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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 1589 by gezelter, Sun Jul 10 16:05:34 2011 UTC

# Line 42 | Line 42
42   #include "math/SquareMatrix3.hpp"
43   #include "nonbonded/NonBondedInteraction.hpp"
44   #include "brains/SnapshotManager.hpp"
45 + #include "brains/PairList.hpp"
46  
47   using namespace std;
48   namespace OpenMD {
# Line 54 | Line 55 | namespace OpenMD {
55    void ForceMatrixDecomposition::distributeInitialData() {
56      snap_ = sman_->getCurrentSnapshot();
57      storageLayout_ = sman_->getStorageLayout();
58 +    ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
60 <    nGroups_ = snap_->getNumberOfCutoffGroups();
60 >    
61 >    nGroups_ = info_->getNLocalCutoffGroups();
62 >    // gather the information for atomtype IDs (atids):
63 >    idents = info_->getIdentArray();
64 >    AtomLocalToGlobal = info_->getGlobalAtomIndices();
65 >    cgLocalToGlobal = info_->getGlobalGroupIndices();
66 >    vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67  
68 +    massFactors = info_->getMassFactors();
69 +
70 +    PairList* excludes = info_->getExcludedInteractions();
71 +    PairList* oneTwo = info_->getOneTwoInteractions();
72 +    PairList* oneThree = info_->getOneThreeInteractions();
73 +    PairList* oneFour = info_->getOneFourInteractions();
74 +
75   #ifdef IS_MPI
76  
77      AtomCommIntRow = new Communicator<Row,int>(nLocal_);
78      AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
79      AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
80      AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
81 +    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
82  
83      AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
84      AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
85      AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
86      AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
87 +    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
88  
89      cgCommIntRow = new Communicator<Row,int>(nGroups_);
90      cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
# Line 88 | Line 105 | namespace OpenMD {
105      cgRowData.setStorageLayout(DataStorage::dslPosition);
106      cgColData.resize(nGroupsInCol_);
107      cgColData.setStorageLayout(DataStorage::dslPosition);
108 +        
109 +    identsRow.resize(nAtomsInRow_);
110 +    identsCol.resize(nAtomsInCol_);
111      
112 <    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
113 <                                      vector<RealType> (nAtomsInRow_, 0.0));
94 <    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
95 <                                      vector<RealType> (nAtomsInCol_, 0.0));
96 <
97 <
98 <    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
115 <    // gather the information for atomtype IDs (atids):
116 <    vector<int> identsLocal = info_->getIdentArray();
117 <    identsRow.reserve(nAtomsInRow_);
118 <    identsCol.reserve(nAtomsInCol_);
119 <    
120 <    AtomCommIntRow->gather(identsLocal, identsRow);
121 <    AtomCommIntColumn->gather(identsLocal, identsCol);
122 <    
123 <    AtomLocalToGlobal = info_->getGlobalAtomIndices();
115 >    // allocate memory for the parallel objects
116 >    AtomRowToGlobal.resize(nAtomsInRow_);
117 >    AtomColToGlobal.resize(nAtomsInCol_);
118 >    cgRowToGlobal.resize(nGroupsInRow_);
119 >    cgColToGlobal.resize(nGroupsInCol_);
120 >    massFactorsRow.resize(nAtomsInRow_);
121 >    massFactorsCol.resize(nAtomsInCol_);
122 >    pot_row.resize(nAtomsInRow_);
123 >    pot_col.resize(nAtomsInCol_);
124 >
125      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
126      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
127      
112 –    cgLocalToGlobal = info_->getGlobalGroupIndices();
128      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
129      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
130  
131 <    // still need:
132 <    // topoDist
133 <    // exclude
131 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
132 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
133 >
134 >    groupListRow_.clear();
135 >    groupListRow_.resize(nGroupsInRow_);
136 >    for (int i = 0; i < nGroupsInRow_; i++) {
137 >      int gid = cgRowToGlobal[i];
138 >      for (int j = 0; j < nAtomsInRow_; j++) {
139 >        int aid = AtomRowToGlobal[j];
140 >        if (globalGroupMembership[aid] == gid)
141 >          groupListRow_[i].push_back(j);
142 >      }      
143 >    }
144 >
145 >    groupListCol_.clear();
146 >    groupListCol_.resize(nGroupsInCol_);
147 >    for (int i = 0; i < nGroupsInCol_; i++) {
148 >      int gid = cgColToGlobal[i];
149 >      for (int j = 0; j < nAtomsInCol_; j++) {
150 >        int aid = AtomColToGlobal[j];
151 >        if (globalGroupMembership[aid] == gid)
152 >          groupListCol_[i].push_back(j);
153 >      }      
154 >    }
155 >
156 >    excludesForAtom.clear();
157 >    excludesForAtom.resize(nAtomsInRow_);
158 >    toposForAtom.clear();
159 >    toposForAtom.resize(nAtomsInRow_);
160 >    topoDist.clear();
161 >    topoDist.resize(nAtomsInRow_);
162 >    for (int i = 0; i < nAtomsInRow_; i++) {
163 >      int iglob = AtomRowToGlobal[i];
164 >
165 >      for (int j = 0; j < nAtomsInCol_; j++) {
166 >        int jglob = AtomColToGlobal[j];
167 >
168 >        if (excludes->hasPair(iglob, jglob))
169 >          excludesForAtom[i].push_back(j);      
170 >        
171 >        if (oneTwo->hasPair(iglob, jglob)) {
172 >          toposForAtom[i].push_back(j);
173 >          topoDist[i].push_back(1);
174 >        } else {
175 >          if (oneThree->hasPair(iglob, jglob)) {
176 >            toposForAtom[i].push_back(j);
177 >            topoDist[i].push_back(2);
178 >          } else {
179 >            if (oneFour->hasPair(iglob, jglob)) {
180 >              toposForAtom[i].push_back(j);
181 >              topoDist[i].push_back(3);
182 >            }
183 >          }
184 >        }
185 >      }      
186 >    }
187 >
188 > #endif
189 >
190 >    groupList_.clear();
191 >    groupList_.resize(nGroups_);
192 >    for (int i = 0; i < nGroups_; i++) {
193 >      int gid = cgLocalToGlobal[i];
194 >      for (int j = 0; j < nLocal_; j++) {
195 >        int aid = AtomLocalToGlobal[j];
196 >        if (globalGroupMembership[aid] == gid) {
197 >          groupList_[i].push_back(j);
198 >        }
199 >      }      
200 >    }
201 >
202 >    excludesForAtom.clear();
203 >    excludesForAtom.resize(nLocal_);
204 >    toposForAtom.clear();
205 >    toposForAtom.resize(nLocal_);
206 >    topoDist.clear();
207 >    topoDist.resize(nLocal_);
208 >
209 >    for (int i = 0; i < nLocal_; i++) {
210 >      int iglob = AtomLocalToGlobal[i];
211 >
212 >      for (int j = 0; j < nLocal_; j++) {
213 >        int jglob = AtomLocalToGlobal[j];
214 >
215 >        if (excludes->hasPair(iglob, jglob))
216 >          excludesForAtom[i].push_back(j);              
217 >        
218 >        if (oneTwo->hasPair(iglob, jglob)) {
219 >          toposForAtom[i].push_back(j);
220 >          topoDist[i].push_back(1);
221 >        } else {
222 >          if (oneThree->hasPair(iglob, jglob)) {
223 >            toposForAtom[i].push_back(j);
224 >            topoDist[i].push_back(2);
225 >          } else {
226 >            if (oneFour->hasPair(iglob, jglob)) {
227 >              toposForAtom[i].push_back(j);
228 >              topoDist[i].push_back(3);
229 >            }
230 >          }
231 >        }
232 >      }      
233 >    }
234 >    
235 >    createGtypeCutoffMap();
236 >
237 >  }
238 >  
239 >  void ForceMatrixDecomposition::createGtypeCutoffMap() {
240 >    
241 >    RealType tol = 1e-6;
242 >    RealType rc;
243 >    int atid;
244 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
245 >    map<int, RealType> atypeCutoff;
246 >      
247 >    for (set<AtomType*>::iterator at = atypes.begin();
248 >         at != atypes.end(); ++at){
249 >      atid = (*at)->getIdent();
250 >      if (userChoseCutoff_)
251 >        atypeCutoff[atid] = userCutoff_;
252 >      else
253 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
254 >    }
255 >
256 >    vector<RealType> gTypeCutoffs;
257 >    // first we do a single loop over the cutoff groups to find the
258 >    // largest cutoff for any atypes present in this group.
259 > #ifdef IS_MPI
260 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
261 >    groupRowToGtype.resize(nGroupsInRow_);
262 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
263 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
264 >      for (vector<int>::iterator ia = atomListRow.begin();
265 >           ia != atomListRow.end(); ++ia) {            
266 >        int atom1 = (*ia);
267 >        atid = identsRow[atom1];
268 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
269 >          groupCutoffRow[cg1] = atypeCutoff[atid];
270 >        }
271 >      }
272 >
273 >      bool gTypeFound = false;
274 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
275 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
276 >          groupRowToGtype[cg1] = gt;
277 >          gTypeFound = true;
278 >        }
279 >      }
280 >      if (!gTypeFound) {
281 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
282 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
283 >      }
284 >      
285 >    }
286 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
287 >    groupColToGtype.resize(nGroupsInCol_);
288 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
289 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
290 >      for (vector<int>::iterator jb = atomListCol.begin();
291 >           jb != atomListCol.end(); ++jb) {            
292 >        int atom2 = (*jb);
293 >        atid = identsCol[atom2];
294 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
295 >          groupCutoffCol[cg2] = atypeCutoff[atid];
296 >        }
297 >      }
298 >      bool gTypeFound = false;
299 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
300 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
301 >          groupColToGtype[cg2] = gt;
302 >          gTypeFound = true;
303 >        }
304 >      }
305 >      if (!gTypeFound) {
306 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
307 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
308 >      }
309 >    }
310 > #else
311 >
312 >    vector<RealType> groupCutoff(nGroups_, 0.0);
313 >    groupToGtype.resize(nGroups_);
314 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
315 >
316 >      groupCutoff[cg1] = 0.0;
317 >      vector<int> atomList = getAtomsInGroupRow(cg1);
318 >
319 >      for (vector<int>::iterator ia = atomList.begin();
320 >           ia != atomList.end(); ++ia) {            
321 >        int atom1 = (*ia);
322 >        atid = idents[atom1];
323 >        if (atypeCutoff[atid] > groupCutoff[cg1]) {
324 >          groupCutoff[cg1] = atypeCutoff[atid];
325 >        }
326 >      }
327 >
328 >      bool gTypeFound = false;
329 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
330 >        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
331 >          groupToGtype[cg1] = gt;
332 >          gTypeFound = true;
333 >        }
334 >      }
335 >      if (!gTypeFound) {
336 >        gTypeCutoffs.push_back( groupCutoff[cg1] );
337 >        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
338 >      }      
339 >    }
340   #endif
341 +
342 +    // Now we find the maximum group cutoff value present in the simulation
343 +
344 +    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
345 +
346 + #ifdef IS_MPI
347 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
348 + #endif
349 +    
350 +    RealType tradRcut = groupMax;
351 +
352 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
353 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
354 +        RealType thisRcut;
355 +        switch(cutoffPolicy_) {
356 +        case TRADITIONAL:
357 +          thisRcut = tradRcut;
358 +          break;
359 +        case MIX:
360 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
361 +          break;
362 +        case MAX:
363 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
364 +          break;
365 +        default:
366 +          sprintf(painCave.errMsg,
367 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
368 +                  "hit an unknown cutoff policy!\n");
369 +          painCave.severity = OPENMD_ERROR;
370 +          painCave.isFatal = 1;
371 +          simError();
372 +          break;
373 +        }
374 +
375 +        pair<int,int> key = make_pair(i,j);
376 +        gTypeCutoffMap[key].first = thisRcut;
377 +
378 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
379 +
380 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
381 +        
382 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
383 +
384 +        // sanity check
385 +        
386 +        if (userChoseCutoff_) {
387 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
388 +            sprintf(painCave.errMsg,
389 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
390 +                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
391 +            painCave.severity = OPENMD_ERROR;
392 +            painCave.isFatal = 1;
393 +            simError();            
394 +          }
395 +        }
396 +      }
397 +    }
398    }
399 +
400 +
401 +  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
402 +    int i, j;  
403 + #ifdef IS_MPI
404 +    i = groupRowToGtype[cg1];
405 +    j = groupColToGtype[cg2];
406 + #else
407 +    i = groupToGtype[cg1];
408 +    j = groupToGtype[cg2];
409 + #endif    
410 +    return gTypeCutoffMap[make_pair(i,j)];
411 +  }
412 +
413 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
414 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
415 +      if (toposForAtom[atom1][j] == atom2)
416 +        return topoDist[atom1][j];
417 +    }
418 +    return 0;
419 +  }
420 +
421 +  void ForceMatrixDecomposition::zeroWorkArrays() {
422 +    pairwisePot = 0.0;
423 +    embeddingPot = 0.0;
424 +
425 + #ifdef IS_MPI
426 +    if (storageLayout_ & DataStorage::dslForce) {
427 +      fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero);
428 +      fill(atomColData.force.begin(), atomColData.force.end(), V3Zero);
429 +    }
430 +
431 +    if (storageLayout_ & DataStorage::dslTorque) {
432 +      fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero);
433 +      fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero);
434 +    }
435      
436 +    fill(pot_row.begin(), pot_row.end(),
437 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
438  
439 +    fill(pot_col.begin(), pot_col.end(),
440 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
441  
442 +    if (storageLayout_ & DataStorage::dslParticlePot) {    
443 +      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
444 +      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
445 +    }
446 +
447 +    if (storageLayout_ & DataStorage::dslDensity) {      
448 +      fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0);
449 +      fill(atomColData.density.begin(), atomColData.density.end(), 0.0);
450 +    }
451 +
452 +    if (storageLayout_ & DataStorage::dslFunctional) {  
453 +      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
454 +      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
455 +    }
456 +
457 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
458 +      fill(atomRowData.functionalDerivative.begin(),
459 +           atomRowData.functionalDerivative.end(), 0.0);
460 +      fill(atomColData.functionalDerivative.begin(),
461 +           atomColData.functionalDerivative.end(), 0.0);
462 +    }
463 +
464 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
465 +      fill(atomRowData.skippedCharge.begin(),
466 +           atomRowData.skippedCharge.end(), 0.0);
467 +      fill(atomColData.skippedCharge.begin(),
468 +           atomColData.skippedCharge.end(), 0.0);
469 +    }
470 +
471 + #else
472 +    
473 +    if (storageLayout_ & DataStorage::dslParticlePot) {      
474 +      fill(snap_->atomData.particlePot.begin(),
475 +           snap_->atomData.particlePot.end(), 0.0);
476 +    }
477 +    
478 +    if (storageLayout_ & DataStorage::dslDensity) {      
479 +      fill(snap_->atomData.density.begin(),
480 +           snap_->atomData.density.end(), 0.0);
481 +    }
482 +    if (storageLayout_ & DataStorage::dslFunctional) {
483 +      fill(snap_->atomData.functional.begin(),
484 +           snap_->atomData.functional.end(), 0.0);
485 +    }
486 +    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
487 +      fill(snap_->atomData.functionalDerivative.begin(),
488 +           snap_->atomData.functionalDerivative.end(), 0.0);
489 +    }
490 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
491 +      fill(snap_->atomData.skippedCharge.begin(),
492 +           snap_->atomData.skippedCharge.end(), 0.0);
493 +    }
494 + #endif
495 +    
496 +  }
497 +
498 +
499    void ForceMatrixDecomposition::distributeData()  {
500      snap_ = sman_->getCurrentSnapshot();
501      storageLayout_ = sman_->getStorageLayout();
# Line 156 | Line 531 | namespace OpenMD {
531   #endif      
532    }
533    
534 +  /* collects information obtained during the pre-pair loop onto local
535 +   * data structures.
536 +   */
537    void ForceMatrixDecomposition::collectIntermediateData() {
538      snap_ = sman_->getCurrentSnapshot();
539      storageLayout_ = sman_->getStorageLayout();
# Line 167 | Line 545 | namespace OpenMD {
545                                 snap_->atomData.density);
546        
547        int n = snap_->atomData.density.size();
548 <      std::vector<RealType> rho_tmp(n, 0.0);
548 >      vector<RealType> rho_tmp(n, 0.0);
549        AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
550        for (int i = 0; i < n; i++)
551          snap_->atomData.density[i] += rho_tmp[i];
552      }
553   #endif
554    }
555 <  
555 >
556 >  /*
557 >   * redistributes information obtained during the pre-pair loop out to
558 >   * row and column-indexed data structures
559 >   */
560    void ForceMatrixDecomposition::distributeIntermediateData() {
561      snap_ = sman_->getCurrentSnapshot();
562      storageLayout_ = sman_->getStorageLayout();
# Line 216 | Line 598 | namespace OpenMD {
598      
599      if (storageLayout_ & DataStorage::dslTorque) {
600  
601 <      int nt = snap_->atomData.force.size();
601 >      int nt = snap_->atomData.torque.size();
602        vector<Vector3d> trq_tmp(nt, V3Zero);
603  
604        AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
605 <      for (int i = 0; i < n; i++) {
605 >      for (int i = 0; i < nt; i++) {
606          snap_->atomData.torque[i] += trq_tmp[i];
607          trq_tmp[i] = 0.0;
608        }
609        
610        AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
611 <      for (int i = 0; i < n; i++)
611 >      for (int i = 0; i < nt; i++)
612          snap_->atomData.torque[i] += trq_tmp[i];
613      }
614 +
615 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
616 +
617 +      int ns = snap_->atomData.skippedCharge.size();
618 +      vector<RealType> skch_tmp(ns, 0.0);
619 +
620 +      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
621 +      for (int i = 0; i < ns; i++) {
622 +        snap_->atomData.skippedCharge[i] = skch_tmp[i];
623 +        skch_tmp[i] = 0.0;
624 +      }
625 +      
626 +      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
627 +      for (int i = 0; i < ns; i++)
628 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
629 +    }
630      
631      nLocal_ = snap_->getNumberOfAtoms();
632  
633 <    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
634 <                                       vector<RealType> (nLocal_, 0.0));
633 >    vector<potVec> pot_temp(nLocal_,
634 >                            Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
635 >
636 >    // scatter/gather pot_row into the members of my column
637 >          
638 >    AtomCommPotRow->scatter(pot_row, pot_temp);
639 >
640 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
641 >      pairwisePot += pot_temp[ii];
642      
643 <    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
644 <      AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
645 <      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
646 <        pot_local[i] += pot_temp[i][ii];
647 <      }
648 <    }
643 >    fill(pot_temp.begin(), pot_temp.end(),
644 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
645 >      
646 >    AtomCommPotColumn->scatter(pot_col, pot_temp);    
647 >    
648 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
649 >      pairwisePot += pot_temp[ii];    
650   #endif
651 +
652    }
653  
654 +  int ForceMatrixDecomposition::getNAtomsInRow() {  
655 + #ifdef IS_MPI
656 +    return nAtomsInRow_;
657 + #else
658 +    return nLocal_;
659 + #endif
660 +  }
661 +
662 +  /**
663 +   * returns the list of atoms belonging to this group.  
664 +   */
665 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
666 + #ifdef IS_MPI
667 +    return groupListRow_[cg1];
668 + #else
669 +    return groupList_[cg1];
670 + #endif
671 +  }
672 +
673 +  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
674 + #ifdef IS_MPI
675 +    return groupListCol_[cg2];
676 + #else
677 +    return groupList_[cg2];
678 + #endif
679 +  }
680    
681    Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){
682      Vector3d d;
# Line 284 | Line 717 | namespace OpenMD {
717      
718      snap_->wrapVector(d);
719      return d;    
720 +  }
721 +
722 +  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
723 + #ifdef IS_MPI
724 +    return massFactorsRow[atom1];
725 + #else
726 +    return massFactors[atom1];
727 + #endif
728 +  }
729 +
730 +  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
731 + #ifdef IS_MPI
732 +    return massFactorsCol[atom2];
733 + #else
734 +    return massFactors[atom2];
735 + #endif
736 +
737    }
738      
739    Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){
# Line 299 | Line 749 | namespace OpenMD {
749      return d;    
750    }
751  
752 +  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
753 +    return excludesForAtom[atom1];
754 +  }
755 +
756 +  /**
757 +   * We need to exclude some overcounted interactions that result from
758 +   * the parallel decomposition.
759 +   */
760 +  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
761 +    int unique_id_1, unique_id_2;
762 +
763 + #ifdef IS_MPI
764 +    // in MPI, we have to look up the unique IDs for each atom
765 +    unique_id_1 = AtomRowToGlobal[atom1];
766 +    unique_id_2 = AtomColToGlobal[atom2];
767 +
768 +    // this situation should only arise in MPI simulations
769 +    if (unique_id_1 == unique_id_2) return true;
770 +    
771 +    // this prevents us from doing the pair on multiple processors
772 +    if (unique_id_1 < unique_id_2) {
773 +      if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
774 +    } else {
775 +      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
776 +    }
777 + #endif
778 +    return false;
779 +  }
780 +
781 +  /**
782 +   * We need to handle the interactions for atoms who are involved in
783 +   * the same rigid body as well as some short range interactions
784 +   * (bonds, bends, torsions) differently from other interactions.
785 +   * We'll still visit the pairwise routines, but with a flag that
786 +   * tells those routines to exclude the pair from direct long range
787 +   * interactions.  Some indirect interactions (notably reaction
788 +   * field) must still be handled for these pairs.
789 +   */
790 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
791 +    int unique_id_2;
792 +    
793 + #ifdef IS_MPI
794 +    // in MPI, we have to look up the unique IDs for the row atom.
795 +    unique_id_2 = AtomColToGlobal[atom2];
796 + #else
797 +    // in the normal loop, the atom numbers are unique
798 +    unique_id_2 = atom2;
799 + #endif
800 +    
801 +    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
802 +         i != excludesForAtom[atom1].end(); ++i) {
803 +      if ( (*i) == unique_id_2 ) return true;
804 +    }
805 +
806 +    return false;
807 +  }
808 +
809 +
810    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
811   #ifdef IS_MPI
812      atomRowData.force[atom1] += fg;
# Line 316 | Line 824 | namespace OpenMD {
824    }
825  
826      // filling interaction blocks with pointers
827 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
828 <    InteractionData idat;
827 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
828 >                                                     int atom1, int atom2) {
829  
830 +    idat.excluded = excludeAtomPair(atom1, atom2);
831 +  
832   #ifdef IS_MPI
833 +    
834 +    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
835 +                             ff_->getAtomType(identsCol[atom2]) );
836 +    
837      if (storageLayout_ & DataStorage::dslAmat) {
838        idat.A1 = &(atomRowData.aMat[atom1]);
839        idat.A2 = &(atomColData.aMat[atom2]);
# Line 340 | Line 854 | namespace OpenMD {
854        idat.rho2 = &(atomColData.density[atom2]);
855      }
856  
857 +    if (storageLayout_ & DataStorage::dslFunctional) {
858 +      idat.frho1 = &(atomRowData.functional[atom1]);
859 +      idat.frho2 = &(atomColData.functional[atom2]);
860 +    }
861 +
862      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
863        idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]);
864        idat.dfrho2 = &(atomColData.functionalDerivative[atom2]);
865      }
866 +
867 +    if (storageLayout_ & DataStorage::dslParticlePot) {
868 +      idat.particlePot1 = &(atomRowData.particlePot[atom1]);
869 +      idat.particlePot2 = &(atomColData.particlePot[atom2]);
870 +    }
871 +
872 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
873 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
874 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
875 +    }
876 +
877   #else
878 +
879 +    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
880 +                             ff_->getAtomType(idents[atom2]) );
881 +
882      if (storageLayout_ & DataStorage::dslAmat) {
883        idat.A1 = &(snap_->atomData.aMat[atom1]);
884        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 360 | Line 894 | namespace OpenMD {
894        idat.t2 = &(snap_->atomData.torque[atom2]);
895      }
896  
897 <    if (storageLayout_ & DataStorage::dslDensity) {
897 >    if (storageLayout_ & DataStorage::dslDensity) {    
898        idat.rho1 = &(snap_->atomData.density[atom1]);
899        idat.rho2 = &(snap_->atomData.density[atom2]);
900      }
901  
902 +    if (storageLayout_ & DataStorage::dslFunctional) {
903 +      idat.frho1 = &(snap_->atomData.functional[atom1]);
904 +      idat.frho2 = &(snap_->atomData.functional[atom2]);
905 +    }
906 +
907      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
908        idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]);
909        idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]);
910      }
911 +
912 +    if (storageLayout_ & DataStorage::dslParticlePot) {
913 +      idat.particlePot1 = &(snap_->atomData.particlePot[atom1]);
914 +      idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
915 +    }
916 +
917 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
918 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
919 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
920 +    }
921   #endif
373 –    return idat;
922    }
923  
924 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
925 <
378 <    InteractionData idat;
924 >  
925 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
926   #ifdef IS_MPI
927 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
928 <      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
929 <      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
930 <    }
931 <    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 <    }
927 >    pot_row[atom1] += 0.5 *  *(idat.pot);
928 >    pot_col[atom2] += 0.5 *  *(idat.pot);
929 >
930 >    atomRowData.force[atom1] += *(idat.f1);
931 >    atomColData.force[atom2] -= *(idat.f1);
932   #else
933 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
934 <      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
935 <      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
936 <    }
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 <    }
933 >    pairwisePot += *(idat.pot);
934 >
935 >    snap_->atomData.force[atom1] += *(idat.f1);
936 >    snap_->atomData.force[atom2] -= *(idat.f1);
937   #endif
938      
939    }
940  
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 –
941    /*
942     * buildNeighborList
943     *
# Line 443 | Line 947 | namespace OpenMD {
947    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
948        
949      vector<pair<int, int> > neighborList;
950 +    groupCutoffs cuts;
951 +    bool doAllPairs = false;
952 +
953   #ifdef IS_MPI
954 <    CellListRow.clear();
955 <    CellListCol.clear();
954 >    cellListRow_.clear();
955 >    cellListCol_.clear();
956   #else
957 <    CellList.clear();
957 >    cellList_.clear();
958   #endif
959  
960 <    // dangerous to not do error checking.
454 <    RealType skinThickness_ = info_->getSimParams()->getSkinThickness();
455 <    RealType rCut_;
456 <
457 <    RealType rList_ = (rCut_ + skinThickness_);
960 >    RealType rList_ = (largestRcut_ + skinThickness_);
961      RealType rl2 = rList_ * rList_;
962      Snapshot* snap_ = sman_->getCurrentSnapshot();
963      Mat3x3d Hmat = snap_->getHmat();
964      Vector3d Hx = Hmat.getColumn(0);
965      Vector3d Hy = Hmat.getColumn(1);
966      Vector3d Hz = Hmat.getColumn(2);
464 –    Vector3i nCells;
967  
968 <    nCells.x() = (int) ( Hx.length() )/ rList_;
969 <    nCells.y() = (int) ( Hy.length() )/ rList_;
970 <    nCells.z() = (int) ( Hz.length() )/ rList_;
968 >    nCells_.x() = (int) ( Hx.length() )/ rList_;
969 >    nCells_.y() = (int) ( Hy.length() )/ rList_;
970 >    nCells_.z() = (int) ( Hz.length() )/ rList_;
971  
972 +    // handle small boxes where the cell offsets can end up repeating cells
973 +    
974 +    if (nCells_.x() < 3) doAllPairs = true;
975 +    if (nCells_.y() < 3) doAllPairs = true;
976 +    if (nCells_.z() < 3) doAllPairs = true;
977 +
978      Mat3x3d invHmat = snap_->getInvHmat();
979      Vector3d rs, scaled, dr;
980      Vector3i whichCell;
981      int cellIndex;
982 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
983  
984   #ifdef IS_MPI
985 <    for (int i = 0; i < nGroupsInRow_; i++) {
986 <      rs = cgRowData.position[i];
987 <      // scaled positions relative to the box vectors
988 <      scaled = invHmat * rs;
989 <      // 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();
985 >    cellListRow_.resize(nCtot);
986 >    cellListCol_.resize(nCtot);
987 > #else
988 >    cellList_.resize(nCtot);
989 > #endif
990  
991 <      // find single index of this cell:
992 <      cellIndex = Vlinear(whichCell, nCells);
492 <      // add this cutoff group to the list of groups in this cell;
493 <      CellListRow[cellIndex].push_back(i);
494 <    }
991 >    if (!doAllPairs) {
992 > #ifdef IS_MPI
993  
994 <    for (int i = 0; i < nGroupsInCol_; i++) {
995 <      rs = cgColData.position[i];
996 <      // scaled positions relative to the box vectors
997 <      scaled = invHmat * rs;
998 <      // wrap the vector back into the unit box by subtracting integer box
999 <      // numbers
1000 <      for (int j = 0; j < 3; j++)
1001 <        scaled[j] -= roundMe(scaled[j]);
1002 <
1003 <      // find xyz-indices of cell that cutoffGroup is in.
1004 <      whichCell.x() = nCells.x() * scaled.x();
1005 <      whichCell.y() = nCells.y() * scaled.y();
1006 <      whichCell.z() = nCells.z() * scaled.z();
1007 <
1008 <      // find single index of this cell:
1009 <      cellIndex = Vlinear(whichCell, nCells);
1010 <      // add this cutoff group to the list of groups in this cell;
1011 <      CellListCol[cellIndex].push_back(i);
1012 <    }
994 >      for (int i = 0; i < nGroupsInRow_; i++) {
995 >        rs = cgRowData.position[i];
996 >        
997 >        // scaled positions relative to the box vectors
998 >        scaled = invHmat * rs;
999 >        
1000 >        // wrap the vector back into the unit box by subtracting integer box
1001 >        // numbers
1002 >        for (int j = 0; j < 3; j++) {
1003 >          scaled[j] -= roundMe(scaled[j]);
1004 >          scaled[j] += 0.5;
1005 >        }
1006 >        
1007 >        // find xyz-indices of cell that cutoffGroup is in.
1008 >        whichCell.x() = nCells_.x() * scaled.x();
1009 >        whichCell.y() = nCells_.y() * scaled.y();
1010 >        whichCell.z() = nCells_.z() * scaled.z();
1011 >        
1012 >        // find single index of this cell:
1013 >        cellIndex = Vlinear(whichCell, nCells_);
1014 >        
1015 >        // add this cutoff group to the list of groups in this cell;
1016 >        cellListRow_[cellIndex].push_back(i);
1017 >      }
1018 >      
1019 >      for (int i = 0; i < nGroupsInCol_; i++) {
1020 >        rs = cgColData.position[i];
1021 >        
1022 >        // scaled positions relative to the box vectors
1023 >        scaled = invHmat * rs;
1024 >        
1025 >        // wrap the vector back into the unit box by subtracting integer box
1026 >        // numbers
1027 >        for (int j = 0; j < 3; j++) {
1028 >          scaled[j] -= roundMe(scaled[j]);
1029 >          scaled[j] += 0.5;
1030 >        }
1031 >        
1032 >        // find xyz-indices of cell that cutoffGroup is in.
1033 >        whichCell.x() = nCells_.x() * scaled.x();
1034 >        whichCell.y() = nCells_.y() * scaled.y();
1035 >        whichCell.z() = nCells_.z() * scaled.z();
1036 >        
1037 >        // find single index of this cell:
1038 >        cellIndex = Vlinear(whichCell, nCells_);
1039 >        
1040 >        // add this cutoff group to the list of groups in this cell;
1041 >        cellListCol_[cellIndex].push_back(i);
1042 >      }
1043   #else
1044 <    for (int i = 0; i < nGroups_; i++) {
1045 <      rs = snap_->cgData.position[i];
1046 <      // scaled positions relative to the box vectors
1047 <      scaled = invHmat * rs;
1048 <      // wrap the vector back into the unit box by subtracting integer box
1049 <      // numbers
1050 <      for (int j = 0; j < 3; j++)
1051 <        scaled[j] -= roundMe(scaled[j]);
1052 <
1053 <      // find xyz-indices of cell that cutoffGroup is in.
1054 <      whichCell.x() = nCells.x() * scaled.x();
1055 <      whichCell.y() = nCells.y() * scaled.y();
1056 <      whichCell.z() = nCells.z() * scaled.z();
1057 <
1058 <      // find single index of this cell:
1059 <      cellIndex = Vlinear(whichCell, nCells);
1060 <      // add this cutoff group to the list of groups in this cell;
1061 <      CellList[cellIndex].push_back(i);
1062 <    }
1044 >      for (int i = 0; i < nGroups_; i++) {
1045 >        rs = snap_->cgData.position[i];
1046 >        
1047 >        // scaled positions relative to the box vectors
1048 >        scaled = invHmat * rs;
1049 >        
1050 >        // wrap the vector back into the unit box by subtracting integer box
1051 >        // numbers
1052 >        for (int j = 0; j < 3; j++) {
1053 >          scaled[j] -= roundMe(scaled[j]);
1054 >          scaled[j] += 0.5;
1055 >        }
1056 >        
1057 >        // find xyz-indices of cell that cutoffGroup is in.
1058 >        whichCell.x() = nCells_.x() * scaled.x();
1059 >        whichCell.y() = nCells_.y() * scaled.y();
1060 >        whichCell.z() = nCells_.z() * scaled.z();
1061 >        
1062 >        // find single index of this cell:
1063 >        cellIndex = Vlinear(whichCell, nCells_);      
1064 >        
1065 >        // add this cutoff group to the list of groups in this cell;
1066 >        cellList_[cellIndex].push_back(i);
1067 >      }
1068   #endif
1069  
1070 <
1071 <
1072 <    for (int m1z = 0; m1z < nCells.z(); m1z++) {
1073 <      for (int m1y = 0; m1y < nCells.y(); m1y++) {
1074 <        for (int m1x = 0; m1x < nCells.x(); m1x++) {
1075 <          Vector3i m1v(m1x, m1y, m1z);
1076 <          int m1 = Vlinear(m1v, nCells);
1077 <          for (int offset = 0; offset < nOffset_; offset++) {
1078 <            Vector3i m2v = m1v + cellOffsets_[offset];
1079 <
1080 <            if (m2v.x() >= nCells.x()) {
1081 <              m2v.x() = 0;          
1082 <            } else if (m2v.x() < 0) {
1083 <              m2v.x() = nCells.x() - 1;
1084 <            }
1085 <
1086 <            if (m2v.y() >= nCells.y()) {
1087 <              m2v.y() = 0;          
1088 <            } else if (m2v.y() < 0) {
1089 <              m2v.y() = nCells.y() - 1;
1090 <            }
1091 <
1092 <            if (m2v.z() >= nCells.z()) {
1093 <              m2v.z() = 0;          
1094 <            } else if (m2v.z() < 0) {
1095 <              m2v.z() = nCells.z() - 1;
1096 <            }
1097 <
1098 <            int m2 = Vlinear (m2v, nCells);
1099 <
1070 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1071 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1072 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1073 >            Vector3i m1v(m1x, m1y, m1z);
1074 >            int m1 = Vlinear(m1v, nCells_);
1075 >            
1076 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1077 >                 os != cellOffsets_.end(); ++os) {
1078 >              
1079 >              Vector3i m2v = m1v + (*os);
1080 >              
1081 >              if (m2v.x() >= nCells_.x()) {
1082 >                m2v.x() = 0;          
1083 >              } else if (m2v.x() < 0) {
1084 >                m2v.x() = nCells_.x() - 1;
1085 >              }
1086 >              
1087 >              if (m2v.y() >= nCells_.y()) {
1088 >                m2v.y() = 0;          
1089 >              } else if (m2v.y() < 0) {
1090 >                m2v.y() = nCells_.y() - 1;
1091 >              }
1092 >              
1093 >              if (m2v.z() >= nCells_.z()) {
1094 >                m2v.z() = 0;          
1095 >              } else if (m2v.z() < 0) {
1096 >                m2v.z() = nCells_.z() - 1;
1097 >              }
1098 >              
1099 >              int m2 = Vlinear (m2v, nCells_);
1100 >              
1101   #ifdef IS_MPI
1102 <            for (vector<int>::iterator j1 = CellListRow[m1].begin();
1103 <                 j1 != CellListRow[m1].end(); ++j1) {
1104 <              for (vector<int>::iterator j2 = CellListCol[m2].begin();
1105 <                   j2 != CellListCol[m2].end(); ++j2) {
1106 <                              
1107 <                // Always do this if we're in different cells or if
1108 <                // we're in the same cell and the global index of the
1109 <                // j2 cutoff group is less than the j1 cutoff group
1110 <
1111 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1112 <                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1113 <                  snap_->wrapVector(dr);
1114 <                  if (dr.lengthSquare() < rl2) {
1115 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1102 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1103 >                   j1 != cellListRow_[m1].end(); ++j1) {
1104 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1105 >                     j2 != cellListCol_[m2].end(); ++j2) {
1106 >                  
1107 >                  // Always do this if we're in different cells or if
1108 >                  // we're in the same cell and the global index of the
1109 >                  // j2 cutoff group is less than the j1 cutoff group
1110 >                  
1111 >                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1112 >                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1113 >                    snap_->wrapVector(dr);
1114 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1115 >                    if (dr.lengthSquare() < cuts.third) {
1116 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1117 >                    }
1118                    }
1119                  }
1120                }
585 –            }
1121   #else
1122 <            for (vector<int>::iterator j1 = CellList[m1].begin();
1123 <                 j1 != CellList[m1].end(); ++j1) {
1124 <              for (vector<int>::iterator j2 = CellList[m2].begin();
1125 <                   j2 != CellList[m2].end(); ++j2) {
1126 <                              
1127 <                // Always do this if we're in different cells or if
1128 <                // we're in the same cell and the global index of the
1129 <                // j2 cutoff group is less than the j1 cutoff group
1130 <
1131 <                if (m2 != m1 || (*j2) < (*j1)) {
1132 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1133 <                  snap_->wrapVector(dr);
1134 <                  if (dr.lengthSquare() < rl2) {
1135 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1122 >              
1123 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1124 >                   j1 != cellList_[m1].end(); ++j1) {
1125 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1126 >                     j2 != cellList_[m2].end(); ++j2) {
1127 >                  
1128 >                  // Always do this if we're in different cells or if
1129 >                  // we're in the same cell and the global index of the
1130 >                  // j2 cutoff group is less than the j1 cutoff group
1131 >                  
1132 >                  if (m2 != m1 || (*j2) < (*j1)) {
1133 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1134 >                    snap_->wrapVector(dr);
1135 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1136 >                    if (dr.lengthSquare() < cuts.third) {
1137 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1138 >                    }
1139                    }
1140                  }
1141                }
604 –            }
1142   #endif
1143 +            }
1144            }
1145          }
1146        }
1147 +    } else {
1148 +      // branch to do all cutoff group pairs
1149 + #ifdef IS_MPI
1150 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1151 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1152 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1153 +          snap_->wrapVector(dr);
1154 +          cuts = getGroupCutoffs( j1, j2 );
1155 +          if (dr.lengthSquare() < cuts.third) {
1156 +            neighborList.push_back(make_pair(j1, j2));
1157 +          }
1158 +        }
1159 +      }
1160 + #else
1161 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1162 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1163 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1164 +          snap_->wrapVector(dr);
1165 +          cuts = getGroupCutoffs( j1, j2 );
1166 +          if (dr.lengthSquare() < cuts.third) {
1167 +            neighborList.push_back(make_pair(j1, j2));
1168 +          }
1169 +        }
1170 +      }        
1171 + #endif
1172      }
1173 +      
1174 +    // save the local cutoff group positions for the check that is
1175 +    // done on each loop:
1176 +    saved_CG_positions_.clear();
1177 +    for (int i = 0; i < nGroups_; i++)
1178 +      saved_CG_positions_.push_back(snap_->cgData.position[i]);
1179 +    
1180      return neighborList;
1181    }
1182   } //end namespace OpenMD

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