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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 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC vs.
Revision 1589 by gezelter, Sun Jul 10 16:05:34 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      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 111 | Line 112 | namespace OpenMD {
112      AtomCommIntRow->gather(idents, identsRow);
113      AtomCommIntColumn->gather(idents, identsCol);
114      
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      
# Line 142 | Line 153 | namespace OpenMD {
153        }      
154      }
155  
156 <    skipsForAtom.clear();
157 <    skipsForAtom.resize(nAtomsInRow_);
156 >    excludesForAtom.clear();
157 >    excludesForAtom.resize(nAtomsInRow_);
158      toposForAtom.clear();
159      toposForAtom.resize(nAtomsInRow_);
160      topoDist.clear();
# Line 154 | Line 165 | namespace OpenMD {
165        for (int j = 0; j < nAtomsInCol_; j++) {
166          int jglob = AtomColToGlobal[j];
167  
168 <        if (excludes.hasPair(iglob, jglob))
169 <          skipsForAtom[i].push_back(j);      
168 >        if (excludes->hasPair(iglob, jglob))
169 >          excludesForAtom[i].push_back(j);      
170          
171 <        if (oneTwo.hasPair(iglob, jglob)) {
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)) {
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)) {
179 >            if (oneFour->hasPair(iglob, jglob)) {
180                toposForAtom[i].push_back(j);
181                topoDist[i].push_back(3);
182              }
# Line 188 | Line 199 | namespace OpenMD {
199        }      
200      }
201  
202 <    skipsForAtom.clear();
203 <    skipsForAtom.resize(nLocal_);
202 >    excludesForAtom.clear();
203 >    excludesForAtom.resize(nLocal_);
204      toposForAtom.clear();
205      toposForAtom.resize(nLocal_);
206      topoDist.clear();
# Line 201 | Line 212 | namespace OpenMD {
212        for (int j = 0; j < nLocal_; j++) {
213          int jglob = AtomLocalToGlobal[j];
214  
215 <        if (excludes.hasPair(iglob, jglob))
216 <          skipsForAtom[i].push_back(j);              
215 >        if (excludes->hasPair(iglob, jglob))
216 >          excludesForAtom[i].push_back(j);              
217          
218 <        if (oneTwo.hasPair(iglob, jglob)) {
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)) {
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)) {
226 >            if (oneFour->hasPair(iglob, jglob)) {
227                toposForAtom[i].push_back(j);
228                topoDist[i].push_back(3);
229              }
# Line 222 | Line 233 | namespace OpenMD {
233      }
234      
235      createGtypeCutoffMap();
236 +
237    }
238    
239    void ForceMatrixDecomposition::createGtypeCutoffMap() {
240 <
240 >    
241      RealType tol = 1e-6;
242      RealType rc;
243      int atid;
244      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
245 <    vector<RealType> atypeCutoff;
234 <    atypeCutoff.resize( atypes.size() );
245 >    map<int, RealType> atypeCutoff;
246        
247      for (set<AtomType*>::iterator at = atypes.begin();
248           at != atypes.end(); ++at){
249        atid = (*at)->getIdent();
250 <
240 <      if (userChoseCutoff_)
250 >      if (userChoseCutoff_)
251          atypeCutoff[atid] = userCutoff_;
252 <      else
252 >      else
253          atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
254      }
255  
256      vector<RealType> gTypeCutoffs;
247 –
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
# Line 302 | Line 311 | namespace OpenMD {
311  
312      vector<RealType> groupCutoff(nGroups_, 0.0);
313      groupToGtype.resize(nGroups_);
305 –
306 –    cerr << "nGroups = " << nGroups_ << "\n";
314      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
315  
316        groupCutoff[cg1] = 0.0;
# Line 332 | Line 339 | namespace OpenMD {
339      }
340   #endif
341  
335 –    cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n";
342      // Now we find the maximum group cutoff value present in the simulation
343  
344      RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
# Line 453 | Line 459 | namespace OpenMD {
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
# Line 474 | Line 487 | namespace OpenMD {
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    }
# Line 581 | 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();
# Line 716 | Line 749 | namespace OpenMD {
749      return d;    
750    }
751  
752 <  vector<int> ForceMatrixDecomposition::getSkipsForAtom(int atom1) {
753 <    return skipsForAtom[atom1];
752 >  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
753 >    return excludesForAtom[atom1];
754    }
755  
756    /**
757 <   * There are a number of reasons to skip a pair or a
725 <   * particle. Mostly we do this to exclude atoms who are involved in
726 <   * short range interactions (bonds, bends, torsions), but we also
727 <   * need to exclude some overcounted interactions that result from
757 >   * We need to exclude some overcounted interactions that result from
758     * the parallel decomposition.
759     */
760    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
# Line 744 | Line 774 | namespace OpenMD {
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
749 –    unique_id_1 = atom1;
798      unique_id_2 = atom2;
799   #endif
800      
801 <    for (vector<int>::iterator i = skipsForAtom[atom1].begin();
802 <         i != skipsForAtom[atom1].end(); ++i) {
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  
# Line 777 | Line 825 | namespace OpenMD {
825  
826      // filling interaction blocks with pointers
827    void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
828 <                                                     int atom1, int atom2) {    
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]),
# Line 818 | Line 869 | namespace OpenMD {
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]),
# Line 858 | Line 914 | namespace OpenMD {
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
922    }
923  
# Line 875 | Line 935 | namespace OpenMD {
935      snap_->atomData.force[atom1] += *(idat.f1);
936      snap_->atomData.force[atom2] -= *(idat.f1);
937   #endif
938 <
938 >    
939    }
940  
881 –
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]) );
888 –
889 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
890 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
891 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
892 –    }
893 –    if (storageLayout_ & DataStorage::dslTorque) {
894 –      idat.t1 = &(atomRowData.torque[atom1]);
895 –      idat.t2 = &(atomColData.torque[atom2]);
896 –    }
897 – #else
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]);
903 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
904 –    }
905 –    if (storageLayout_ & DataStorage::dslTorque) {
906 –      idat.t1 = &(snap_->atomData.torque[atom1]);
907 –      idat.t2 = &(snap_->atomData.torque[atom2]);
908 –    }
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 –
941    /*
942     * buildNeighborList
943     *
# Line 931 | Line 948 | namespace OpenMD {
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();
# Line 950 | Line 969 | namespace OpenMD {
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;
# Line 963 | Line 988 | namespace OpenMD {
988      cellList_.resize(nCtot);
989   #endif
990  
991 +    if (!doAllPairs) {
992   #ifdef IS_MPI
967 –    for (int i = 0; i < nGroupsInRow_; i++) {
968 –      rs = cgRowData.position[i];
993  
994 <      // scaled positions relative to the box vectors
995 <      scaled = invHmat * rs;
996 <
997 <      // wrap the vector back into the unit box by subtracting integer box
998 <      // numbers
999 <      for (int j = 0; j < 3; j++) {
1000 <        scaled[j] -= roundMe(scaled[j]);
1001 <        scaled[j] += 0.5;
1002 <      }
1003 <    
1004 <      // find xyz-indices of cell that cutoffGroup is in.
1005 <      whichCell.x() = nCells_.x() * scaled.x();
1006 <      whichCell.y() = nCells_.y() * scaled.y();
1007 <      whichCell.z() = nCells_.z() * scaled.z();
1008 <
1009 <      // find single index of this cell:
1010 <      cellIndex = Vlinear(whichCell, nCells_);
1011 <
1012 <      // add this cutoff group to the list of groups in this cell;
1013 <      cellListRow_[cellIndex].push_back(i);
1014 <    }
1015 <
1016 <    for (int i = 0; i < nGroupsInCol_; i++) {
1017 <      rs = cgColData.position[i];
1018 <
1019 <      // scaled positions relative to the box vectors
1020 <      scaled = invHmat * rs;
1021 <
1022 <      // wrap the vector back into the unit box by subtracting integer box
1023 <      // numbers
1024 <      for (int j = 0; j < 3; j++) {
1025 <        scaled[j] -= roundMe(scaled[j]);
1026 <        scaled[j] += 0.5;
1027 <      }
1028 <
1029 <      // find xyz-indices of cell that cutoffGroup is in.
1030 <      whichCell.x() = nCells_.x() * scaled.x();
1031 <      whichCell.y() = nCells_.y() * scaled.y();
1032 <      whichCell.z() = nCells_.z() * scaled.z();
1033 <
1034 <      // find single index of this cell:
1035 <      cellIndex = Vlinear(whichCell, nCells_);
1036 <
1037 <      // add this cutoff group to the list of groups in this cell;
1038 <      cellListCol_[cellIndex].push_back(i);
1039 <    }
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 <
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;
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        }
1029 –
1030 –      // find xyz-indices of cell that cutoffGroup is in.
1031 –      whichCell.x() = nCells_.x() * scaled.x();
1032 –      whichCell.y() = nCells_.y() * scaled.y();
1033 –      whichCell.z() = nCells_.z() * scaled.z();
1034 –
1035 –      // find single index of this cell:
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 –    }
1068   #endif
1069  
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_);
1048 <
1049 <          for (vector<Vector3i>::iterator os = cellOffsets_.begin();
1050 <               os != cellOffsets_.end(); ++os) {
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 <            Vector3i m2v = m1v + (*os);
1077 <            
1078 <            if (m2v.x() >= nCells_.x()) {
1079 <              m2v.x() = 0;          
1080 <            } else if (m2v.x() < 0) {
1081 <              m2v.x() = nCells_.x() - 1;
1082 <            }
1083 <            
1084 <            if (m2v.y() >= nCells_.y()) {
1085 <              m2v.y() = 0;          
1086 <            } else if (m2v.y() < 0) {
1087 <              m2v.y() = nCells_.y() - 1;
1088 <            }
1089 <            
1090 <            if (m2v.z() >= nCells_.z()) {
1091 <              m2v.z() = 0;          
1092 <            } else if (m2v.z() < 0) {
1093 <              m2v.z() = nCells_.z() - 1;
1094 <            }
1095 <            
1096 <            int m2 = Vlinear (m2v, nCells_);
1097 <
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 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1115 <                  if (dr.lengthSquare() < cuts.third) {
1116 <                    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                }
1093 –            }
1121   #else
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)));
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                }
1114 –            }
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 <    
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 <  
1179 >    
1180      return neighborList;
1181    }
1182   } //end namespace OpenMD

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