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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 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC vs.
Revision 1583 by gezelter, Thu Jun 16 22:00:08 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();
64 >    idents = 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);
111 >    AtomCommIntRow->gather(idents, identsRow);
112 >    AtomCommIntColumn->gather(idents, identsCol);
113      
114      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
115      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
# 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];
198 –      for (int j = 0; j < nLocal_; j++) {
199 –        int jglob = AtomLocalToGlobal[j];        
200 –        if (excludes.hasPair(iglob, jglob))
201 –          skipsForLocalAtom[i].push_back(j);      
202 –      }      
203 –    }
200  
205 –    toposForLocalAtom.clear();
206 –    toposForLocalAtom.reserve(nLocal_);
207 –    for (int i = 0; i < nLocal_; i++) {
208 –      int iglob = AtomLocalToGlobal[i];
209 –      int nTopos = 0;
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 >          skipsForAtom[i].push_back(j);              
206 >        
207          if (oneTwo.hasPair(iglob, jglob)) {
208 <          toposForLocalAtom[i].push_back(j);
209 <          topoDistLocal[i][nTopos] = 1;
210 <          nTopos++;
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          }
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 –        }
221        }      
222 <    }    
223 <
222 >    }
223 >    
224 >    createGtypeCutoffMap();
225    }
226    
227    void ForceMatrixDecomposition::createGtypeCutoffMap() {
# Line 236 | Line 231 | namespace OpenMD {
231      int atid;
232      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
233      vector<RealType> atypeCutoff;
234 <    atypeCutoff.reserve( atypes.size() );
235 <
236 <    for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at){
237 <      rc = interactionMan_->getSuggestedCutoffRadius(*at);
234 >    atypeCutoff.resize( atypes.size() );
235 >      
236 >    for (set<AtomType*>::iterator at = atypes.begin();
237 >         at != atypes.end(); ++at){
238        atid = (*at)->getIdent();
239 <      atypeCutoff[atid] = rc;
239 >
240 >      if (userChoseCutoff_)
241 >        atypeCutoff[atid] = userCutoff_;
242 >      else
243 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
244      }
245  
246      vector<RealType> gTypeCutoffs;
# Line 250 | Line 249 | namespace OpenMD {
249      // largest cutoff for any atypes present in this group.
250   #ifdef IS_MPI
251      vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0);
252 +    groupRowToGtype.resize(nGroupsInRow_);
253      for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) {
254        vector<int> atomListRow = getAtomsInGroupRow(cg1);
255        for (vector<int>::iterator ia = atomListRow.begin();
# Line 275 | Line 275 | namespace OpenMD {
275        
276      }
277      vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0);
278 +    groupColToGtype.resize(nGroupsInCol_);
279      for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) {
280        vector<int> atomListCol = getAtomsInGroupColumn(cg2);
281        for (vector<int>::iterator jb = atomListCol.begin();
# Line 298 | Line 299 | namespace OpenMD {
299        }
300      }
301   #else
302 +
303      vector<RealType> groupCutoff(nGroups_, 0.0);
304 +    groupToGtype.resize(nGroups_);
305 +
306 +    cerr << "nGroups = " << nGroups_ << "\n";
307      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
308 +
309        groupCutoff[cg1] = 0.0;
310        vector<int> atomList = getAtomsInGroupRow(cg1);
311 +
312        for (vector<int>::iterator ia = atomList.begin();
313             ia != atomList.end(); ++ia) {            
314          int atom1 = (*ia);
315 <        atid = identsLocal[atom1];
315 >        atid = idents[atom1];
316          if (atypeCutoff[atid] > groupCutoff[cg1]) {
317            groupCutoff[cg1] = atypeCutoff[atid];
318          }
# Line 325 | Line 332 | namespace OpenMD {
332      }
333   #endif
334  
335 +    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
336      // Now we find the maximum group cutoff value present in the simulation
337  
338 <    vector<RealType>::iterator groupMaxLoc = max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
331 <    RealType groupMax = *groupMaxLoc;
338 >    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
339  
340   #ifdef IS_MPI
341      MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
# Line 337 | Line 344 | namespace OpenMD {
344      RealType tradRcut = groupMax;
345  
346      for (int i = 0; i < gTypeCutoffs.size();  i++) {
347 <      for (int j = 0; j < gTypeCutoffs.size();  j++) {
341 <        
347 >      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
348          RealType thisRcut;
349          switch(cutoffPolicy_) {
350          case TRADITIONAL:
351            thisRcut = tradRcut;
352 +          break;
353          case MIX:
354            thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]);
355 +          break;
356          case MAX:
357            thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]);
358 +          break;
359          default:
360            sprintf(painCave.errMsg,
361                    "ForceMatrixDecomposition::createGtypeCutoffMap "
362                    "hit an unknown cutoff policy!\n");
363            painCave.severity = OPENMD_ERROR;
364            painCave.isFatal = 1;
365 <          simError();              
365 >          simError();
366 >          break;
367          }
368  
369          pair<int,int> key = make_pair(i,j);
# Line 371 | Line 381 | namespace OpenMD {
381            if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
382              sprintf(painCave.errMsg,
383                      "ForceMatrixDecomposition::createGtypeCutoffMap "
384 <                    "user-specified rCut does not match computed group Cutoff\n");
384 >                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
385              painCave.severity = OPENMD_ERROR;
386              painCave.isFatal = 1;
387              simError();            
# Line 383 | Line 393 | namespace OpenMD {
393  
394  
395    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
396 <    int i, j;
387 <
396 >    int i, j;  
397   #ifdef IS_MPI
398      i = groupRowToGtype[cg1];
399      j = groupColToGtype[cg2];
400   #else
401      i = groupToGtype[cg1];
402      j = groupToGtype[cg2];
403 < #endif
395 <    
403 > #endif    
404      return gTypeCutoffMap[make_pair(i,j)];
405    }
406  
407 +  int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
408 +    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
409 +      if (toposForAtom[atom1][j] == atom2)
410 +        return topoDist[atom1][j];
411 +    }
412 +    return 0;
413 +  }
414  
415    void ForceMatrixDecomposition::zeroWorkArrays() {
416 <
417 <    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
403 <      longRangePot_[j] = 0.0;
404 <    }
416 >    pairwisePot = 0.0;
417 >    embeddingPot = 0.0;
418  
419   #ifdef IS_MPI
420      if (storageLayout_ & DataStorage::dslForce) {
# Line 418 | Line 431 | namespace OpenMD {
431           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
432  
433      fill(pot_col.begin(), pot_col.end(),
434 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
422 <    
423 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
434 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
435  
436      if (storageLayout_ & DataStorage::dslParticlePot) {    
437        fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
# Line 594 | Line 605 | namespace OpenMD {
605      AtomCommPotRow->scatter(pot_row, pot_temp);
606  
607      for (int ii = 0;  ii < pot_temp.size(); ii++ )
608 <      pot_local += pot_temp[ii];
608 >      pairwisePot += pot_temp[ii];
609      
610      fill(pot_temp.begin(), pot_temp.end(),
611           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
# Line 602 | Line 613 | namespace OpenMD {
613      AtomCommPotColumn->scatter(pot_col, pot_temp);    
614      
615      for (int ii = 0;  ii < pot_temp.size(); ii++ )
616 <      pot_local += pot_temp[ii];
606 <    
616 >      pairwisePot += pot_temp[ii];    
617   #endif
618 +
619    }
620  
621    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 679 | Line 690 | namespace OpenMD {
690   #ifdef IS_MPI
691      return massFactorsRow[atom1];
692   #else
693 <    return massFactorsLocal[atom1];
693 >    return massFactors[atom1];
694   #endif
695    }
696  
# Line 687 | Line 698 | namespace OpenMD {
698   #ifdef IS_MPI
699      return massFactorsCol[atom2];
700   #else
701 <    return massFactorsLocal[atom2];
701 >    return massFactors[atom2];
702   #endif
703  
704    }
# Line 705 | Line 716 | namespace OpenMD {
716      return d;    
717    }
718  
719 <  vector<int> ForceMatrixDecomposition::getSkipsForRowAtom(int atom1) {
720 < #ifdef IS_MPI
710 <    return skipsForRowAtom[atom1];
711 < #else
712 <    return skipsForLocalAtom[atom1];
713 < #endif
719 >  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
720 >    return skipsForAtom[atom1];
721    }
722  
723    /**
# Line 743 | Line 750 | namespace OpenMD {
750      unique_id_2 = atom2;
751   #endif
752      
753 < #ifdef IS_MPI
754 <    for (vector<int>::iterator i = skipsForRowAtom[atom1].begin();
748 <         i != skipsForRowAtom[atom1].end(); ++i) {
753 >    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
754 >         i != skipsForAtom[atom1].end(); ++i) {
755        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];
756      }
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
757  
758 <    // zero is default for unconnected (i.e. normal) pair interactions
772 <    return 0;
758 >    return false;
759    }
760  
761 +
762    void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){
763   #ifdef IS_MPI
764      atomRowData.force[atom1] += fg;
# Line 789 | Line 776 | namespace OpenMD {
776    }
777  
778      // filling interaction blocks with pointers
779 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
780 <    InteractionData idat;
794 <
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]) );
799 –
785      
786      if (storageLayout_ & DataStorage::dslAmat) {
787        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 835 | Line 820 | namespace OpenMD {
820  
821   #else
822  
823 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
824 <                             ff_->getAtomType(identsLocal[atom2]) );
823 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
824 >                             ff_->getAtomType(idents[atom2]) );
825  
826      if (storageLayout_ & DataStorage::dslAmat) {
827        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 853 | Line 838 | namespace OpenMD {
838        idat.t2 = &(snap_->atomData.torque[atom2]);
839      }
840  
841 <    if (storageLayout_ & DataStorage::dslDensity) {
841 >    if (storageLayout_ & DataStorage::dslDensity) {    
842        idat.rho1 = &(snap_->atomData.density[atom1]);
843        idat.rho2 = &(snap_->atomData.density[atom2]);
844      }
# Line 874 | Line 859 | namespace OpenMD {
859      }
860  
861   #endif
877 –    return idat;
862    }
863  
864    
865 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
865 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
866   #ifdef IS_MPI
867      pot_row[atom1] += 0.5 *  *(idat.pot);
868      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 886 | Line 870 | namespace OpenMD {
870      atomRowData.force[atom1] += *(idat.f1);
871      atomColData.force[atom2] -= *(idat.f1);
872   #else
873 <    longRangePot_ += *(idat.pot);
874 <    
873 >    pairwisePot += *(idat.pot);
874 >
875      snap_->atomData.force[atom1] += *(idat.f1);
876      snap_->atomData.force[atom2] -= *(idat.f1);
877   #endif
# Line 895 | Line 879 | namespace OpenMD {
879    }
880  
881  
882 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
883 <
884 <    InteractionData idat;
882 >  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
883 >                                              int atom1, int atom2) {
884 >    // Still Missing:: skippedCharge fill must be added to DataStorage
885   #ifdef IS_MPI
886      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
887                               ff_->getAtomType(identsCol[atom2]) );
# Line 911 | Line 895 | namespace OpenMD {
895        idat.t2 = &(atomColData.torque[atom2]);
896      }
897   #else
898 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
899 <                             ff_->getAtomType(identsLocal[atom2]) );
898 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
899 >                             ff_->getAtomType(idents[atom2]) );
900  
901      if (storageLayout_ & DataStorage::dslElectroFrame) {
902        idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
# Line 925 | Line 909 | namespace OpenMD {
909   #endif    
910    }
911  
912 +
913 +  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
914 + #ifdef IS_MPI
915 +    pot_row[atom1] += 0.5 *  *(idat.pot);
916 +    pot_col[atom2] += 0.5 *  *(idat.pot);
917 + #else
918 +    pairwisePot += *(idat.pot);  
919 + #endif
920 +
921 +  }
922 +
923 +
924    /*
925     * buildNeighborList
926     *
# Line 958 | Line 954 | namespace OpenMD {
954      Vector3d rs, scaled, dr;
955      Vector3i whichCell;
956      int cellIndex;
957 +    int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
958 +
959 + #ifdef IS_MPI
960 +    cellListRow_.resize(nCtot);
961 +    cellListCol_.resize(nCtot);
962 + #else
963 +    cellList_.resize(nCtot);
964 + #endif
965  
966   #ifdef IS_MPI
967      for (int i = 0; i < nGroupsInRow_; i++) {
968        rs = cgRowData.position[i];
969 +
970        // scaled positions relative to the box vectors
971        scaled = invHmat * rs;
972 +
973        // wrap the vector back into the unit box by subtracting integer box
974        // numbers
975 <      for (int j = 0; j < 3; j++)
975 >      for (int j = 0; j < 3; j++) {
976          scaled[j] -= roundMe(scaled[j]);
977 +        scaled[j] += 0.5;
978 +      }
979      
980        // find xyz-indices of cell that cutoffGroup is in.
981        whichCell.x() = nCells_.x() * scaled.x();
# Line 976 | Line 984 | namespace OpenMD {
984  
985        // find single index of this cell:
986        cellIndex = Vlinear(whichCell, nCells_);
987 +
988        // add this cutoff group to the list of groups in this cell;
989        cellListRow_[cellIndex].push_back(i);
990      }
991  
992      for (int i = 0; i < nGroupsInCol_; i++) {
993        rs = cgColData.position[i];
994 +
995        // scaled positions relative to the box vectors
996        scaled = invHmat * rs;
997 +
998        // wrap the vector back into the unit box by subtracting integer box
999        // numbers
1000 <      for (int j = 0; j < 3; j++)
1000 >      for (int j = 0; j < 3; j++) {
1001          scaled[j] -= roundMe(scaled[j]);
1002 +        scaled[j] += 0.5;
1003 +      }
1004  
1005        // find xyz-indices of cell that cutoffGroup is in.
1006        whichCell.x() = nCells_.x() * scaled.x();
# Line 996 | Line 1009 | namespace OpenMD {
1009  
1010        // find single index of this cell:
1011        cellIndex = Vlinear(whichCell, nCells_);
1012 +
1013        // add this cutoff group to the list of groups in this cell;
1014        cellListCol_[cellIndex].push_back(i);
1015      }
1016   #else
1017      for (int i = 0; i < nGroups_; i++) {
1018        rs = snap_->cgData.position[i];
1019 +
1020        // scaled positions relative to the box vectors
1021        scaled = invHmat * rs;
1022 +
1023        // wrap the vector back into the unit box by subtracting integer box
1024        // numbers
1025 <      for (int j = 0; j < 3; j++)
1025 >      for (int j = 0; j < 3; j++) {
1026          scaled[j] -= roundMe(scaled[j]);
1027 +        scaled[j] += 0.5;
1028 +      }
1029  
1030        // find xyz-indices of cell that cutoffGroup is in.
1031        whichCell.x() = nCells_.x() * scaled.x();
# Line 1015 | Line 1033 | namespace OpenMD {
1033        whichCell.z() = nCells_.z() * scaled.z();
1034  
1035        // find single index of this cell:
1036 <      cellIndex = Vlinear(whichCell, nCells_);
1036 >      cellIndex = Vlinear(whichCell, nCells_);      
1037 >
1038        // add this cutoff group to the list of groups in this cell;
1039        cellList_[cellIndex].push_back(i);
1040      }
# Line 1073 | Line 1092 | namespace OpenMD {
1092                }
1093              }
1094   #else
1095 +
1096              for (vector<int>::iterator j1 = cellList_[m1].begin();
1097                   j1 != cellList_[m1].end(); ++j1) {
1098                for (vector<int>::iterator j2 = cellList_[m2].begin();
1099                     j2 != cellList_[m2].end(); ++j2) {
1100 <                              
1100 >
1101                  // Always do this if we're in different cells or if
1102                  // we're in the same cell and the global index of the
1103                  // j2 cutoff group is less than the j1 cutoff group
# Line 1097 | Line 1117 | namespace OpenMD {
1117          }
1118        }
1119      }
1120 <
1120 >    
1121      // save the local cutoff group positions for the check that is
1122      // done on each loop:
1123      saved_CG_positions_.clear();
1124      for (int i = 0; i < nGroups_; i++)
1125        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1126 <
1126 >  
1127      return neighborList;
1128    }
1129   } //end namespace OpenMD

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