
498 <      AtomCommMatrixI->gather(snap->atomData.electroFrame,
499 <                             snap->atomIData.electroFrame);
500 <      AtomCommMatrixJ->gather(snap->atomData.electroFrame,
501 <                             snap->atomJData.electroFrame);
497 >    if (storageLayout_ & DataStorage::dslElectroFrame) {
498 >      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
499 >                                atomRowData.electroFrame);
500 >      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
501 >                                   atomColData.electroFrame);
502      }
503   #endif      
504    }
505    
506 <  void ForceDecomposition::collectIntermediateData() {
506 >  /* collects information obtained during the pre-pair loop onto local
507 >   * data structures.
508 >   */
509 >  void ForceMatrixDecomposition::collectIntermediateData() {
510 >    snap_ = sman_->getCurrentSnapshot();
511 >    storageLayout_ = sman_->getStorageLayout();
512   #ifdef IS_MPI
105 –    Snapshot* snap = sman_->getCurrentSnapshot();
106 –    // gather up the atomic positions
513      
514 <    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
515 <      AtomCommRealI->scatter(snap->atomIData.density,
516 <                            snap->atomData.density);
517 <      std::vector<RealType> rho_tmp;
518 <      int n = snap->getNumberOfAtoms();
519 <      rho_tmp.reserve( n );
520 <      AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
514 >    if (storageLayout_ & DataStorage::dslDensity) {
515 >      
516 >      AtomCommRealRow->scatter(atomRowData.density,
517 >                               snap_->atomData.density);
518 >      
519 >      int n = snap_->atomData.density.size();
520 >      vector<RealType> rho_tmp(n, 0.0);
521 >      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
522        for (int i = 0; i < n; i++)
523 <        snap->atomData.density[i] += rho_tmp[i];
523 >        snap_->atomData.density[i] += rho_tmp[i];
524      }
525   #endif
526    }
527 <  
528 <  void ForceDecomposition::distributeIntermediateData() {
527 >
528 >  /*
529 >   * redistributes information obtained during the pre-pair loop out to
530 >   * row and column-indexed data structures
531 >   */
532 >  void ForceMatrixDecomposition::distributeIntermediateData() {
533 >    snap_ = sman_->getCurrentSnapshot();
534 >    storageLayout_ = sman_->getStorageLayout();
535   #ifdef IS_MPI
536 <    Snapshot* snap = sman_->getCurrentSnapshot();
537 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
538 <      AtomCommRealI->gather(snap->atomData.functional,
539 <                           snap->atomIData.functional);
540 <      AtomCommRealJ->gather(snap->atomData.functional,
128 <                           snap->atomJData.functional);
536 >    if (storageLayout_ & DataStorage::dslFunctional) {
537 >      AtomCommRealRow->gather(snap_->atomData.functional,
538 >                              atomRowData.functional);
539 >      AtomCommRealColumn->gather(snap_->atomData.functional,
540 >                                 atomColData.functional);
541      }
542      
543 <    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
544 <      AtomCommRealI->gather(snap->atomData.functionalDerivative,
545 <                           snap->atomIData.functionalDerivative);
546 <      AtomCommRealJ->gather(snap->atomData.functionalDerivative,
547 <                           snap->atomJData.functionalDerivative);
543 >    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
544 >      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
545 >                              atomRowData.functionalDerivative);
546 >      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
547 >                                 atomColData.functionalDerivative);
548      }
549   #endif
550    }
551    
552    
553 <  void ForceDecomposition::collectData() {
553 >  void ForceMatrixDecomposition::collectData() {
554 >    snap_ = sman_->getCurrentSnapshot();
555 >    storageLayout_ = sman_->getStorageLayout();
556 > #ifdef IS_MPI    
557 >    int n = snap_->atomData.force.size();
558 >    vector<Vector3d> frc_tmp(n, V3Zero);
559 >    
560 >    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
561 >    for (int i = 0; i < n; i++) {
562 >      snap_->atomData.force[i] += frc_tmp[i];
563 >      frc_tmp[i] = 0.0;
564 >    }
565 >    
566 >    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
567 >    for (int i = 0; i < n; i++)
568 >      snap_->atomData.force[i] += frc_tmp[i];
569 >    
570 >    
571 >    if (storageLayout_ & DataStorage::dslTorque) {
572 >
573 >      int nt = snap_->atomData.force.size();
574 >      vector<Vector3d> trq_tmp(nt, V3Zero);
575 >
576 >      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
577 >      for (int i = 0; i < n; i++) {
578 >        snap_->atomData.torque[i] += trq_tmp[i];
579 >        trq_tmp[i] = 0.0;
580 >      }
581 >      
582 >      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
583 >      for (int i = 0; i < n; i++)
584 >        snap_->atomData.torque[i] += trq_tmp[i];
585 >    }
586 >    
587 >    nLocal_ = snap_->getNumberOfAtoms();
588 >
589 >    vector<potVec> pot_temp(nLocal_,
590 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
591 >
592 >    // scatter/gather pot_row into the members of my column
593 >          
594 >    AtomCommPotRow->scatter(pot_row, pot_temp);
595 >
596 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
597 >      pot_local += pot_temp[ii];
598 >    
599 >    fill(pot_temp.begin(), pot_temp.end(),
600 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
601 >      
602 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
603 >    
604 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
605 >      pot_local += pot_temp[ii];
606 >    
607 > #endif
608 >  }
609 >
610 >  int ForceMatrixDecomposition::getNAtomsInRow() {  
611   #ifdef IS_MPI
612 +    return nAtomsInRow_;
613 + #else
614 +    return nLocal_;
615 + #endif
616 +  }
617 +
618 +  /**
619 +   * returns the list of atoms belonging to this group.  
620 +   */
621 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
622 + #ifdef IS_MPI
623 +    return groupListRow_[cg1];
624 + #else
625 +    return groupList_[cg1];
626 + #endif
627 +  }
628 +
629 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
630 + #ifdef IS_MPI
631 +    return groupListCol_[cg2];
632 + #else
633 +    return groupList_[cg2];
634 + #endif
635 +  }
636 +  
637 +  Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
638 +    Vector3d d;
639 +    
640 + #ifdef IS_MPI
641 +    d = cgColData.position[cg2] - cgRowData.position[cg1];
642 + #else
643 +    d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
644 + #endif
645 +    
646 +    snap_->wrapVector(d);
647 +    return d;    
648 +  }
649 +
650 +
651 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
652 +
653 +    Vector3d d;
654 +    
655 + #ifdef IS_MPI
656 +    d = cgRowData.position[cg1] - atomRowData.position[atom1];
657 + #else
658 +    d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
659 + #endif
660 +
661 +    snap_->wrapVector(d);
662 +    return d;    
663 +  }
664 +  
665 +  Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){
666 +    Vector3d d;
667 +    
668 + #ifdef IS_MPI
669 +    d = cgColData.position[cg2] - atomColData.position[atom2];
670 + #else
671 +    d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
672 + #endif
673 +    
674 +    snap_->wrapVector(d);
675 +    return d;    
676 +  }
677 +
678 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
679 + #ifdef IS_MPI
680 +    return massFactorsRow[atom1];
681 + #else
682 +    return massFactorsLocal[atom1];
683 + #endif
684 +  }
685 +
686 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
687 + #ifdef IS_MPI
688 +    return massFactorsCol[atom2];
689 + #else
690 +    return massFactorsLocal[atom2];
691 + #endif
692 +
693 +  }
694 +    
695 +  Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
696 +    Vector3d d;
697 +    
698 + #ifdef IS_MPI
699 +    d = atomColData.position[atom2] - atomRowData.position[atom1];
700 + #else
701 +    d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
702 + #endif
703 +
704 +    snap_->wrapVector(d);
705 +    return d;    
706 +  }
707 +
708 +  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
709 + #ifdef IS_MPI
710 +    return skipsForRowAtom[atom1];
711 + #else
712 +    return skipsForLocalAtom[atom1];
713 + #endif
714 +  }
715 +
716 +  /**
717 +   * There are a number of reasons to skip a pair or a
718 +   * particle. Mostly we do this to exclude atoms who are involved in
719 +   * short range interactions (bonds, bends, torsions), but we also
720 +   * need to exclude some overcounted interactions that result from
721 +   * the parallel decomposition.
722 +   */
723 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
724 +    int unique_id_1, unique_id_2;
725 +
726 + #ifdef IS_MPI
727 +    // in MPI, we have to look up the unique IDs for each atom
728 +    unique_id_1 = AtomRowToGlobal[atom1];
729 +    unique_id_2 = AtomColToGlobal[atom2];
730 +
731 +    // this situation should only arise in MPI simulations
732 +    if (unique_id_1 == unique_id_2) return true;
733 +    
734 +    // this prevents us from doing the pair on multiple processors
735 +    if (unique_id_1 < unique_id_2) {
736 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
737 +    } else {
738 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
739 +    }
740 + #else
741 +    // in the normal loop, the atom numbers are unique
742 +    unique_id_1 = atom1;
743 +    unique_id_2 = atom2;
744 + #endif
745 +    
746 + #ifdef IS_MPI
747 +    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748 +         i != skipsForRowAtom[atom1].end(); ++i) {
749 +      if ( (*i) == unique_id_2 ) return true;
750 +    }    
751 + #else
752 +    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
753 +         i != skipsForLocalAtom[atom1].end(); ++i) {
754 +      if ( (*i) == unique_id_2 ) return true;
755 +    }    
756 + #endif
757 +  }
758 +
759 +  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
760 +    
761 + #ifdef IS_MPI
762 +    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
763 +      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
764 +    }
765 + #else
766 +    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
767 +      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
768 +    }
769 + #endif
770 +
771 +    // zero is default for unconnected (i.e. normal) pair interactions
772 +    return 0;
773 +  }
774 +
775 +  void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
776 + #ifdef IS_MPI
777 +    atomRowData.force[atom1] += fg;
778 + #else
779 +    snap_->atomData.force[atom1] += fg;
780 + #endif
781 +  }
782 +
783 +  void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){
784 + #ifdef IS_MPI
785 +    atomColData.force[atom2] += fg;
786 + #else
787 +    snap_->atomData.force[atom2] += fg;
788 + #endif
789 +  }
790 +
791 +    // filling interaction blocks with pointers
792 +  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
793 +    InteractionData idat;
794 +
795 + #ifdef IS_MPI
796 +    
797 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
798 +                             ff_->getAtomType(identsCol[atom2]) );
799 +
800 +    
801 +    if (storageLayout_ & DataStorage::dslAmat) {
802 +      idat.A1 = &(atomRowData.aMat[atom1]);
803 +      idat.A2 = &(atomColData.aMat[atom2]);
804 +    }
805 +    
806 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
807 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
808 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
809 +    }
810 +
811 +    if (storageLayout_ & DataStorage::dslTorque) {
812 +      idat.t1 = &(atomRowData.torque[atom1]);
813 +      idat.t2 = &(atomColData.torque[atom2]);
814 +    }
815 +
816 +    if (storageLayout_ & DataStorage::dslDensity) {
817 +      idat.rho1 = &(atomRowData.density[atom1]);
818 +      idat.rho2 = &(atomColData.density[atom2]);
819 +    }
820 +
821 +    if (storageLayout_ & DataStorage::dslFunctional) {
822 +      idat.frho1 = &(atomRowData.functional[atom1]);
823 +      idat.frho2 = &(atomColData.functional[atom2]);
824 +    }
825 +
826 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
827 +      idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
828 +      idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
829 +    }
830 +
831 +    if (storageLayout_ & DataStorage::dslParticlePot) {
832 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
833 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
834 +    }
835 +
836 + #else
837 +
838 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
839 +                             ff_->getAtomType(identsLocal[atom2]) );
840 +
841 +    if (storageLayout_ & DataStorage::dslAmat) {
842 +      idat.A1 = &(snap_->atomData.aMat[atom1]);
843 +      idat.A2 = &(snap_->atomData.aMat[atom2]);
844 +    }
845 +
846 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
847 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
848 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
849 +    }
850 +
851 +    if (storageLayout_ & DataStorage::dslTorque) {
852 +      idat.t1 = &(snap_->atomData.torque[atom1]);
853 +      idat.t2 = &(snap_->atomData.torque[atom2]);
854 +    }
855 +
856 +    if (storageLayout_ & DataStorage::dslDensity) {
857 +      idat.rho1 = &(snap_->atomData.density[atom1]);
858 +      idat.rho2 = &(snap_->atomData.density[atom2]);
859 +    }
860 +
861 +    if (storageLayout_ & DataStorage::dslFunctional) {
862 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
863 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
864 +    }
865 +
866 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
867 +      idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
868 +      idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
869 +    }
870 +
871 +    if (storageLayout_ & DataStorage::dslParticlePot) {
872 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
873 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
874 +    }
875 +
876   #endif
877 +    return idat;
878    }
879 +
880    
881 +  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
882 + #ifdef IS_MPI
883 +    pot_row[atom1] += 0.5 *  *(idat.pot);
884 +    pot_col[atom2] += 0.5 *  *(idat.pot);
885 +
886 +    atomRowData.force[atom1] += *(idat.f1);
887 +    atomColData.force[atom2] -= *(idat.f1);
888 + #else
889 +    longRangePot_ += *(idat.pot);
890 +    
891 +    snap_->atomData.force[atom1] += *(idat.f1);
892 +    snap_->atomData.force[atom2] -= *(idat.f1);
893 + #endif
894 +
895 +  }
896 +
897 +
898 +  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
899 +
900 +    InteractionData idat;
901 + #ifdef IS_MPI
902 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
903 +                             ff_->getAtomType(identsCol[atom2]) );
904 +
905 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
906 +      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
907 +      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
908 +    }
909 +    if (storageLayout_ & DataStorage::dslTorque) {
910 +      idat.t1 = &(atomRowData.torque[atom1]);
911 +      idat.t2 = &(atomColData.torque[atom2]);
912 +    }
913 + #else
914 +    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
915 +                             ff_->getAtomType(identsLocal[atom2]) );
916 +
917 +    if (storageLayout_ & DataStorage::dslElectroFrame) {
918 +      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
919 +      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
920 +    }
921 +    if (storageLayout_ & DataStorage::dslTorque) {
922 +      idat.t1 = &(snap_->atomData.torque[atom1]);
923 +      idat.t2 = &(snap_->atomData.torque[atom2]);
924 +    }
925 + #endif    
926 +  }
927 +
928 +  /*
929 +   * buildNeighborList
930 +   *
931 +   * first element of pair is row-indexed CutoffGroup
932 +   * second element of pair is column-indexed CutoffGroup
933 +   */
934 +  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
935 +      
936 +    vector<pair<int, int> > neighborList;
937 +    groupCutoffs cuts;
938 + #ifdef IS_MPI
939 +    cellListRow_.clear();
940 +    cellListCol_.clear();
941 + #else
942 +    cellList_.clear();
943 + #endif
944 +
945 +    RealType rList_ = (largestRcut_ + skinThickness_);
946 +    RealType rl2 = rList_ * rList_;
947 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
948 +    Mat3x3d Hmat = snap_->getHmat();
949 +    Vector3d Hx = Hmat.getColumn(0);
950 +    Vector3d Hy = Hmat.getColumn(1);
951 +    Vector3d Hz = Hmat.getColumn(2);
952 +
953 +    nCells_.x() = (int) ( Hx.length() )/ rList_;
954 +    nCells_.y() = (int) ( Hy.length() )/ rList_;
955 +    nCells_.z() = (int) ( Hz.length() )/ rList_;
956 +
957 +    Mat3x3d invHmat = snap_->getInvHmat();
958 +    Vector3d rs, scaled, dr;
959 +    Vector3i whichCell;
960 +    int cellIndex;
961 +
962 + #ifdef IS_MPI
963 +    for (int i = 0; i < nGroupsInRow_; i++) {
964 +      rs = cgRowData.position[i];
965 +      // scaled positions relative to the box vectors
966 +      scaled = invHmat * rs;
967 +      // wrap the vector back into the unit box by subtracting integer box
968 +      // numbers
969 +      for (int j = 0; j < 3; j++)
970 +        scaled[j] -= roundMe(scaled[j]);
971 +    
972 +      // find xyz-indices of cell that cutoffGroup is in.
973 +      whichCell.x() = nCells_.x() * scaled.x();
974 +      whichCell.y() = nCells_.y() * scaled.y();
975 +      whichCell.z() = nCells_.z() * scaled.z();
976 +
977 +      // find single index of this cell:
978 +      cellIndex = Vlinear(whichCell, nCells_);
979 +      // add this cutoff group to the list of groups in this cell;
980 +      cellListRow_[cellIndex].push_back(i);
981 +    }
982 +
983 +    for (int i = 0; i < nGroupsInCol_; i++) {
984 +      rs = cgColData.position[i];
985 +      // scaled positions relative to the box vectors
986 +      scaled = invHmat * rs;
987 +      // wrap the vector back into the unit box by subtracting integer box
988 +      // numbers
989 +      for (int j = 0; j < 3; j++)
990 +        scaled[j] -= roundMe(scaled[j]);
991 +
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 +      // add this cutoff group to the list of groups in this cell;
1000 +      cellListCol_[cellIndex].push_back(i);
1001 +    }
1002 + #else
1003 +    for (int i = 0; i < nGroups_; i++) {
1004 +      rs = snap_->cgData.position[i];
1005 +      // scaled positions relative to the box vectors
1006 +      scaled = invHmat * rs;
1007 +      // wrap the vector back into the unit box by subtracting integer box
1008 +      // numbers
1009 +      for (int j = 0; j < 3; j++)
1010 +        scaled[j] -= roundMe(scaled[j]);
1011 +
1012 +      // find xyz-indices of cell that cutoffGroup is in.
1013 +      whichCell.x() = nCells_.x() * scaled.x();
1014 +      whichCell.y() = nCells_.y() * scaled.y();
1015 +      whichCell.z() = nCells_.z() * scaled.z();
1016 +
1017 +      // find single index of this cell:
1018 +      cellIndex = Vlinear(whichCell, nCells_);
1019 +      // add this cutoff group to the list of groups in this cell;
1020 +      cellList_[cellIndex].push_back(i);
1021 +    }
1022 + #endif
1023 +
1024 +    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1025 +      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1026 +        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1027 +          Vector3i m1v(m1x, m1y, m1z);
1028 +          int m1 = Vlinear(m1v, nCells_);
1029 +
1030 +          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1031 +               os != cellOffsets_.end(); ++os) {
1032 +            
1033 +            Vector3i m2v = m1v + (*os);
1034 +            
1035 +            if (m2v.x() >= nCells_.x()) {
1036 +              m2v.x() = 0;          
1037 +            } else if (m2v.x() < 0) {
1038 +              m2v.x() = nCells_.x() - 1;
1039 +            }
1040 +            
1041 +            if (m2v.y() >= nCells_.y()) {
1042 +              m2v.y() = 0;          
1043 +            } else if (m2v.y() < 0) {
1044 +              m2v.y() = nCells_.y() - 1;
1045 +            }
1046 +            
1047 +            if (m2v.z() >= nCells_.z()) {
1048 +              m2v.z() = 0;          
1049 +            } else if (m2v.z() < 0) {
1050 +              m2v.z() = nCells_.z() - 1;
1051 +            }
1052 +            
1053 +            int m2 = Vlinear (m2v, nCells_);
1054 +
1055 + #ifdef IS_MPI
1056 +            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1057 +                 j1 != cellListRow_[m1].end(); ++j1) {
1058 +              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1059 +                   j2 != cellListCol_[m2].end(); ++j2) {
1060 +                              
1061 +                // Always do this if we're in different cells or if
1062 +                // we're in the same cell and the global index of the
1063 +                // j2 cutoff group is less than the j1 cutoff group
1064 +
1065 +                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1066 +                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1067 +                  snap_->wrapVector(dr);
1068 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1069 +                  if (dr.lengthSquare() < cuts.third) {
1070 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1071 +                  }
1072 +                }
1073 +              }
1074 +            }
1075 + #else
1076 +            for (vector<int>::iterator j1 = cellList_[m1].begin();
1077 +                 j1 != cellList_[m1].end(); ++j1) {
1078 +              for (vector<int>::iterator j2 = cellList_[m2].begin();
1079 +                   j2 != cellList_[m2].end(); ++j2) {
1080 +                              
1081 +                // Always do this if we're in different cells or if
1082 +                // we're in the same cell and the global index of the
1083 +                // j2 cutoff group is less than the j1 cutoff group
1084 +
1085 +                if (m2 != m1 || (*j2) < (*j1)) {
1086 +                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1087 +                  snap_->wrapVector(dr);
1088 +                  cuts = getGroupCutoffs( (*j1), (*j2) );
1089 +                  if (dr.lengthSquare() < cuts.third) {
1090 +                    neighborList.push_back(make_pair((*j1), (*j2)));
1091 +                  }
1092 +                }
1093 +              }
1094 +            }
1095 + #endif
1096 +          }
1097 +        }
1098 +      }
1099 +    }
1100 +
1101 +    // save the local cutoff group positions for the check that is
1102 +    // done on each loop:
1103 +    saved_CG_positions_.clear();
1104 +    for (int i = 0; i < nGroups_; i++)
1105 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1106 +
1107 +    return neighborList;
1108 +  }
1109   } //end namespace OpenMD

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