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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 1588 by gezelter, Sat Jul 9 15:05:59 2011 UTC vs.
Revision 1612 by gezelter, Fri Aug 12 19:59:56 2011 UTC

# Line 47 | Line 47 | namespace OpenMD {
47   using namespace std;
48   namespace OpenMD {
49  
50 +  ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {
51 +
52 +    // In a parallel computation, row and colum scans must visit all
53 +    // surrounding cells (not just the 14 upper triangular blocks that
54 +    // are used when the processor can see all pairs)
55 + #ifdef IS_MPI
56 +    cellOffsets_.clear();
57 +    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
58 +    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
59 +    cellOffsets_.push_back( Vector3i( 1,-1,-1) );                          
60 +    cellOffsets_.push_back( Vector3i(-1, 0,-1) );
61 +    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
62 +    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
63 +    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
64 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );      
65 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
66 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
67 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
68 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
69 +    cellOffsets_.push_back( Vector3i(-1, 0, 0) );      
70 +    cellOffsets_.push_back( Vector3i( 0, 0, 0) );
71 +    cellOffsets_.push_back( Vector3i( 1, 0, 0) );
72 +    cellOffsets_.push_back( Vector3i(-1, 1, 0) );
73 +    cellOffsets_.push_back( Vector3i( 0, 1, 0) );
74 +    cellOffsets_.push_back( Vector3i( 1, 1, 0) );
75 +    cellOffsets_.push_back( Vector3i(-1,-1, 1) );
76 +    cellOffsets_.push_back( Vector3i( 0,-1, 1) );
77 +    cellOffsets_.push_back( Vector3i( 1,-1, 1) );
78 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
79 +    cellOffsets_.push_back( Vector3i( 0, 0, 1) );
80 +    cellOffsets_.push_back( Vector3i( 1, 0, 1) );
81 +    cellOffsets_.push_back( Vector3i(-1, 1, 1) );
82 +    cellOffsets_.push_back( Vector3i( 0, 1, 1) );
83 +    cellOffsets_.push_back( Vector3i( 1, 1, 1) );
84 + #endif    
85 +  }
86 +
87 +
88    /**
89     * distributeInitialData is essentially a copy of the older fortran
90     * SimulationSetup
91     */
54 –  
92    void ForceMatrixDecomposition::distributeInitialData() {
93      snap_ = sman_->getCurrentSnapshot();
94      storageLayout_ = sman_->getStorageLayout();
# Line 74 | Line 111 | namespace OpenMD {
111  
112   #ifdef IS_MPI
113  
114 <    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
115 <    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_);
114 >    MPI::Intracomm row = rowComm.getComm();
115 >    MPI::Intracomm col = colComm.getComm();
116  
117 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
118 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
119 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
120 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
121 <    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
117 >    AtomPlanIntRow = new Plan<int>(row, nLocal_);
118 >    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
119 >    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
120 >    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
121 >    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
122  
123 <    cgCommIntRow = new Communicator<Row,int>(nGroups_);
124 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
125 <    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
126 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
123 >    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
124 >    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
125 >    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
126 >    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
127 >    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
128  
129 <    nAtomsInRow_ = AtomCommIntRow->getSize();
130 <    nAtomsInCol_ = AtomCommIntColumn->getSize();
131 <    nGroupsInRow_ = cgCommIntRow->getSize();
132 <    nGroupsInCol_ = cgCommIntColumn->getSize();
129 >    cgPlanIntRow = new Plan<int>(row, nGroups_);
130 >    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
131 >    cgPlanIntColumn = new Plan<int>(col, nGroups_);
132 >    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
133  
134 +    nAtomsInRow_ = AtomPlanIntRow->getSize();
135 +    nAtomsInCol_ = AtomPlanIntColumn->getSize();
136 +    nGroupsInRow_ = cgPlanIntRow->getSize();
137 +    nGroupsInCol_ = cgPlanIntColumn->getSize();
138 +
139      // Modify the data storage objects with the correct layouts and sizes:
140      atomRowData.resize(nAtomsInRow_);
141      atomRowData.setStorageLayout(storageLayout_);
# Line 109 | Line 149 | namespace OpenMD {
149      identsRow.resize(nAtomsInRow_);
150      identsCol.resize(nAtomsInCol_);
151      
152 <    AtomCommIntRow->gather(idents, identsRow);
153 <    AtomCommIntColumn->gather(idents, identsCol);
152 >    AtomPlanIntRow->gather(idents, identsRow);
153 >    AtomPlanIntColumn->gather(idents, identsCol);
154      
155 <    vector<int>::iterator it;
156 <    for (it = AtomLocalToGlobal.begin(); it != AtomLocalToGlobal.end(); ++it) {
157 <      cerr << "my AtomLocalToGlobal = " << (*it) << "\n";
118 <    }
119 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
120 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
121 <    
122 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
123 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
155 >    // allocate memory for the parallel objects
156 >    atypesRow.resize(nAtomsInRow_);
157 >    atypesCol.resize(nAtomsInCol_);
158  
159 <    AtomCommRealRow->gather(massFactors, massFactorsRow);
160 <    AtomCommRealColumn->gather(massFactors, massFactorsCol);
159 >    for (int i = 0; i < nAtomsInRow_; i++)
160 >      atypesRow[i] = ff_->getAtomType(identsRow[i]);
161 >    for (int i = 0; i < nAtomsInCol_; i++)
162 >      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
163  
164 +    pot_row.resize(nAtomsInRow_);
165 +    pot_col.resize(nAtomsInCol_);
166 +
167 +    AtomRowToGlobal.resize(nAtomsInRow_);
168 +    AtomColToGlobal.resize(nAtomsInCol_);
169 +    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
170 +    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
171 +
172 +    cgRowToGlobal.resize(nGroupsInRow_);
173 +    cgColToGlobal.resize(nGroupsInCol_);
174 +    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
175 +    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
176 +
177 +    massFactorsRow.resize(nAtomsInRow_);
178 +    massFactorsCol.resize(nAtomsInCol_);
179 +    AtomPlanRealRow->gather(massFactors, massFactorsRow);
180 +    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
181 +
182      groupListRow_.clear();
183      groupListRow_.resize(nGroupsInRow_);
184      for (int i = 0; i < nGroupsInRow_; i++) {
# Line 181 | Line 235 | namespace OpenMD {
235  
236   #endif
237  
238 +    // allocate memory for the parallel objects
239 +    atypesLocal.resize(nLocal_);
240 +
241 +    for (int i = 0; i < nLocal_; i++)
242 +      atypesLocal[i] = ff_->getAtomType(idents[i]);
243 +
244      groupList_.clear();
245      groupList_.resize(nGroups_);
246      for (int i = 0; i < nGroups_; i++) {
# Line 233 | Line 293 | namespace OpenMD {
293    void ForceMatrixDecomposition::createGtypeCutoffMap() {
294      
295      RealType tol = 1e-6;
296 +    largestRcut_ = 0.0;
297      RealType rc;
298      int atid;
299      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
300 +    
301      map<int, RealType> atypeCutoff;
302        
303      for (set<AtomType*>::iterator at = atypes.begin();
# Line 243 | Line 305 | namespace OpenMD {
305        atid = (*at)->getIdent();
306        if (userChoseCutoff_)
307          atypeCutoff[atid] = userCutoff_;
308 <      else
308 >      else
309          atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
310      }
311 <
311 >    
312      vector<RealType> gTypeCutoffs;
313      // first we do a single loop over the cutoff groups to find the
314      // largest cutoff for any atypes present in this group.
# Line 306 | Line 368 | namespace OpenMD {
368      vector<RealType> groupCutoff(nGroups_, 0.0);
369      groupToGtype.resize(nGroups_);
370      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
309 –
371        groupCutoff[cg1] = 0.0;
372        vector<int> atomList = getAtomsInGroupRow(cg1);
312 –
373        for (vector<int>::iterator ia = atomList.begin();
374             ia != atomList.end(); ++ia) {            
375          int atom1 = (*ia);
376          atid = idents[atom1];
377 <        if (atypeCutoff[atid] > groupCutoff[cg1]) {
377 >        if (atypeCutoff[atid] > groupCutoff[cg1])
378            groupCutoff[cg1] = atypeCutoff[atid];
319 –        }
379        }
380 <
380 >      
381        bool gTypeFound = false;
382        for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
383          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
# Line 326 | Line 385 | namespace OpenMD {
385            gTypeFound = true;
386          }
387        }
388 <      if (!gTypeFound) {
388 >      if (!gTypeFound) {      
389          gTypeCutoffs.push_back( groupCutoff[cg1] );
390          groupToGtype[cg1] = gTypeCutoffs.size() - 1;
391        }      
# Line 335 | Line 394 | namespace OpenMD {
394  
395      // Now we find the maximum group cutoff value present in the simulation
396  
397 <    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
397 >    RealType groupMax = *max_element(gTypeCutoffs.begin(),
398 >                                     gTypeCutoffs.end());
399  
400   #ifdef IS_MPI
401 <    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
401 >    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
402 >                              MPI::MAX);
403   #endif
404      
405      RealType tradRcut = groupMax;
# Line 368 | Line 429 | namespace OpenMD {
429  
430          pair<int,int> key = make_pair(i,j);
431          gTypeCutoffMap[key].first = thisRcut;
371 –
432          if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
373 –
433          gTypeCutoffMap[key].second = thisRcut*thisRcut;
375 –        
434          gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
377 –
435          // sanity check
436          
437          if (userChoseCutoff_) {
# Line 434 | Line 491 | namespace OpenMD {
491           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
492  
493      if (storageLayout_ & DataStorage::dslParticlePot) {    
494 <      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
495 <      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
494 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
495 >           0.0);
496 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
497 >           0.0);
498      }
499  
500      if (storageLayout_ & DataStorage::dslDensity) {      
# Line 444 | Line 503 | namespace OpenMD {
503      }
504  
505      if (storageLayout_ & DataStorage::dslFunctional) {  
506 <      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
507 <      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
506 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
507 >           0.0);
508 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
509 >           0.0);
510      }
511  
512      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
# Line 462 | Line 523 | namespace OpenMD {
523             atomColData.skippedCharge.end(), 0.0);
524      }
525  
526 < #else
527 <    
526 > #endif
527 >    // even in parallel, we need to zero out the local arrays:
528 >
529      if (storageLayout_ & DataStorage::dslParticlePot) {      
530        fill(snap_->atomData.particlePot.begin(),
531             snap_->atomData.particlePot.end(), 0.0);
# Line 485 | Line 547 | namespace OpenMD {
547        fill(snap_->atomData.skippedCharge.begin(),
548             snap_->atomData.skippedCharge.end(), 0.0);
549      }
488 – #endif
550      
551    }
552  
# Line 496 | Line 557 | namespace OpenMD {
557   #ifdef IS_MPI
558      
559      // gather up the atomic positions
560 <    AtomCommVectorRow->gather(snap_->atomData.position,
560 >    AtomPlanVectorRow->gather(snap_->atomData.position,
561                                atomRowData.position);
562 <    AtomCommVectorColumn->gather(snap_->atomData.position,
562 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
563                                   atomColData.position);
564      
565      // gather up the cutoff group positions
566 <    cgCommVectorRow->gather(snap_->cgData.position,
566 >
567 >    cgPlanVectorRow->gather(snap_->cgData.position,
568                              cgRowData.position);
569 <    cgCommVectorColumn->gather(snap_->cgData.position,
569 >
570 >    cgPlanVectorColumn->gather(snap_->cgData.position,
571                                 cgColData.position);
572 +
573      
574      // if needed, gather the atomic rotation matrices
575      if (storageLayout_ & DataStorage::dslAmat) {
576 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
576 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
577                                  atomRowData.aMat);
578 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
578 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
579                                     atomColData.aMat);
580      }
581      
582      // if needed, gather the atomic eletrostatic frames
583      if (storageLayout_ & DataStorage::dslElectroFrame) {
584 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
584 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
585                                  atomRowData.electroFrame);
586 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
586 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
587                                     atomColData.electroFrame);
588      }
589 +
590   #endif      
591    }
592    
# Line 535 | Line 600 | namespace OpenMD {
600      
601      if (storageLayout_ & DataStorage::dslDensity) {
602        
603 <      AtomCommRealRow->scatter(atomRowData.density,
603 >      AtomPlanRealRow->scatter(atomRowData.density,
604                                 snap_->atomData.density);
605        
606        int n = snap_->atomData.density.size();
607        vector<RealType> rho_tmp(n, 0.0);
608 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
608 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
609        for (int i = 0; i < n; i++)
610          snap_->atomData.density[i] += rho_tmp[i];
611      }
# Line 556 | Line 621 | namespace OpenMD {
621      storageLayout_ = sman_->getStorageLayout();
622   #ifdef IS_MPI
623      if (storageLayout_ & DataStorage::dslFunctional) {
624 <      AtomCommRealRow->gather(snap_->atomData.functional,
624 >      AtomPlanRealRow->gather(snap_->atomData.functional,
625                                atomRowData.functional);
626 <      AtomCommRealColumn->gather(snap_->atomData.functional,
626 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
627                                   atomColData.functional);
628      }
629      
630      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
631 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
631 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
632                                atomRowData.functionalDerivative);
633 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
633 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
634                                   atomColData.functionalDerivative);
635      }
636   #endif
# Line 579 | Line 644 | namespace OpenMD {
644      int n = snap_->atomData.force.size();
645      vector<Vector3d> frc_tmp(n, V3Zero);
646      
647 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
647 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
648      for (int i = 0; i < n; i++) {
649        snap_->atomData.force[i] += frc_tmp[i];
650        frc_tmp[i] = 0.0;
651      }
652      
653 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
654 <    for (int i = 0; i < n; i++)
653 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
654 >    for (int i = 0; i < n; i++) {
655        snap_->atomData.force[i] += frc_tmp[i];
656 <    
657 <    
656 >    }
657 >        
658      if (storageLayout_ & DataStorage::dslTorque) {
659  
660        int nt = snap_->atomData.torque.size();
661        vector<Vector3d> trq_tmp(nt, V3Zero);
662  
663 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
663 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
664        for (int i = 0; i < nt; i++) {
665          snap_->atomData.torque[i] += trq_tmp[i];
666          trq_tmp[i] = 0.0;
667        }
668        
669 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
669 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
670        for (int i = 0; i < nt; i++)
671          snap_->atomData.torque[i] += trq_tmp[i];
672      }
# Line 611 | Line 676 | namespace OpenMD {
676        int ns = snap_->atomData.skippedCharge.size();
677        vector<RealType> skch_tmp(ns, 0.0);
678  
679 <      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
679 >      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
680        for (int i = 0; i < ns; i++) {
681 <        snap_->atomData.skippedCharge[i] = skch_tmp[i];
681 >        snap_->atomData.skippedCharge[i] += skch_tmp[i];
682          skch_tmp[i] = 0.0;
683        }
684        
685 <      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
685 >      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
686        for (int i = 0; i < ns; i++)
687          snap_->atomData.skippedCharge[i] += skch_tmp[i];
688      }
# Line 629 | Line 694 | namespace OpenMD {
694  
695      // scatter/gather pot_row into the members of my column
696            
697 <    AtomCommPotRow->scatter(pot_row, pot_temp);
697 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
698  
699      for (int ii = 0;  ii < pot_temp.size(); ii++ )
700        pairwisePot += pot_temp[ii];
# Line 637 | Line 702 | namespace OpenMD {
702      fill(pot_temp.begin(), pot_temp.end(),
703           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
704        
705 <    AtomCommPotColumn->scatter(pot_col, pot_temp);    
705 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
706      
707      for (int ii = 0;  ii < pot_temp.size(); ii++ )
708        pairwisePot += pot_temp[ii];    
709 +    
710 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
711 +      RealType ploc1 = pairwisePot[ii];
712 +      RealType ploc2 = 0.0;
713 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
714 +      pairwisePot[ii] = ploc2;
715 +    }
716 +
717   #endif
718  
719    }
# Line 753 | Line 826 | namespace OpenMD {
826     */
827    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
828      int unique_id_1, unique_id_2;
829 <
829 >    
830   #ifdef IS_MPI
831      // in MPI, we have to look up the unique IDs for each atom
832      unique_id_1 = AtomRowToGlobal[atom1];
# Line 783 | Line 856 | namespace OpenMD {
856     */
857    bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
858      int unique_id_2;
786 –    
859   #ifdef IS_MPI
860      // in MPI, we have to look up the unique IDs for the row atom.
861      unique_id_2 = AtomColToGlobal[atom2];
# Line 824 | Line 896 | namespace OpenMD {
896      idat.excluded = excludeAtomPair(atom1, atom2);
897    
898   #ifdef IS_MPI
899 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
900 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
901 +    //                         ff_->getAtomType(identsCol[atom2]) );
902      
828 –    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
829 –                             ff_->getAtomType(identsCol[atom2]) );
830 –    
903      if (storageLayout_ & DataStorage::dslAmat) {
904        idat.A1 = &(atomRowData.aMat[atom1]);
905        idat.A2 = &(atomColData.aMat[atom2]);
# Line 870 | Line 942 | namespace OpenMD {
942  
943   #else
944  
945 <    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
946 <                             ff_->getAtomType(idents[atom2]) );
945 >    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
946 >    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
947 >    //                         ff_->getAtomType(idents[atom2]) );
948  
949      if (storageLayout_ & DataStorage::dslAmat) {
950        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 1009 | Line 1082 | namespace OpenMD {
1082          // add this cutoff group to the list of groups in this cell;
1083          cellListRow_[cellIndex].push_back(i);
1084        }
1012 –      
1085        for (int i = 0; i < nGroupsInCol_; i++) {
1086          rs = cgColData.position[i];
1087          
# Line 1034 | Line 1106 | namespace OpenMD {
1106          // add this cutoff group to the list of groups in this cell;
1107          cellListCol_[cellIndex].push_back(i);
1108        }
1109 +    
1110   #else
1111        for (int i = 0; i < nGroups_; i++) {
1112          rs = snap_->cgData.position[i];
# Line 1054 | Line 1127 | namespace OpenMD {
1127          whichCell.z() = nCells_.z() * scaled.z();
1128          
1129          // find single index of this cell:
1130 <        cellIndex = Vlinear(whichCell, nCells_);      
1130 >        cellIndex = Vlinear(whichCell, nCells_);
1131          
1132          // add this cutoff group to the list of groups in this cell;
1133          cellList_[cellIndex].push_back(i);
1134        }
1135 +
1136   #endif
1137  
1138        for (int m1z = 0; m1z < nCells_.z(); m1z++) {
# Line 1071 | Line 1145 | namespace OpenMD {
1145                   os != cellOffsets_.end(); ++os) {
1146                
1147                Vector3i m2v = m1v + (*os);
1148 <              
1148 >            
1149 >
1150                if (m2v.x() >= nCells_.x()) {
1151                  m2v.x() = 0;          
1152                } else if (m2v.x() < 0) {
# Line 1089 | Line 1164 | namespace OpenMD {
1164                } else if (m2v.z() < 0) {
1165                  m2v.z() = nCells_.z() - 1;
1166                }
1167 <              
1167 >
1168                int m2 = Vlinear (m2v, nCells_);
1169                
1170   #ifdef IS_MPI
# Line 1098 | Line 1173 | namespace OpenMD {
1173                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1174                       j2 != cellListCol_[m2].end(); ++j2) {
1175                    
1176 <                  // Always do this if we're in different cells or if
1177 <                  // we're in the same cell and the global index of the
1178 <                  // j2 cutoff group is less than the j1 cutoff group
1179 <                  
1180 <                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1181 <                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1182 <                    snap_->wrapVector(dr);
1183 <                    cuts = getGroupCutoffs( (*j1), (*j2) );
1184 <                    if (dr.lengthSquare() < cuts.third) {
1110 <                      neighborList.push_back(make_pair((*j1), (*j2)));
1111 <                    }
1112 <                  }
1176 >                  // In parallel, we need to visit *all* pairs of row
1177 >                  // & column indicies and will divide labor in the
1178 >                  // force evaluation later.
1179 >                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1180 >                  snap_->wrapVector(dr);
1181 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1182 >                  if (dr.lengthSquare() < cuts.third) {
1183 >                    neighborList.push_back(make_pair((*j1), (*j2)));
1184 >                  }                  
1185                  }
1186                }
1187   #else

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