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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 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC vs.
Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC

# Line 57 | Line 57 | namespace OpenMD {
57      storageLayout_ = sman_->getStorageLayout();
58      ff_ = info_->getForceField();
59      nLocal_ = snap_->getNumberOfAtoms();
60 <
60 >    
61      nGroups_ = info_->getNLocalCutoffGroups();
62 –    cerr << "in dId, nGroups = " << nGroups_ << "\n";
62      // gather the information for atomtype IDs (atids):
63 <    identsLocal = info_->getIdentArray();
63 >    idents = info_->getIdentArray();
64      AtomLocalToGlobal = info_->getGlobalAtomIndices();
65      cgLocalToGlobal = info_->getGlobalGroupIndices();
66      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
67 +
68      massFactors = info_->getMassFactors();
69 –    PairList excludes = info_->getExcludedInteractions();
70 –    PairList oneTwo = info_->getOneTwoInteractions();
71 –    PairList oneThree = info_->getOneThreeInteractions();
72 –    PairList oneFour = info_->getOneFourInteractions();
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_);
# Line 108 | Line 109 | namespace OpenMD {
109      identsRow.resize(nAtomsInRow_);
110      identsCol.resize(nAtomsInCol_);
111      
112 <    AtomCommIntRow->gather(identsLocal, identsRow);
113 <    AtomCommIntColumn->gather(identsLocal, identsCol);
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
115      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
# Line 142 | Line 143 | namespace OpenMD {
143        }      
144      }
145  
146 <    skipsForAtom.clear();
147 <    skipsForAtom.resize(nAtomsInRow_);
146 >    excludesForAtom.clear();
147 >    excludesForAtom.resize(nAtomsInRow_);
148      toposForAtom.clear();
149      toposForAtom.resize(nAtomsInRow_);
150      topoDist.clear();
# Line 154 | Line 155 | namespace OpenMD {
155        for (int j = 0; j < nAtomsInCol_; j++) {
156          int jglob = AtomColToGlobal[j];
157  
158 <        if (excludes.hasPair(iglob, jglob))
159 <          skipsForAtom[i].push_back(j);      
158 >        if (excludes->hasPair(iglob, jglob))
159 >          excludesForAtom[i].push_back(j);      
160          
161 <        if (oneTwo.hasPair(iglob, jglob)) {
161 >        if (oneTwo->hasPair(iglob, jglob)) {
162            toposForAtom[i].push_back(j);
163            topoDist[i].push_back(1);
164          } else {
165 <          if (oneThree.hasPair(iglob, jglob)) {
165 >          if (oneThree->hasPair(iglob, jglob)) {
166              toposForAtom[i].push_back(j);
167              topoDist[i].push_back(2);
168            } else {
169 <            if (oneFour.hasPair(iglob, jglob)) {
169 >            if (oneFour->hasPair(iglob, jglob)) {
170                toposForAtom[i].push_back(j);
171                topoDist[i].push_back(3);
172              }
# Line 188 | Line 189 | namespace OpenMD {
189        }      
190      }
191  
192 <    skipsForAtom.clear();
193 <    skipsForAtom.resize(nLocal_);
192 >    excludesForAtom.clear();
193 >    excludesForAtom.resize(nLocal_);
194      toposForAtom.clear();
195      toposForAtom.resize(nLocal_);
196      topoDist.clear();
# Line 201 | Line 202 | namespace OpenMD {
202        for (int j = 0; j < nLocal_; j++) {
203          int jglob = AtomLocalToGlobal[j];
204  
205 <        if (excludes.hasPair(iglob, jglob))
206 <          skipsForAtom[i].push_back(j);              
205 >        if (excludes->hasPair(iglob, jglob))
206 >          excludesForAtom[i].push_back(j);              
207          
208 <        if (oneTwo.hasPair(iglob, jglob)) {
208 >        if (oneTwo->hasPair(iglob, jglob)) {
209            toposForAtom[i].push_back(j);
210            topoDist[i].push_back(1);
211          } else {
212 <          if (oneThree.hasPair(iglob, jglob)) {
212 >          if (oneThree->hasPair(iglob, jglob)) {
213              toposForAtom[i].push_back(j);
214              topoDist[i].push_back(2);
215            } else {
216 <            if (oneFour.hasPair(iglob, jglob)) {
216 >            if (oneFour->hasPair(iglob, jglob)) {
217                toposForAtom[i].push_back(j);
218                topoDist[i].push_back(3);
219              }
# Line 222 | Line 223 | namespace OpenMD {
223      }
224      
225      createGtypeCutoffMap();
226 +
227    }
228    
229    void ForceMatrixDecomposition::createGtypeCutoffMap() {
230 <
230 >    
231      RealType tol = 1e-6;
232      RealType rc;
233      int atid;
234      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
235 <    vector<RealType> atypeCutoff;
236 <    atypeCutoff.resize( atypes.size() );
235 <
235 >    map<int, RealType> atypeCutoff;
236 >      
237      for (set<AtomType*>::iterator at = atypes.begin();
238           at != atypes.end(); ++at){
238 –      rc = interactionMan_->getSuggestedCutoffRadius(*at);
239        atid = (*at)->getIdent();
240 <      atypeCutoff[atid] = rc;
240 >      if (userChoseCutoff_)
241 >        atypeCutoff[atid] = userCutoff_;
242 >      else
243 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
244      }
245  
246      vector<RealType> gTypeCutoffs;
244 –
247      // first we do a single loop over the cutoff groups to find the
248      // largest cutoff for any atypes present in this group.
249   #ifdef IS_MPI
# Line 299 | Line 301 | namespace OpenMD {
301  
302      vector<RealType> groupCutoff(nGroups_, 0.0);
303      groupToGtype.resize(nGroups_);
302 –
303 –    cerr << "nGroups = " << nGroups_ << "\n";
304      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
305  
306        groupCutoff[cg1] = 0.0;
# Line 309 | Line 309 | namespace OpenMD {
309        for (vector<int>::iterator ia = atomList.begin();
310             ia != atomList.end(); ++ia) {            
311          int atom1 = (*ia);
312 <        atid = identsLocal[atom1];
312 >        atid = idents[atom1];
313          if (atypeCutoff[atid] > groupCutoff[cg1]) {
314            groupCutoff[cg1] = atypeCutoff[atid];
315          }
# Line 329 | Line 329 | namespace OpenMD {
329      }
330   #endif
331  
332 –    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
332      // Now we find the maximum group cutoff value present in the simulation
333  
334      RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
# Line 378 | Line 377 | namespace OpenMD {
377            if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
378              sprintf(painCave.errMsg,
379                      "ForceMatrixDecomposition::createGtypeCutoffMap "
380 <                    "user-specified rCut does not match computed group Cutoff\n");
380 >                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
381              painCave.severity = OPENMD_ERROR;
382              painCave.isFatal = 1;
383              simError();            
# Line 410 | Line 409 | namespace OpenMD {
409    }
410  
411    void ForceMatrixDecomposition::zeroWorkArrays() {
412 <
413 <    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
415 <      longRangePot_[j] = 0.0;
416 <    }
412 >    pairwisePot = 0.0;
413 >    embeddingPot = 0.0;
414  
415   #ifdef IS_MPI
416      if (storageLayout_ & DataStorage::dslForce) {
# Line 430 | Line 427 | namespace OpenMD {
427           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
428  
429      fill(pot_col.begin(), pot_col.end(),
430 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434 <    
435 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
430 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
431  
432      if (storageLayout_ & DataStorage::dslParticlePot) {    
433        fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
# Line 456 | Line 451 | namespace OpenMD {
451             atomColData.functionalDerivative.end(), 0.0);
452      }
453  
454 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
455 +      fill(atomRowData.skippedCharge.begin(),
456 +           atomRowData.skippedCharge.end(), 0.0);
457 +      fill(atomColData.skippedCharge.begin(),
458 +           atomColData.skippedCharge.end(), 0.0);
459 +    }
460 +
461   #else
462      
463      if (storageLayout_ & DataStorage::dslParticlePot) {      
# Line 475 | Line 477 | namespace OpenMD {
477        fill(snap_->atomData.functionalDerivative.begin(),
478             snap_->atomData.functionalDerivative.end(), 0.0);
479      }
480 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {      
481 +      fill(snap_->atomData.skippedCharge.begin(),
482 +           snap_->atomData.skippedCharge.end(), 0.0);
483 +    }
484   #endif
485      
486    }
# Line 582 | Line 588 | namespace OpenMD {
588      
589      if (storageLayout_ & DataStorage::dslTorque) {
590  
591 <      int nt = snap_->atomData.force.size();
591 >      int nt = snap_->atomData.torque.size();
592        vector<Vector3d> trq_tmp(nt, V3Zero);
593  
594        AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
595 <      for (int i = 0; i < n; i++) {
595 >      for (int i = 0; i < nt; i++) {
596          snap_->atomData.torque[i] += trq_tmp[i];
597          trq_tmp[i] = 0.0;
598        }
599        
600        AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
601 <      for (int i = 0; i < n; i++)
601 >      for (int i = 0; i < nt; i++)
602          snap_->atomData.torque[i] += trq_tmp[i];
603      }
604 +
605 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
606 +
607 +      int ns = snap_->atomData.skippedCharge.size();
608 +      vector<RealType> skch_tmp(ns, 0.0);
609 +
610 +      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
611 +      for (int i = 0; i < ns; i++) {
612 +        snap_->atomData.skippedCharge[i] = skch_tmp[i];
613 +        skch_tmp[i] = 0.0;
614 +      }
615 +      
616 +      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
617 +      for (int i = 0; i < ns; i++)
618 +        snap_->atomData.skippedCharge[i] += skch_tmp[i];
619 +    }
620      
621      nLocal_ = snap_->getNumberOfAtoms();
622  
# Line 606 | Line 628 | namespace OpenMD {
628      AtomCommPotRow->scatter(pot_row, pot_temp);
629  
630      for (int ii = 0;  ii < pot_temp.size(); ii++ )
631 <      pot_local += pot_temp[ii];
631 >      pairwisePot += pot_temp[ii];
632      
633      fill(pot_temp.begin(), pot_temp.end(),
634           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
# Line 614 | Line 636 | namespace OpenMD {
636      AtomCommPotColumn->scatter(pot_col, pot_temp);    
637      
638      for (int ii = 0;  ii < pot_temp.size(); ii++ )
639 <      pot_local += pot_temp[ii];
618 <    
639 >      pairwisePot += pot_temp[ii];    
640   #endif
641 +
642    }
643  
644    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 717 | Line 739 | namespace OpenMD {
739      return d;    
740    }
741  
742 <  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
743 <    return skipsForAtom[atom1];
742 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
743 >    return excludesForAtom[atom1];
744    }
745  
746    /**
747 <   * There are a number of reasons to skip a pair or a
726 <   * particle. Mostly we do this to exclude atoms who are involved in
727 <   * short range interactions (bonds, bends, torsions), but we also
728 <   * need to exclude some overcounted interactions that result from
747 >   * We need to exclude some overcounted interactions that result from
748     * the parallel decomposition.
749     */
750    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
# Line 745 | Line 764 | namespace OpenMD {
764      } else {
765        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
766      }
767 + #endif
768 +    return false;
769 +  }
770 +
771 +  /**
772 +   * We need to handle the interactions for atoms who are involved in
773 +   * the same rigid body as well as some short range interactions
774 +   * (bonds, bends, torsions) differently from other interactions.
775 +   * We'll still visit the pairwise routines, but with a flag that
776 +   * tells those routines to exclude the pair from direct long range
777 +   * interactions.  Some indirect interactions (notably reaction
778 +   * field) must still be handled for these pairs.
779 +   */
780 +  bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
781 +    int unique_id_2;
782 +    
783 + #ifdef IS_MPI
784 +    // in MPI, we have to look up the unique IDs for the row atom.
785 +    unique_id_2 = AtomColToGlobal[atom2];
786   #else
787      // in the normal loop, the atom numbers are unique
750 –    unique_id_1 = atom1;
788      unique_id_2 = atom2;
789   #endif
790      
791 <    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
792 <         i != skipsForAtom[atom1].end(); ++i) {
791 >    for (vector<int>::iterator i = excludesForAtom[atom1].begin();
792 >         i != excludesForAtom[atom1].end(); ++i) {
793        if ( (*i) == unique_id_2 ) return true;
794 <    }    
794 >    }
795  
796 +    return false;
797    }
798  
799  
# Line 776 | Line 814 | namespace OpenMD {
814    }
815  
816      // filling interaction blocks with pointers
817 <  void ForceMatrixDecomposition::fillInteractionData(InteractionData idat,
818 <                                                     int atom1, int atom2) {    
817 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
818 >                                                     int atom1, int atom2) {
819 >
820 >    idat.excluded = excludeAtomPair(atom1, atom2);
821 >  
822   #ifdef IS_MPI
823      
824      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
# Line 818 | Line 859 | namespace OpenMD {
859        idat.particlePot2 = &(atomColData.particlePot[atom2]);
860      }
861  
862 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {              
863 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
864 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
865 +    }
866 +
867   #else
868  
869 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
870 <                             ff_->getAtomType(identsLocal[atom2]) );
869 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
870 >                             ff_->getAtomType(idents[atom2]) );
871  
872      if (storageLayout_ & DataStorage::dslAmat) {
873        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 838 | Line 884 | namespace OpenMD {
884        idat.t2 = &(snap_->atomData.torque[atom2]);
885      }
886  
887 <    if (storageLayout_ & DataStorage::dslDensity) {
887 >    if (storageLayout_ & DataStorage::dslDensity) {    
888        idat.rho1 = &(snap_->atomData.density[atom1]);
889        idat.rho2 = &(snap_->atomData.density[atom2]);
890      }
# Line 858 | Line 904 | namespace OpenMD {
904        idat.particlePot2 = &(snap_->atomData.particlePot[atom2]);
905      }
906  
907 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
908 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
909 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
910 +    }
911   #endif
912    }
913  
914    
915 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
915 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
916   #ifdef IS_MPI
917      pot_row[atom1] += 0.5 *  *(idat.pot);
918      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 870 | Line 920 | namespace OpenMD {
920      atomRowData.force[atom1] += *(idat.f1);
921      atomColData.force[atom2] -= *(idat.f1);
922   #else
923 <    longRangePot_ += *(idat.pot);
924 <    
923 >    pairwisePot += *(idat.pot);
924 >
925      snap_->atomData.force[atom1] += *(idat.f1);
926      snap_->atomData.force[atom2] -= *(idat.f1);
927   #endif
928 <
928 >    
929    }
930  
881 –
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]) );
887 –
888 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
889 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
890 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
891 –    }
892 –    if (storageLayout_ & DataStorage::dslTorque) {
893 –      idat.t1 = &(atomRowData.torque[atom1]);
894 –      idat.t2 = &(atomColData.torque[atom2]);
895 –    }
896 – #else
897 –    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
898 –                             ff_->getAtomType(identsLocal[atom2]) );
899 –
900 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
901 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
902 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
903 –    }
904 –    if (storageLayout_ & DataStorage::dslTorque) {
905 –      idat.t1 = &(snap_->atomData.torque[atom1]);
906 –      idat.t2 = &(snap_->atomData.torque[atom2]);
907 –    }
908 – #endif    
909 –  }
910 –
931    /*
932     * buildNeighborList
933     *
# Line 918 | Line 938 | namespace OpenMD {
938        
939      vector<pair<int, int> > neighborList;
940      groupCutoffs cuts;
941 +    bool doAllPairs = false;
942 +
943   #ifdef IS_MPI
944      cellListRow_.clear();
945      cellListCol_.clear();
# Line 937 | Line 959 | namespace OpenMD {
959      nCells_.y() = (int) ( Hy.length() )/ rList_;
960      nCells_.z() = (int) ( Hz.length() )/ rList_;
961  
962 +    // handle small boxes where the cell offsets can end up repeating cells
963 +    
964 +    if (nCells_.x() < 3) doAllPairs = true;
965 +    if (nCells_.y() < 3) doAllPairs = true;
966 +    if (nCells_.z() < 3) doAllPairs = true;
967 +
968      Mat3x3d invHmat = snap_->getInvHmat();
969      Vector3d rs, scaled, dr;
970      Vector3i whichCell;
971      int cellIndex;
972      int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
973  
946 –    cerr << "flag1\n";
974   #ifdef IS_MPI
975      cellListRow_.resize(nCtot);
976      cellListCol_.resize(nCtot);
977   #else
978      cellList_.resize(nCtot);
979   #endif
980 <    cerr << "flag2\n";
980 >
981 >    if (!doAllPairs) {
982   #ifdef IS_MPI
955 –    for (int i = 0; i < nGroupsInRow_; i++) {
956 –      rs = cgRowData.position[i];
983  
984 <      // scaled positions relative to the box vectors
985 <      scaled = invHmat * rs;
986 <
987 <      // wrap the vector back into the unit box by subtracting integer box
988 <      // numbers
989 <      for (int j = 0; j < 3; j++) {
990 <        scaled[j] -= roundMe(scaled[j]);
991 <        scaled[j] += 0.5;
992 <      }
993 <    
994 <      // find xyz-indices of cell that cutoffGroup is in.
995 <      whichCell.x() = nCells_.x() * scaled.x();
996 <      whichCell.y() = nCells_.y() * scaled.y();
997 <      whichCell.z() = nCells_.z() * scaled.z();
998 <
999 <      // find single index of this cell:
1000 <      cellIndex = Vlinear(whichCell, nCells_);
1001 <
1002 <      // add this cutoff group to the list of groups in this cell;
1003 <      cellListRow_[cellIndex].push_back(i);
1004 <    }
1005 <
1006 <    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++) {
989 <        scaled[j] -= roundMe(scaled[j]);
990 <        scaled[j] += 0.5;
984 >      for (int i = 0; i < nGroupsInRow_; i++) {
985 >        rs = cgRowData.position[i];
986 >        
987 >        // scaled positions relative to the box vectors
988 >        scaled = invHmat * rs;
989 >        
990 >        // wrap the vector back into the unit box by subtracting integer box
991 >        // numbers
992 >        for (int j = 0; j < 3; j++) {
993 >          scaled[j] -= roundMe(scaled[j]);
994 >          scaled[j] += 0.5;
995 >        }
996 >        
997 >        // find xyz-indices of cell that cutoffGroup is in.
998 >        whichCell.x() = nCells_.x() * scaled.x();
999 >        whichCell.y() = nCells_.y() * scaled.y();
1000 >        whichCell.z() = nCells_.z() * scaled.z();
1001 >        
1002 >        // find single index of this cell:
1003 >        cellIndex = Vlinear(whichCell, nCells_);
1004 >        
1005 >        // add this cutoff group to the list of groups in this cell;
1006 >        cellListRow_[cellIndex].push_back(i);
1007        }
1008 <
1009 <      // find xyz-indices of cell that cutoffGroup is in.
1010 <      whichCell.x() = nCells_.x() * scaled.x();
1011 <      whichCell.y() = nCells_.y() * scaled.y();
1012 <      whichCell.z() = nCells_.z() * scaled.z();
1013 <
1014 <      // find single index of this cell:
1015 <      cellIndex = Vlinear(whichCell, nCells_);
1016 <
1017 <      // add this cutoff group to the list of groups in this cell;
1018 <      cellListCol_[cellIndex].push_back(i);
1019 <    }
1008 >      
1009 >      for (int i = 0; i < nGroupsInCol_; i++) {
1010 >        rs = cgColData.position[i];
1011 >        
1012 >        // scaled positions relative to the box vectors
1013 >        scaled = invHmat * rs;
1014 >        
1015 >        // wrap the vector back into the unit box by subtracting integer box
1016 >        // numbers
1017 >        for (int j = 0; j < 3; j++) {
1018 >          scaled[j] -= roundMe(scaled[j]);
1019 >          scaled[j] += 0.5;
1020 >        }
1021 >        
1022 >        // find xyz-indices of cell that cutoffGroup is in.
1023 >        whichCell.x() = nCells_.x() * scaled.x();
1024 >        whichCell.y() = nCells_.y() * scaled.y();
1025 >        whichCell.z() = nCells_.z() * scaled.z();
1026 >        
1027 >        // find single index of this cell:
1028 >        cellIndex = Vlinear(whichCell, nCells_);
1029 >        
1030 >        // add this cutoff group to the list of groups in this cell;
1031 >        cellListCol_[cellIndex].push_back(i);
1032 >      }
1033   #else
1034 <    for (int i = 0; i < nGroups_; i++) {
1035 <      rs = snap_->cgData.position[i];
1036 <
1037 <      // scaled positions relative to the box vectors
1038 <      scaled = invHmat * rs;
1039 <
1040 <      // wrap the vector back into the unit box by subtracting integer box
1041 <      // numbers
1042 <      for (int j = 0; j < 3; j++) {
1043 <        scaled[j] -= roundMe(scaled[j]);
1044 <        scaled[j] += 0.5;
1034 >      for (int i = 0; i < nGroups_; i++) {
1035 >        rs = snap_->cgData.position[i];
1036 >        
1037 >        // scaled positions relative to the box vectors
1038 >        scaled = invHmat * rs;
1039 >        
1040 >        // wrap the vector back into the unit box by subtracting integer box
1041 >        // numbers
1042 >        for (int j = 0; j < 3; j++) {
1043 >          scaled[j] -= roundMe(scaled[j]);
1044 >          scaled[j] += 0.5;
1045 >        }
1046 >        
1047 >        // find xyz-indices of cell that cutoffGroup is in.
1048 >        whichCell.x() = nCells_.x() * scaled.x();
1049 >        whichCell.y() = nCells_.y() * scaled.y();
1050 >        whichCell.z() = nCells_.z() * scaled.z();
1051 >        
1052 >        // find single index of this cell:
1053 >        cellIndex = Vlinear(whichCell, nCells_);      
1054 >        
1055 >        // add this cutoff group to the list of groups in this cell;
1056 >        cellList_[cellIndex].push_back(i);
1057        }
1017 –
1018 –      // find xyz-indices of cell that cutoffGroup is in.
1019 –      whichCell.x() = nCells_.x() * scaled.x();
1020 –      whichCell.y() = nCells_.y() * scaled.y();
1021 –      whichCell.z() = nCells_.z() * scaled.z();
1022 –
1023 –      // find single index of this cell:
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 –    }
1058   #endif
1059  
1060 <    for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1061 <      for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1062 <        for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1063 <          Vector3i m1v(m1x, m1y, m1z);
1064 <          int m1 = Vlinear(m1v, nCells_);
1036 <
1037 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1038 <               os != cellOffsets_.end(); ++os) {
1060 >      for (int m1z = 0; m1z < nCells_.z(); m1z++) {
1061 >        for (int m1y = 0; m1y < nCells_.y(); m1y++) {
1062 >          for (int m1x = 0; m1x < nCells_.x(); m1x++) {
1063 >            Vector3i m1v(m1x, m1y, m1z);
1064 >            int m1 = Vlinear(m1v, nCells_);
1065              
1066 <            Vector3i m2v = m1v + (*os);
1067 <            
1068 <            if (m2v.x() >= nCells_.x()) {
1069 <              m2v.x() = 0;          
1070 <            } else if (m2v.x() < 0) {
1071 <              m2v.x() = nCells_.x() - 1;
1072 <            }
1073 <            
1074 <            if (m2v.y() >= nCells_.y()) {
1075 <              m2v.y() = 0;          
1076 <            } else if (m2v.y() < 0) {
1077 <              m2v.y() = nCells_.y() - 1;
1078 <            }
1079 <            
1080 <            if (m2v.z() >= nCells_.z()) {
1081 <              m2v.z() = 0;          
1082 <            } else if (m2v.z() < 0) {
1083 <              m2v.z() = nCells_.z() - 1;
1084 <            }
1085 <            
1086 <            int m2 = Vlinear (m2v, nCells_);
1087 <
1066 >            for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1067 >                 os != cellOffsets_.end(); ++os) {
1068 >              
1069 >              Vector3i m2v = m1v + (*os);
1070 >              
1071 >              if (m2v.x() >= nCells_.x()) {
1072 >                m2v.x() = 0;          
1073 >              } else if (m2v.x() < 0) {
1074 >                m2v.x() = nCells_.x() - 1;
1075 >              }
1076 >              
1077 >              if (m2v.y() >= nCells_.y()) {
1078 >                m2v.y() = 0;          
1079 >              } else if (m2v.y() < 0) {
1080 >                m2v.y() = nCells_.y() - 1;
1081 >              }
1082 >              
1083 >              if (m2v.z() >= nCells_.z()) {
1084 >                m2v.z() = 0;          
1085 >              } else if (m2v.z() < 0) {
1086 >                m2v.z() = nCells_.z() - 1;
1087 >              }
1088 >              
1089 >              int m2 = Vlinear (m2v, nCells_);
1090 >              
1091   #ifdef IS_MPI
1092 <            for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1093 <                 j1 != cellListRow_[m1].end(); ++j1) {
1094 <              for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1095 <                   j2 != cellListCol_[m2].end(); ++j2) {
1096 <                              
1097 <                // Always do this if we're in different cells or if
1098 <                // we're in the same cell and the global index of the
1099 <                // j2 cutoff group is less than the j1 cutoff group
1100 <
1101 <                if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1102 <                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1103 <                  snap_->wrapVector(dr);
1104 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1105 <                  if (dr.lengthSquare() < cuts.third) {
1106 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1092 >              for (vector<int>::iterator j1 = cellListRow_[m1].begin();
1093 >                   j1 != cellListRow_[m1].end(); ++j1) {
1094 >                for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1095 >                     j2 != cellListCol_[m2].end(); ++j2) {
1096 >                  
1097 >                  // Always do this if we're in different cells or if
1098 >                  // we're in the same cell and the global index of the
1099 >                  // j2 cutoff group is less than the j1 cutoff group
1100 >                  
1101 >                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1102 >                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1103 >                    snap_->wrapVector(dr);
1104 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1105 >                    if (dr.lengthSquare() < cuts.third) {
1106 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1107 >                    }
1108                    }
1109                  }
1110                }
1081 –            }
1111   #else
1112 <
1113 <            for (vector<int>::iterator j1 = cellList_[m1].begin();
1114 <                 j1 != cellList_[m1].end(); ++j1) {
1115 <              for (vector<int>::iterator j2 = cellList_[m2].begin();
1116 <                   j2 != cellList_[m2].end(); ++j2) {
1117 <
1118 <                // Always do this if we're in different cells or if
1119 <                // we're in the same cell and the global index of the
1120 <                // j2 cutoff group is less than the j1 cutoff group
1121 <
1122 <                if (m2 != m1 || (*j2) < (*j1)) {
1123 <                  dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1124 <                  snap_->wrapVector(dr);
1125 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1126 <                  if (dr.lengthSquare() < cuts.third) {
1127 <                    neighborList.push_back(make_pair((*j1), (*j2)));
1112 >              
1113 >              for (vector<int>::iterator j1 = cellList_[m1].begin();
1114 >                   j1 != cellList_[m1].end(); ++j1) {
1115 >                for (vector<int>::iterator j2 = cellList_[m2].begin();
1116 >                     j2 != cellList_[m2].end(); ++j2) {
1117 >                  
1118 >                  // Always do this if we're in different cells or if
1119 >                  // we're in the same cell and the global index of the
1120 >                  // j2 cutoff group is less than the j1 cutoff group
1121 >                  
1122 >                  if (m2 != m1 || (*j2) < (*j1)) {
1123 >                    dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1124 >                    snap_->wrapVector(dr);
1125 >                    cuts = getGroupCutoffs( (*j1), (*j2) );
1126 >                    if (dr.lengthSquare() < cuts.third) {
1127 >                      neighborList.push_back(make_pair((*j1), (*j2)));
1128 >                    }
1129                    }
1130                  }
1131                }
1102 –            }
1132   #endif
1133 +            }
1134            }
1135          }
1136        }
1137 +    } else {
1138 +      // branch to do all cutoff group pairs
1139 + #ifdef IS_MPI
1140 +      for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1141 +        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1142 +          dr = cgColData.position[j2] - cgRowData.position[j1];
1143 +          snap_->wrapVector(dr);
1144 +          cuts = getGroupCutoffs( j1, j2 );
1145 +          if (dr.lengthSquare() < cuts.third) {
1146 +            neighborList.push_back(make_pair(j1, j2));
1147 +          }
1148 +        }
1149 +      }
1150 + #else
1151 +      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1152 +        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1153 +          dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1154 +          snap_->wrapVector(dr);
1155 +          cuts = getGroupCutoffs( j1, j2 );
1156 +          if (dr.lengthSquare() < cuts.third) {
1157 +            neighborList.push_back(make_pair(j1, j2));
1158 +          }
1159 +        }
1160 +      }        
1161 + #endif
1162      }
1163 <    
1163 >      
1164      // save the local cutoff group positions for the check that is
1165      // done on each loop:
1166      saved_CG_positions_.clear();

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