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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 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC vs.
Revision 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC

# Line 57 | Line 57 | namespace OpenMD {
57      storageLayout_ = sman_->getStorageLayout();
58      ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
60 –    nGroups_ = snap_->getNumberOfCutoffGroups();
60  
61 +    nGroups_ = info_->getNLocalCutoffGroups();
62 +    cerr << "in dId, nGroups = " << nGroups_ << "\n";
63      // gather the information for atomtype IDs (atids):
64      identsLocal = info_->getIdentArray();
65      AtomLocalToGlobal = info_->getGlobalAtomIndices();
66      cgLocalToGlobal = info_->getGlobalGroupIndices();
67      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68 <    vector<RealType> massFactorsLocal = info_->getMassFactors();
68 >    massFactors = info_->getMassFactors();
69      PairList excludes = info_->getExcludedInteractions();
70      PairList oneTwo = info_->getOneTwoInteractions();
71      PairList oneThree = info_->getOneThreeInteractions();
# Line 104 | Line 105 | namespace OpenMD {
105      cgColData.resize(nGroupsInCol_);
106      cgColData.setStorageLayout(DataStorage::dslPosition);
107          
108 <    identsRow.reserve(nAtomsInRow_);
109 <    identsCol.reserve(nAtomsInCol_);
108 >    identsRow.resize(nAtomsInRow_);
109 >    identsCol.resize(nAtomsInCol_);
110      
111      AtomCommIntRow->gather(identsLocal, identsRow);
112      AtomCommIntColumn->gather(identsLocal, identsCol);
# Line 116 | Line 117 | namespace OpenMD {
117      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
118      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
119  
120 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
121 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
120 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
121 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
122  
123      groupListRow_.clear();
124 <    groupListRow_.reserve(nGroupsInRow_);
124 >    groupListRow_.resize(nGroupsInRow_);
125      for (int i = 0; i < nGroupsInRow_; i++) {
126        int gid = cgRowToGlobal[i];
127        for (int j = 0; j < nAtomsInRow_; j++) {
# Line 131 | Line 132 | namespace OpenMD {
132      }
133  
134      groupListCol_.clear();
135 <    groupListCol_.reserve(nGroupsInCol_);
135 >    groupListCol_.resize(nGroupsInCol_);
136      for (int i = 0; i < nGroupsInCol_; i++) {
137        int gid = cgColToGlobal[i];
138        for (int j = 0; j < nAtomsInCol_; j++) {
# Line 141 | Line 142 | namespace OpenMD {
142        }      
143      }
144  
145 <    skipsForRowAtom.clear();
146 <    skipsForRowAtom.reserve(nAtomsInRow_);
145 >    skipsForAtom.clear();
146 >    skipsForAtom.resize(nAtomsInRow_);
147 >    toposForAtom.clear();
148 >    toposForAtom.resize(nAtomsInRow_);
149 >    topoDist.clear();
150 >    topoDist.resize(nAtomsInRow_);
151      for (int i = 0; i < nAtomsInRow_; i++) {
152        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 –    }
153  
155 –    toposForRowAtom.clear();
156 –    toposForRowAtom.reserve(nAtomsInRow_);
157 –    for (int i = 0; i < nAtomsInRow_; i++) {
158 –      int iglob = AtomRowToGlobal[i];
159 –      int nTopos = 0;
154        for (int j = 0; j < nAtomsInCol_; j++) {
155 <        int jglob = AtomColToGlobal[j];        
155 >        int jglob = AtomColToGlobal[j];
156 >
157 >        if (excludes.hasPair(iglob, jglob))
158 >          skipsForAtom[i].push_back(j);      
159 >        
160          if (oneTwo.hasPair(iglob, jglob)) {
161 <          toposForRowAtom[i].push_back(j);
162 <          topoDistRow[i][nTopos] = 1;
163 <          nTopos++;
161 >          toposForAtom[i].push_back(j);
162 >          topoDist[i].push_back(1);
163 >        } else {
164 >          if (oneThree.hasPair(iglob, jglob)) {
165 >            toposForAtom[i].push_back(j);
166 >            topoDist[i].push_back(2);
167 >          } else {
168 >            if (oneFour.hasPair(iglob, jglob)) {
169 >              toposForAtom[i].push_back(j);
170 >              topoDist[i].push_back(3);
171 >            }
172 >          }
173          }
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 –        }
174        }      
175      }
176  
177   #endif
178  
179      groupList_.clear();
180 <    groupList_.reserve(nGroups_);
180 >    groupList_.resize(nGroups_);
181      for (int i = 0; i < nGroups_; i++) {
182        int gid = cgLocalToGlobal[i];
183        for (int j = 0; j < nLocal_; j++) {
184          int aid = AtomLocalToGlobal[j];
185 <        if (globalGroupMembership[aid] == gid)
185 >        if (globalGroupMembership[aid] == gid) {
186            groupList_[i].push_back(j);
187 +        }
188        }      
189      }
190  
191 <    skipsForLocalAtom.clear();
192 <    skipsForLocalAtom.reserve(nLocal_);
191 >    skipsForAtom.clear();
192 >    skipsForAtom.resize(nLocal_);
193 >    toposForAtom.clear();
194 >    toposForAtom.resize(nLocal_);
195 >    topoDist.clear();
196 >    topoDist.resize(nLocal_);
197  
198      for (int i = 0; i < nLocal_; i++) {
199        int iglob = AtomLocalToGlobal[i];
200 +
201        for (int j = 0; j < nLocal_; j++) {
202 <        int jglob = AtomLocalToGlobal[j];        
202 >        int jglob = AtomLocalToGlobal[j];
203 >
204          if (excludes.hasPair(iglob, jglob))
205 <          skipsForLocalAtom[i].push_back(j);      
205 >          skipsForAtom[i].push_back(j);              
206 >        
207 >        if (oneTwo.hasPair(iglob, jglob)) {
208 >          toposForAtom[i].push_back(j);
209 >          topoDist[i].push_back(1);
210 >        } else {
211 >          if (oneThree.hasPair(iglob, jglob)) {
212 >            toposForAtom[i].push_back(j);
213 >            topoDist[i].push_back(2);
214 >          } else {
215 >            if (oneFour.hasPair(iglob, jglob)) {
216 >              toposForAtom[i].push_back(j);
217 >              topoDist[i].push_back(3);
218 >            }
219 >          }
220 >        }
221        }      
222      }
223 +    
224 +    createGtypeCutoffMap();
225 +  }
226 +  
227 +  void ForceMatrixDecomposition::createGtypeCutoffMap() {
228  
229 <    toposForLocalAtom.clear();
230 <    toposForLocalAtom.reserve(nLocal_);
231 <    for (int i = 0; i < nLocal_; i++) {
232 <      int iglob = AtomLocalToGlobal[i];
233 <      int nTopos = 0;
234 <      for (int j = 0; j < nLocal_; j++) {
235 <        int jglob = AtomLocalToGlobal[j];        
236 <        if (oneTwo.hasPair(iglob, jglob)) {
237 <          toposForLocalAtom[i].push_back(j);
238 <          topoDistLocal[i][nTopos] = 1;
239 <          nTopos++;
229 >    RealType tol = 1e-6;
230 >    RealType rc;
231 >    int atid;
232 >    set<AtomType*> atypes = info_->getSimulatedAtomTypes();
233 >    vector<RealType> atypeCutoff;
234 >    atypeCutoff.resize( atypes.size() );
235 >
236 >    for (set<AtomType*>::iterator at = atypes.begin();
237 >         at != atypes.end(); ++at){
238 >      rc = interactionMan_->getSuggestedCutoffRadius(*at);
239 >      atid = (*at)->getIdent();
240 >      atypeCutoff[atid] = rc;
241 >    }
242 >
243 >    vector<RealType> gTypeCutoffs;
244 >
245 >    // first we do a single loop over the cutoff groups to find the
246 >    // largest cutoff for any atypes present in this group.
247 > #ifdef IS_MPI
248 >    vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
249 >    groupRowToGtype.resize(nGroupsInRow_);
250 >    for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
251 >      vector<int> atomListRow = getAtomsInGroupRow(cg1);
252 >      for (vector<int>::iterator ia = atomListRow.begin();
253 >           ia != atomListRow.end(); ++ia) {            
254 >        int atom1 = (*ia);
255 >        atid = identsRow[atom1];
256 >        if (atypeCutoff[atid] > groupCutoffRow[cg1]) {
257 >          groupCutoffRow[cg1] = atypeCutoff[atid];
258          }
259 <        if (oneThree.hasPair(iglob, jglob)) {
260 <          toposForLocalAtom[i].push_back(j);
261 <          topoDistLocal[i][nTopos] = 2;
262 <          nTopos++;
259 >      }
260 >
261 >      bool gTypeFound = false;
262 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
263 >        if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) {
264 >          groupRowToGtype[cg1] = gt;
265 >          gTypeFound = true;
266 >        }
267 >      }
268 >      if (!gTypeFound) {
269 >        gTypeCutoffs.push_back( groupCutoffRow[cg1] );
270 >        groupRowToGtype[cg1] = gTypeCutoffs.size() - 1;
271 >      }
272 >      
273 >    }
274 >    vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
275 >    groupColToGtype.resize(nGroupsInCol_);
276 >    for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
277 >      vector<int> atomListCol = getAtomsInGroupColumn(cg2);
278 >      for (vector<int>::iterator jb = atomListCol.begin();
279 >           jb != atomListCol.end(); ++jb) {            
280 >        int atom2 = (*jb);
281 >        atid = identsCol[atom2];
282 >        if (atypeCutoff[atid] > groupCutoffCol[cg2]) {
283 >          groupCutoffCol[cg2] = atypeCutoff[atid];
284          }
285 <        if (oneFour.hasPair(iglob, jglob)) {
286 <          toposForLocalAtom[i].push_back(j);
287 <          topoDistLocal[i][nTopos] = 3;
288 <          nTopos++;
285 >      }
286 >      bool gTypeFound = false;
287 >      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
288 >        if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) {
289 >          groupColToGtype[cg2] = gt;
290 >          gTypeFound = true;
291 >        }
292 >      }
293 >      if (!gTypeFound) {
294 >        gTypeCutoffs.push_back( groupCutoffCol[cg2] );
295 >        groupColToGtype[cg2] = gTypeCutoffs.size() - 1;
296 >      }
297 >    }
298 > #else
299 >
300 >    vector<RealType> groupCutoff(nGroups_, 0.0);
301 >    groupToGtype.resize(nGroups_);
302 >
303 >    cerr << "nGroups = " << nGroups_ << "\n";
304 >    for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305 >
306 >      groupCutoff[cg1] = 0.0;
307 >      vector<int> atomList = getAtomsInGroupRow(cg1);
308 >
309 >      for (vector<int>::iterator ia = atomList.begin();
310 >           ia != atomList.end(); ++ia) {            
311 >        int atom1 = (*ia);
312 >        atid = identsLocal[atom1];
313 >        if (atypeCutoff[atid] > groupCutoff[cg1]) {
314 >          groupCutoff[cg1] = atypeCutoff[atid];
315          }
316 +      }
317 +
318 +      bool gTypeFound = false;
319 +      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
320 +        if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
321 +          groupToGtype[cg1] = gt;
322 +          gTypeFound = true;
323 +        }
324 +      }
325 +      if (!gTypeFound) {
326 +        gTypeCutoffs.push_back( groupCutoff[cg1] );
327 +        groupToGtype[cg1] = gTypeCutoffs.size() - 1;
328        }      
329 +    }
330 + #endif
331 +
332 +    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
333 +    // Now we find the maximum group cutoff value present in the simulation
334 +
335 +    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
336 +
337 + #ifdef IS_MPI
338 +    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
339 + #endif
340 +    
341 +    RealType tradRcut = groupMax;
342 +
343 +    for (int i = 0; i < gTypeCutoffs.size();  i++) {
344 +      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
345 +        RealType thisRcut;
346 +        switch(cutoffPolicy_) {
347 +        case TRADITIONAL:
348 +          thisRcut = tradRcut;
349 +          break;
350 +        case MIX:
351 +          thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
352 +          break;
353 +        case MAX:
354 +          thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
355 +          break;
356 +        default:
357 +          sprintf(painCave.errMsg,
358 +                  "ForceMatrixDecomposition::createGtypeCutoffMap "
359 +                  "hit an unknown cutoff policy!\n");
360 +          painCave.severity = OPENMD_ERROR;
361 +          painCave.isFatal = 1;
362 +          simError();
363 +          break;
364 +        }
365 +
366 +        pair<int,int> key = make_pair(i,j);
367 +        gTypeCutoffMap[key].first = thisRcut;
368 +
369 +        if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
370 +
371 +        gTypeCutoffMap[key].second = thisRcut*thisRcut;
372 +        
373 +        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
374 +
375 +        // sanity check
376 +        
377 +        if (userChoseCutoff_) {
378 +          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
379 +            sprintf(painCave.errMsg,
380 +                    "ForceMatrixDecomposition::createGtypeCutoffMap "
381 +                    "user-specified rCut does not match computed group Cutoff\n");
382 +            painCave.severity = OPENMD_ERROR;
383 +            painCave.isFatal = 1;
384 +            simError();            
385 +          }
386 +        }
387 +      }
388      }
389    }
390 <  
390 >
391 >
392 >  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
393 >    int i, j;  
394 > #ifdef IS_MPI
395 >    i = groupRowToGtype[cg1];
396 >    j = groupColToGtype[cg2];
397 > #else
398 >    i = groupToGtype[cg1];
399 >    j = groupToGtype[cg2];
400 > #endif    
401 >    return gTypeCutoffMap[make_pair(i,j)];
402 >  }
403 >
404 >  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
405 >    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
406 >      if (toposForAtom[atom1][j] == atom2)
407 >        return topoDist[atom1][j];
408 >    }
409 >    return 0;
410 >  }
411 >
412    void ForceMatrixDecomposition::zeroWorkArrays() {
413  
414      for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
# Line 510 | Line 691 | namespace OpenMD {
691   #ifdef IS_MPI
692      return massFactorsRow[atom1];
693   #else
694 <    return massFactorsLocal[atom1];
694 >    return massFactors[atom1];
695   #endif
696    }
697  
# Line 518 | Line 699 | namespace OpenMD {
699   #ifdef IS_MPI
700      return massFactorsCol[atom2];
701   #else
702 <    return massFactorsLocal[atom2];
702 >    return massFactors[atom2];
703   #endif
704  
705    }
# Line 536 | Line 717 | namespace OpenMD {
717      return d;    
718    }
719  
720 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
721 < #ifdef IS_MPI
541 <    return skipsForRowAtom[atom1];
542 < #else
543 <    return skipsForLocalAtom[atom1];
544 < #endif
720 >  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
721 >    return skipsForAtom[atom1];
722    }
723  
724    /**
# Line 574 | Line 751 | namespace OpenMD {
751      unique_id_2 = atom2;
752   #endif
753      
754 < #ifdef IS_MPI
755 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
579 <         i != skipsForRowAtom[atom1].end(); ++i) {
754 >    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
755 >         i != skipsForAtom[atom1].end(); ++i) {
756        if ( (*i) == unique_id_2 ) return true;
757      }    
582 – #else
583 –    for (vector<int>::iterator i = skipsForLocalAtom[atom1].begin();
584 –         i != skipsForLocalAtom[atom1].end(); ++i) {
585 –      if ( (*i) == unique_id_2 ) return true;
586 –    }    
587 – #endif
588 –  }
758  
590 –  int ForceMatrixDecomposition::getTopoDistance(int atom1, int atom2) {
591 –    
592 – #ifdef IS_MPI
593 –    for (int i = 0; i < toposForRowAtom[atom1].size(); i++) {
594 –      if ( toposForRowAtom[atom1][i] == atom2 ) return topoDistRow[atom1][i];
595 –    }
596 – #else
597 –    for (int i = 0; i < toposForLocalAtom[atom1].size(); i++) {
598 –      if ( toposForLocalAtom[atom1][i] == atom2 ) return topoDistLocal[atom1][i];
599 –    }
600 – #endif
601 –
602 –    // zero is default for unconnected (i.e. normal) pair interactions
603 –    return 0;
759    }
760  
761 +
762    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
763   #ifdef IS_MPI
764      atomRowData.force[atom1] += fg;
# Line 620 | Line 776 | namespace OpenMD {
776    }
777  
778      // filling interaction blocks with pointers
779 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
780 <    InteractionData idat;
625 <
779 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData idat,
780 >                                                     int atom1, int atom2) {    
781   #ifdef IS_MPI
782      
783      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
784                               ff_->getAtomType(identsCol[atom2]) );
630 –
785      
786      if (storageLayout_ & DataStorage::dslAmat) {
787        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 705 | Line 859 | namespace OpenMD {
859      }
860  
861   #endif
708 –    return idat;
862    }
863  
864    
# Line 726 | Line 879 | namespace OpenMD {
879    }
880  
881  
882 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
883 <
731 <    InteractionData idat;
882 >  void ForceMatrixDecomposition::fillSkipData(InteractionData idat,
883 >                                              int atom1, int atom2) {
884   #ifdef IS_MPI
885      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
886                               ff_->getAtomType(identsCol[atom2]) );
# Line 765 | Line 917 | namespace OpenMD {
917    vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
918        
919      vector<pair<int, int> > neighborList;
920 +    groupCutoffs cuts;
921   #ifdef IS_MPI
922      cellListRow_.clear();
923      cellListCol_.clear();
# Line 772 | Line 925 | namespace OpenMD {
925      cellList_.clear();
926   #endif
927  
928 <    // dangerous to not do error checking.
776 <    RealType rCut_;
777 <
778 <    RealType rList_ = (rCut_ + skinThickness_);
928 >    RealType rList_ = (largestRcut_ + skinThickness_);
929      RealType rl2 = rList_ * rList_;
930      Snapshot* snap_ = sman_->getCurrentSnapshot();
931      Mat3x3d Hmat = snap_->getHmat();
# Line 791 | Line 941 | namespace OpenMD {
941      Vector3d rs, scaled, dr;
942      Vector3i whichCell;
943      int cellIndex;
944 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
945  
946 +    cerr << "flag1\n";
947   #ifdef IS_MPI
948 +    cellListRow_.resize(nCtot);
949 +    cellListCol_.resize(nCtot);
950 + #else
951 +    cellList_.resize(nCtot);
952 + #endif
953 +    cerr << "flag2\n";
954 + #ifdef IS_MPI
955      for (int i = 0; i < nGroupsInRow_; i++) {
956        rs = cgRowData.position[i];
957 +
958        // scaled positions relative to the box vectors
959        scaled = invHmat * rs;
960 +
961        // wrap the vector back into the unit box by subtracting integer box
962        // numbers
963 <      for (int j = 0; j < 3; j++)
963 >      for (int j = 0; j < 3; j++) {
964          scaled[j] -= roundMe(scaled[j]);
965 +        scaled[j] += 0.5;
966 +      }
967      
968        // find xyz-indices of cell that cutoffGroup is in.
969        whichCell.x() = nCells_.x() * scaled.x();
# Line 809 | Line 972 | namespace OpenMD {
972  
973        // find single index of this cell:
974        cellIndex = Vlinear(whichCell, nCells_);
975 +
976        // add this cutoff group to the list of groups in this cell;
977        cellListRow_[cellIndex].push_back(i);
978      }
979  
980      for (int i = 0; i < nGroupsInCol_; i++) {
981        rs = cgColData.position[i];
982 +
983        // scaled positions relative to the box vectors
984        scaled = invHmat * rs;
985 +
986        // wrap the vector back into the unit box by subtracting integer box
987        // numbers
988 <      for (int j = 0; j < 3; j++)
988 >      for (int j = 0; j < 3; j++) {
989          scaled[j] -= roundMe(scaled[j]);
990 +        scaled[j] += 0.5;
991 +      }
992  
993        // find xyz-indices of cell that cutoffGroup is in.
994        whichCell.x() = nCells_.x() * scaled.x();
# Line 829 | Line 997 | namespace OpenMD {
997  
998        // find single index of this cell:
999        cellIndex = Vlinear(whichCell, nCells_);
1000 +
1001        // add this cutoff group to the list of groups in this cell;
1002        cellListCol_[cellIndex].push_back(i);
1003      }
1004   #else
1005      for (int i = 0; i < nGroups_; i++) {
1006        rs = snap_->cgData.position[i];
1007 +
1008        // scaled positions relative to the box vectors
1009        scaled = invHmat * rs;
1010 +
1011        // wrap the vector back into the unit box by subtracting integer box
1012        // numbers
1013 <      for (int j = 0; j < 3; j++)
1013 >      for (int j = 0; j < 3; j++) {
1014          scaled[j] -= roundMe(scaled[j]);
1015 +        scaled[j] += 0.5;
1016 +      }
1017  
1018        // find xyz-indices of cell that cutoffGroup is in.
1019        whichCell.x() = nCells_.x() * scaled.x();
# Line 848 | Line 1021 | namespace OpenMD {
1021        whichCell.z() = nCells_.z() * scaled.z();
1022  
1023        // find single index of this cell:
1024 <      cellIndex = Vlinear(whichCell, nCells_);
1024 >      cellIndex = Vlinear(whichCell, nCells_);      
1025 >
1026        // add this cutoff group to the list of groups in this cell;
1027        cellList_[cellIndex].push_back(i);
1028      }
# Line 898 | Line 1072 | namespace OpenMD {
1072                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1073                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1074                    snap_->wrapVector(dr);
1075 <                  if (dr.lengthSquare() < rl2) {
1075 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1076 >                  if (dr.lengthSquare() < cuts.third) {
1077                      neighborList.push_back(make_pair((*j1), (*j2)));
1078                    }
1079                  }
1080                }
1081              }
1082   #else
1083 +
1084              for (vector<int>::iterator j1 = cellList_[m1].begin();
1085                   j1 != cellList_[m1].end(); ++j1) {
1086                for (vector<int>::iterator j2 = cellList_[m2].begin();
1087                     j2 != cellList_[m2].end(); ++j2) {
1088 <                              
1088 >
1089                  // Always do this if we're in different cells or if
1090                  // we're in the same cell and the global index of the
1091                  // j2 cutoff group is less than the j1 cutoff group
# Line 917 | Line 1093 | namespace OpenMD {
1093                  if (m2 != m1 || (*j2) < (*j1)) {
1094                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1095                    snap_->wrapVector(dr);
1096 <                  if (dr.lengthSquare() < rl2) {
1096 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1097 >                  if (dr.lengthSquare() < cuts.third) {
1098                      neighborList.push_back(make_pair((*j1), (*j2)));
1099                    }
1100                  }
# Line 928 | Line 1105 | namespace OpenMD {
1105          }
1106        }
1107      }
1108 <
1108 >    
1109      // save the local cutoff group positions for the check that is
1110      // done on each loop:
1111      saved_CG_positions_.clear();
1112      for (int i = 0; i < nGroups_; i++)
1113        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1114 <
1114 >    
1115      return neighborList;
1116    }
1117   } //end namespace OpenMD

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