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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 1592 by gezelter, Tue Jul 12 20:33:14 2011 UTC vs.
Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42   #include "parallel/ForceMatrixDecomposition.hpp"
43   #include "math/SquareMatrix3.hpp"
# Line 47 | Line 48 | namespace OpenMD {
48   using namespace std;
49   namespace OpenMD {
50  
51 +  ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
52 +
53 +    // In a parallel computation, row and colum scans must visit all
54 +    // surrounding cells (not just the 14 upper triangular blocks that
55 +    // are used when the processor can see all pairs)
56 + #ifdef IS_MPI
57 +    cellOffsets_.clear();
58 +    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
59 +    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
60 +    cellOffsets_.push_back( Vector3i( 1,-1,-1) );                          
61 +    cellOffsets_.push_back( Vector3i(-1, 0,-1) );
62 +    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
63 +    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
64 +    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
65 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );      
66 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
68 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
69 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
70 +    cellOffsets_.push_back( Vector3i(-1, 0, 0) );      
71 +    cellOffsets_.push_back( Vector3i( 0, 0, 0) );
72 +    cellOffsets_.push_back( Vector3i( 1, 0, 0) );
73 +    cellOffsets_.push_back( Vector3i(-1, 1, 0) );
74 +    cellOffsets_.push_back( Vector3i( 0, 1, 0) );
75 +    cellOffsets_.push_back( Vector3i( 1, 1, 0) );
76 +    cellOffsets_.push_back( Vector3i(-1,-1, 1) );
77 +    cellOffsets_.push_back( Vector3i( 0,-1, 1) );
78 +    cellOffsets_.push_back( Vector3i( 1,-1, 1) );
79 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
80 +    cellOffsets_.push_back( Vector3i( 0, 0, 1) );
81 +    cellOffsets_.push_back( Vector3i( 1, 0, 1) );
82 +    cellOffsets_.push_back( Vector3i(-1, 1, 1) );
83 +    cellOffsets_.push_back( Vector3i( 0, 1, 1) );
84 +    cellOffsets_.push_back( Vector3i( 1, 1, 1) );
85 + #endif    
86 +  }
87 +
88 +
89    /**
90     * distributeInitialData is essentially a copy of the older fortran
91     * SimulationSetup
92     */
54 –  
93    void ForceMatrixDecomposition::distributeInitialData() {
94      snap_ = sman_->getCurrentSnapshot();
95      storageLayout_ = sman_->getStorageLayout();
# Line 74 | Line 112 | namespace OpenMD {
112  
113   #ifdef IS_MPI
114  
115 <    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
116 <    AtomCommRealRow = new Communicator<Row,RealType>(nLocal_);
79 <    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal_);
80 <    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal_);
81 <    AtomCommPotRow = new Communicator<Row,potVec>(nLocal_);
115 >    MPI::Intracomm row = rowComm.getComm();
116 >    MPI::Intracomm col = colComm.getComm();
117  
118 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
119 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
120 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
121 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
122 <    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
118 >    AtomPlanIntRow = new Plan<int>(row, nLocal_);
119 >    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
120 >    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
121 >    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
122 >    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
123  
124 <    cgCommIntRow = new Communicator<Row,int>(nGroups_);
125 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
126 <    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
127 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
124 >    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
125 >    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
126 >    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
127 >    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
128 >    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
129  
130 <    nAtomsInRow_ = AtomCommIntRow->getSize();
131 <    nAtomsInCol_ = AtomCommIntColumn->getSize();
132 <    nGroupsInRow_ = cgCommIntRow->getSize();
133 <    nGroupsInCol_ = cgCommIntColumn->getSize();
130 >    cgPlanIntRow = new Plan<int>(row, nGroups_);
131 >    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
132 >    cgPlanIntColumn = new Plan<int>(col, nGroups_);
133 >    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
134  
135 +    nAtomsInRow_ = AtomPlanIntRow->getSize();
136 +    nAtomsInCol_ = AtomPlanIntColumn->getSize();
137 +    nGroupsInRow_ = cgPlanIntRow->getSize();
138 +    nGroupsInCol_ = cgPlanIntColumn->getSize();
139 +
140      // Modify the data storage objects with the correct layouts and sizes:
141      atomRowData.resize(nAtomsInRow_);
142      atomRowData.setStorageLayout(storageLayout_);
# Line 109 | Line 150 | namespace OpenMD {
150      identsRow.resize(nAtomsInRow_);
151      identsCol.resize(nAtomsInCol_);
152      
153 <    AtomCommIntRow->gather(idents, identsRow);
154 <    AtomCommIntColumn->gather(idents, identsCol);
153 >    AtomPlanIntRow->gather(idents, identsRow);
154 >    AtomPlanIntColumn->gather(idents, identsCol);
155      
156      // allocate memory for the parallel objects
157      atypesRow.resize(nAtomsInRow_);
# Line 126 | Line 167 | namespace OpenMD {
167  
168      AtomRowToGlobal.resize(nAtomsInRow_);
169      AtomColToGlobal.resize(nAtomsInCol_);
170 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
171 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
172 <    
170 >    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
171 >    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
172 >
173      cgRowToGlobal.resize(nGroupsInRow_);
174      cgColToGlobal.resize(nGroupsInCol_);
175 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
175 >    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176 >    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177  
178      massFactorsRow.resize(nAtomsInRow_);
179      massFactorsCol.resize(nAtomsInCol_);
180 <    AtomCommRealRow->gather(massFactors, massFactorsRow);
181 <    AtomCommRealColumn->gather(massFactors, massFactorsCol);
180 >    AtomPlanRealRow->gather(massFactors, massFactorsRow);
181 >    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
182  
183      groupListRow_.clear();
184      groupListRow_.resize(nGroupsInRow_);
# Line 193 | Line 234 | namespace OpenMD {
234        }      
235      }
236  
237 < #endif
197 <
198 <    // allocate memory for the parallel objects
199 <    atypesLocal.resize(nLocal_);
200 <
201 <    for (int i = 0; i < nLocal_; i++)
202 <      atypesLocal[i] = ff_->getAtomType(idents[i]);
203 <
204 <    groupList_.clear();
205 <    groupList_.resize(nGroups_);
206 <    for (int i = 0; i < nGroups_; i++) {
207 <      int gid = cgLocalToGlobal[i];
208 <      for (int j = 0; j < nLocal_; j++) {
209 <        int aid = AtomLocalToGlobal[j];
210 <        if (globalGroupMembership[aid] == gid) {
211 <          groupList_[i].push_back(j);
212 <        }
213 <      }      
214 <    }
215 <
237 > #else
238      excludesForAtom.clear();
239      excludesForAtom.resize(nLocal_);
240      toposForAtom.clear();
# Line 245 | Line 267 | namespace OpenMD {
267          }
268        }      
269      }
270 <    
270 > #endif
271 >
272 >    // allocate memory for the parallel objects
273 >    atypesLocal.resize(nLocal_);
274 >
275 >    for (int i = 0; i < nLocal_; i++)
276 >      atypesLocal[i] = ff_->getAtomType(idents[i]);
277 >
278 >    groupList_.clear();
279 >    groupList_.resize(nGroups_);
280 >    for (int i = 0; i < nGroups_; i++) {
281 >      int gid = cgLocalToGlobal[i];
282 >      for (int j = 0; j < nLocal_; j++) {
283 >        int aid = AtomLocalToGlobal[j];
284 >        if (globalGroupMembership[aid] == gid) {
285 >          groupList_[i].push_back(j);
286 >        }
287 >      }      
288 >    }
289 >
290 >
291      createGtypeCutoffMap();
292  
293    }
# Line 517 | Line 559 | namespace OpenMD {
559   #ifdef IS_MPI
560      
561      // gather up the atomic positions
562 <    AtomCommVectorRow->gather(snap_->atomData.position,
562 >    AtomPlanVectorRow->gather(snap_->atomData.position,
563                                atomRowData.position);
564 <    AtomCommVectorColumn->gather(snap_->atomData.position,
564 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
565                                   atomColData.position);
566      
567      // gather up the cutoff group positions
568 <    cgCommVectorRow->gather(snap_->cgData.position,
568 >
569 >    cgPlanVectorRow->gather(snap_->cgData.position,
570                              cgRowData.position);
571 <    cgCommVectorColumn->gather(snap_->cgData.position,
571 >
572 >    cgPlanVectorColumn->gather(snap_->cgData.position,
573                                 cgColData.position);
574 +
575      
576      // if needed, gather the atomic rotation matrices
577      if (storageLayout_ & DataStorage::dslAmat) {
578 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
578 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
579                                  atomRowData.aMat);
580 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
580 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
581                                     atomColData.aMat);
582      }
583      
584      // if needed, gather the atomic eletrostatic frames
585      if (storageLayout_ & DataStorage::dslElectroFrame) {
586 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
586 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
587                                  atomRowData.electroFrame);
588 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
588 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
589                                     atomColData.electroFrame);
590      }
591  
# Line 557 | Line 602 | namespace OpenMD {
602      
603      if (storageLayout_ & DataStorage::dslDensity) {
604        
605 <      AtomCommRealRow->scatter(atomRowData.density,
605 >      AtomPlanRealRow->scatter(atomRowData.density,
606                                 snap_->atomData.density);
607        
608        int n = snap_->atomData.density.size();
609        vector<RealType> rho_tmp(n, 0.0);
610 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
610 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
611        for (int i = 0; i < n; i++)
612          snap_->atomData.density[i] += rho_tmp[i];
613      }
# Line 578 | Line 623 | namespace OpenMD {
623      storageLayout_ = sman_->getStorageLayout();
624   #ifdef IS_MPI
625      if (storageLayout_ & DataStorage::dslFunctional) {
626 <      AtomCommRealRow->gather(snap_->atomData.functional,
626 >      AtomPlanRealRow->gather(snap_->atomData.functional,
627                                atomRowData.functional);
628 <      AtomCommRealColumn->gather(snap_->atomData.functional,
628 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
629                                   atomColData.functional);
630      }
631      
632      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
633 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
633 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
634                                atomRowData.functionalDerivative);
635 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
635 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
636                                   atomColData.functionalDerivative);
637      }
638   #endif
# Line 601 | Line 646 | namespace OpenMD {
646      int n = snap_->atomData.force.size();
647      vector<Vector3d> frc_tmp(n, V3Zero);
648      
649 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
649 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
650      for (int i = 0; i < n; i++) {
651        snap_->atomData.force[i] += frc_tmp[i];
652        frc_tmp[i] = 0.0;
653      }
654      
655 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
656 <    for (int i = 0; i < n; i++)
655 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
656 >    for (int i = 0; i < n; i++) {
657        snap_->atomData.force[i] += frc_tmp[i];
658 +    }
659          
660      if (storageLayout_ & DataStorage::dslTorque) {
661  
662        int nt = snap_->atomData.torque.size();
663        vector<Vector3d> trq_tmp(nt, V3Zero);
664  
665 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
665 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
666        for (int i = 0; i < nt; i++) {
667          snap_->atomData.torque[i] += trq_tmp[i];
668          trq_tmp[i] = 0.0;
669        }
670        
671 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
671 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
672        for (int i = 0; i < nt; i++)
673          snap_->atomData.torque[i] += trq_tmp[i];
674      }
# Line 632 | Line 678 | namespace OpenMD {
678        int ns = snap_->atomData.skippedCharge.size();
679        vector<RealType> skch_tmp(ns, 0.0);
680  
681 <      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
681 >      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
682        for (int i = 0; i < ns; i++) {
683          snap_->atomData.skippedCharge[i] += skch_tmp[i];
684          skch_tmp[i] = 0.0;
685        }
686        
687 <      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
688 <      for (int i = 0; i < ns; i++)
687 >      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
688 >      for (int i = 0; i < ns; i++)
689          snap_->atomData.skippedCharge[i] += skch_tmp[i];
690 +            
691      }
692      
693      nLocal_ = snap_->getNumberOfAtoms();
# Line 650 | Line 697 | namespace OpenMD {
697  
698      // scatter/gather pot_row into the members of my column
699            
700 <    AtomCommPotRow->scatter(pot_row, pot_temp);
700 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
701  
702      for (int ii = 0;  ii < pot_temp.size(); ii++ )
703        pairwisePot += pot_temp[ii];
# Line 658 | Line 705 | namespace OpenMD {
705      fill(pot_temp.begin(), pot_temp.end(),
706           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
707        
708 <    AtomCommPotColumn->scatter(pot_col, pot_temp);    
708 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
709      
710      for (int ii = 0;  ii < pot_temp.size(); ii++ )
711        pairwisePot += pot_temp[ii];    
712 +    
713 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
714 +      RealType ploc1 = pairwisePot[ii];
715 +      RealType ploc2 = 0.0;
716 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
717 +      pairwisePot[ii] = ploc2;
718 +    }
719 +
720 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
721 +      RealType ploc1 = embeddingPot[ii];
722 +      RealType ploc2 = 0.0;
723 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
724 +      embeddingPot[ii] = ploc2;
725 +    }
726 +
727   #endif
728  
729    }
# Line 774 | Line 836 | namespace OpenMD {
836     */
837    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
838      int unique_id_1, unique_id_2;
839 <
839 >        
840   #ifdef IS_MPI
841      // in MPI, we have to look up the unique IDs for each atom
842      unique_id_1 = AtomRowToGlobal[atom1];
843      unique_id_2 = AtomColToGlobal[atom2];
844 + #else
845 +    unique_id_1 = AtomLocalToGlobal[atom1];
846 +    unique_id_2 = AtomLocalToGlobal[atom2];
847 + #endif  
848  
783 –    // this situation should only arise in MPI simulations
849      if (unique_id_1 == unique_id_2) return true;
850 <    
850 >
851 > #ifdef IS_MPI
852      // this prevents us from doing the pair on multiple processors
853      if (unique_id_1 < unique_id_2) {
854        if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
855      } else {
856 <      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
856 >      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
857      }
858   #endif
859 +    
860      return false;
861    }
862  
# Line 803 | Line 870 | namespace OpenMD {
870     * field) must still be handled for these pairs.
871     */
872    bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
873 <    int unique_id_2;
874 <    
875 < #ifdef IS_MPI
809 <    // in MPI, we have to look up the unique IDs for the row atom.
810 <    unique_id_2 = AtomColToGlobal[atom2];
811 < #else
812 <    // in the normal loop, the atom numbers are unique
813 <    unique_id_2 = atom2;
814 < #endif
873 >
874 >    // excludesForAtom was constructed to use row/column indices in the MPI
875 >    // version, and to use local IDs in the non-MPI version:
876      
877      for (vector<int>::iterator i = excludesForAtom[atom1].begin();
878           i != excludesForAtom[atom1].end(); ++i) {
879 <      if ( (*i) == unique_id_2 ) return true;
879 >      if ( (*i) == atom2 ) return true;
880      }
881  
882      return false;
# Line 1031 | Line 1092 | namespace OpenMD {
1092          // add this cutoff group to the list of groups in this cell;
1093          cellListRow_[cellIndex].push_back(i);
1094        }
1034 –      
1095        for (int i = 0; i < nGroupsInCol_; i++) {
1096          rs = cgColData.position[i];
1097          
# Line 1056 | Line 1116 | namespace OpenMD {
1116          // add this cutoff group to the list of groups in this cell;
1117          cellListCol_[cellIndex].push_back(i);
1118        }
1119 +    
1120   #else
1121        for (int i = 0; i < nGroups_; i++) {
1122          rs = snap_->cgData.position[i];
# Line 1076 | Line 1137 | namespace OpenMD {
1137          whichCell.z() = nCells_.z() * scaled.z();
1138          
1139          // find single index of this cell:
1140 <        cellIndex = Vlinear(whichCell, nCells_);      
1140 >        cellIndex = Vlinear(whichCell, nCells_);
1141          
1142          // add this cutoff group to the list of groups in this cell;
1143          cellList_[cellIndex].push_back(i);
1144        }
1145 +
1146   #endif
1147  
1148        for (int m1z = 0; m1z < nCells_.z(); m1z++) {
# Line 1093 | Line 1155 | namespace OpenMD {
1155                   os != cellOffsets_.end(); ++os) {
1156                
1157                Vector3i m2v = m1v + (*os);
1158 <              
1158 >            
1159 >
1160                if (m2v.x() >= nCells_.x()) {
1161                  m2v.x() = 0;          
1162                } else if (m2v.x() < 0) {
# Line 1111 | Line 1174 | namespace OpenMD {
1174                } else if (m2v.z() < 0) {
1175                  m2v.z() = nCells_.z() - 1;
1176                }
1177 <              
1177 >
1178                int m2 = Vlinear (m2v, nCells_);
1179                
1180   #ifdef IS_MPI
# Line 1120 | Line 1183 | namespace OpenMD {
1183                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1184                       j2 != cellListCol_[m2].end(); ++j2) {
1185                    
1186 <                  // Always do this if we're in different cells or if
1187 <                  // we're in the same cell and the global index of the
1188 <                  // j2 cutoff group is less than the j1 cutoff group
1189 <                  
1190 <                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1191 <                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1192 <                    snap_->wrapVector(dr);
1193 <                    cuts = getGroupCutoffs( (*j1), (*j2) );
1194 <                    if (dr.lengthSquare() < cuts.third) {
1132 <                      neighborList.push_back(make_pair((*j1), (*j2)));
1133 <                    }
1134 <                  }
1186 >                  // In parallel, we need to visit *all* pairs of row
1187 >                  // & column indicies and will divide labor in the
1188 >                  // force evaluation later.
1189 >                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1190 >                  snap_->wrapVector(dr);
1191 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1192 >                  if (dr.lengthSquare() < cuts.third) {
1193 >                    neighborList.push_back(make_pair((*j1), (*j2)));
1194 >                  }                  
1195                  }
1196                }
1197   #else
1138 –              
1198                for (vector<int>::iterator j1 = cellList_[m1].begin();
1199                     j1 != cellList_[m1].end(); ++j1) {
1200                  for (vector<int>::iterator j2 = cellList_[m2].begin();
1201                       j2 != cellList_[m2].end(); ++j2) {
1202 <                  
1202 >    
1203                    // Always do this if we're in different cells or if
1204 <                  // we're in the same cell and the global index of the
1205 <                  // j2 cutoff group is less than the j1 cutoff group
1206 <                  
1207 <                  if (m2 != m1 || (*j2) < (*j1)) {
1204 >                  // we're in the same cell and the global index of
1205 >                  // the j2 cutoff group is greater than or equal to
1206 >                  // the j1 cutoff group.  Note that Rappaport's code
1207 >                  // has a "less than" conditional here, but that
1208 >                  // deals with atom-by-atom computation.  OpenMD
1209 >                  // allows atoms within a single cutoff group to
1210 >                  // interact with each other.
1211 >
1212 >
1213 >
1214 >                  if (m2 != m1 || (*j2) >= (*j1) ) {
1215 >
1216                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1217                      snap_->wrapVector(dr);
1218                      cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1164 | Line 1231 | namespace OpenMD {
1231        // branch to do all cutoff group pairs
1232   #ifdef IS_MPI
1233        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1234 <        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1234 >        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1235            dr = cgColData.position[j2] - cgRowData.position[j1];
1236            snap_->wrapVector(dr);
1237            cuts = getGroupCutoffs( j1, j2 );
# Line 1172 | Line 1239 | namespace OpenMD {
1239              neighborList.push_back(make_pair(j1, j2));
1240            }
1241          }
1242 <      }
1242 >      }      
1243   #else
1244 <      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1245 <        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1244 >      // include all groups here.
1245 >      for (int j1 = 0; j1 < nGroups_; j1++) {
1246 >        // include self group interactions j2 == j1
1247 >        for (int j2 = j1; j2 < nGroups_; j2++) {
1248            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1249            snap_->wrapVector(dr);
1250            cuts = getGroupCutoffs( j1, j2 );
1251            if (dr.lengthSquare() < cuts.third) {
1252              neighborList.push_back(make_pair(j1, j2));
1253            }
1254 <        }
1255 <      }        
1254 >        }    
1255 >      }
1256   #endif
1257      }
1258        

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