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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 1589 by gezelter, Sun Jul 10 16:05:34 2011 UTC vs.
Revision 1593 by gezelter, Fri Jul 15 21:35:14 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_.push_back( Vector3i(-1, 0, 0) );
57 +    cellOffsets_.push_back( Vector3i(-1,-1, 0) );
58 +    cellOffsets_.push_back( Vector3i( 0,-1, 0) );
59 +    cellOffsets_.push_back( Vector3i( 1,-1, 0) );
60 +    cellOffsets_.push_back( Vector3i( 0, 0,-1) );
61 +    cellOffsets_.push_back( Vector3i(-1, 0, 1) );
62 +    cellOffsets_.push_back( Vector3i(-1,-1,-1) );
63 +    cellOffsets_.push_back( Vector3i( 0,-1,-1) );
64 +    cellOffsets_.push_back( Vector3i( 1,-1,-1) );
65 +    cellOffsets_.push_back( Vector3i( 1, 0,-1) );
66 +    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 +    cellOffsets_.push_back( Vector3i( 0, 1,-1) );
68 +    cellOffsets_.push_back( Vector3i(-1, 1,-1) );
69 + #endif    
70 +  }
71 +
72 +
73    /**
74     * distributeInitialData is essentially a copy of the older fortran
75     * SimulationSetup
76     */
54 –  
77    void ForceMatrixDecomposition::distributeInitialData() {
78      snap_ = sman_->getCurrentSnapshot();
79      storageLayout_ = sman_->getStorageLayout();
# Line 74 | Line 96 | namespace OpenMD {
96  
97   #ifdef IS_MPI
98  
99 <    AtomCommIntRow = new Communicator<Row,int>(nLocal_);
100 <    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_);
99 >    MPI::Intracomm row = rowComm.getComm();
100 >    MPI::Intracomm col = colComm.getComm();
101  
102 <    AtomCommIntColumn = new Communicator<Column,int>(nLocal_);
103 <    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal_);
104 <    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal_);
105 <    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal_);
106 <    AtomCommPotColumn = new Communicator<Column,potVec>(nLocal_);
102 >    AtomPlanIntRow = new Plan<int>(row, nLocal_);
103 >    AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
104 >    AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_);
105 >    AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_);
106 >    AtomPlanPotRow = new Plan<potVec>(row, nLocal_);
107  
108 <    cgCommIntRow = new Communicator<Row,int>(nGroups_);
109 <    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups_);
110 <    cgCommIntColumn = new Communicator<Column,int>(nGroups_);
111 <    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups_);
108 >    AtomPlanIntColumn = new Plan<int>(col, nLocal_);
109 >    AtomPlanRealColumn = new Plan<RealType>(col, nLocal_);
110 >    AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_);
111 >    AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_);
112 >    AtomPlanPotColumn = new Plan<potVec>(col, nLocal_);
113  
114 <    nAtomsInRow_ = AtomCommIntRow->getSize();
115 <    nAtomsInCol_ = AtomCommIntColumn->getSize();
116 <    nGroupsInRow_ = cgCommIntRow->getSize();
117 <    nGroupsInCol_ = cgCommIntColumn->getSize();
114 >    cgPlanIntRow = new Plan<int>(row, nGroups_);
115 >    cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_);
116 >    cgPlanIntColumn = new Plan<int>(col, nGroups_);
117 >    cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_);
118  
119 +    nAtomsInRow_ = AtomPlanIntRow->getSize();
120 +    nAtomsInCol_ = AtomPlanIntColumn->getSize();
121 +    nGroupsInRow_ = cgPlanIntRow->getSize();
122 +    nGroupsInCol_ = cgPlanIntColumn->getSize();
123 +
124      // Modify the data storage objects with the correct layouts and sizes:
125      atomRowData.resize(nAtomsInRow_);
126      atomRowData.setStorageLayout(storageLayout_);
# Line 109 | Line 134 | namespace OpenMD {
134      identsRow.resize(nAtomsInRow_);
135      identsCol.resize(nAtomsInCol_);
136      
137 <    AtomCommIntRow->gather(idents, identsRow);
138 <    AtomCommIntColumn->gather(idents, identsCol);
137 >    AtomPlanIntRow->gather(idents, identsRow);
138 >    AtomPlanIntColumn->gather(idents, identsCol);
139      
140      // allocate memory for the parallel objects
141 +    atypesRow.resize(nAtomsInRow_);
142 +    atypesCol.resize(nAtomsInCol_);
143 +
144 +    for (int i = 0; i < nAtomsInRow_; i++)
145 +      atypesRow[i] = ff_->getAtomType(identsRow[i]);
146 +    for (int i = 0; i < nAtomsInCol_; i++)
147 +      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
148 +
149 +    pot_row.resize(nAtomsInRow_);
150 +    pot_col.resize(nAtomsInCol_);
151 +
152      AtomRowToGlobal.resize(nAtomsInRow_);
153      AtomColToGlobal.resize(nAtomsInCol_);
154 +    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
155 +    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
156 +
157 +    cerr << "Atoms in Local:\n";
158 +    for (int i = 0; i < AtomLocalToGlobal.size(); i++) {
159 +      cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n";
160 +    }
161 +    cerr << "Atoms in Row:\n";
162 +    for (int i = 0; i < AtomRowToGlobal.size(); i++) {
163 +      cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n";
164 +    }
165 +    cerr << "Atoms in Col:\n";
166 +    for (int i = 0; i < AtomColToGlobal.size(); i++) {
167 +      cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n";
168 +    }
169 +
170      cgRowToGlobal.resize(nGroupsInRow_);
171      cgColToGlobal.resize(nGroupsInCol_);
172 <    massFactorsRow.resize(nAtomsInRow_);
173 <    massFactorsCol.resize(nAtomsInCol_);
122 <    pot_row.resize(nAtomsInRow_);
123 <    pot_col.resize(nAtomsInCol_);
172 >    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
173 >    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
174  
175 <    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
176 <    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
177 <    
178 <    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
179 <    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
175 >    cerr << "Gruops in Local:\n";
176 >    for (int i = 0; i < cgLocalToGlobal.size(); i++) {
177 >      cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n";
178 >    }
179 >    cerr << "Groups in Row:\n";
180 >    for (int i = 0; i < cgRowToGlobal.size(); i++) {
181 >      cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n";
182 >    }
183 >    cerr << "Groups in Col:\n";
184 >    for (int i = 0; i < cgColToGlobal.size(); i++) {
185 >      cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n";
186 >    }
187 >
188  
189 <    AtomCommRealRow->gather(massFactors, massFactorsRow);
190 <    AtomCommRealColumn->gather(massFactors, massFactorsCol);
189 >    massFactorsRow.resize(nAtomsInRow_);
190 >    massFactorsCol.resize(nAtomsInCol_);
191 >    AtomPlanRealRow->gather(massFactors, massFactorsRow);
192 >    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
193  
194      groupListRow_.clear();
195      groupListRow_.resize(nGroupsInRow_);
# Line 187 | Line 247 | namespace OpenMD {
247  
248   #endif
249  
250 +    // allocate memory for the parallel objects
251 +    atypesLocal.resize(nLocal_);
252 +
253 +    for (int i = 0; i < nLocal_; i++)
254 +      atypesLocal[i] = ff_->getAtomType(idents[i]);
255 +
256      groupList_.clear();
257      groupList_.resize(nGroups_);
258      for (int i = 0; i < nGroups_; i++) {
# Line 239 | Line 305 | namespace OpenMD {
305    void ForceMatrixDecomposition::createGtypeCutoffMap() {
306      
307      RealType tol = 1e-6;
308 +    largestRcut_ = 0.0;
309      RealType rc;
310      int atid;
311      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
312 +    
313      map<int, RealType> atypeCutoff;
314        
315      for (set<AtomType*>::iterator at = atypes.begin();
# Line 249 | Line 317 | namespace OpenMD {
317        atid = (*at)->getIdent();
318        if (userChoseCutoff_)
319          atypeCutoff[atid] = userCutoff_;
320 <      else
320 >      else
321          atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
322      }
323 <
323 >    
324      vector<RealType> gTypeCutoffs;
325      // first we do a single loop over the cutoff groups to find the
326      // largest cutoff for any atypes present in this group.
# Line 312 | Line 380 | namespace OpenMD {
380      vector<RealType> groupCutoff(nGroups_, 0.0);
381      groupToGtype.resize(nGroups_);
382      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
315 –
383        groupCutoff[cg1] = 0.0;
384        vector<int> atomList = getAtomsInGroupRow(cg1);
318 –
385        for (vector<int>::iterator ia = atomList.begin();
386             ia != atomList.end(); ++ia) {            
387          int atom1 = (*ia);
388          atid = idents[atom1];
389 <        if (atypeCutoff[atid] > groupCutoff[cg1]) {
389 >        if (atypeCutoff[atid] > groupCutoff[cg1])
390            groupCutoff[cg1] = atypeCutoff[atid];
325 –        }
391        }
392 <
392 >      
393        bool gTypeFound = false;
394        for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
395          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
# Line 332 | Line 397 | namespace OpenMD {
397            gTypeFound = true;
398          }
399        }
400 <      if (!gTypeFound) {
400 >      if (!gTypeFound) {      
401          gTypeCutoffs.push_back( groupCutoff[cg1] );
402          groupToGtype[cg1] = gTypeCutoffs.size() - 1;
403        }      
# Line 341 | Line 406 | namespace OpenMD {
406  
407      // Now we find the maximum group cutoff value present in the simulation
408  
409 <    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
409 >    RealType groupMax = *max_element(gTypeCutoffs.begin(),
410 >                                     gTypeCutoffs.end());
411  
412   #ifdef IS_MPI
413 <    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
413 >    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
414 >                              MPI::MAX);
415   #endif
416      
417      RealType tradRcut = groupMax;
# Line 374 | Line 441 | namespace OpenMD {
441  
442          pair<int,int> key = make_pair(i,j);
443          gTypeCutoffMap[key].first = thisRcut;
377 –
444          if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
379 –
445          gTypeCutoffMap[key].second = thisRcut*thisRcut;
381 –        
446          gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
383 –
447          // sanity check
448          
449          if (userChoseCutoff_) {
# Line 440 | Line 503 | namespace OpenMD {
503           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
504  
505      if (storageLayout_ & DataStorage::dslParticlePot) {    
506 <      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
507 <      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
506 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
507 >           0.0);
508 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
509 >           0.0);
510      }
511  
512      if (storageLayout_ & DataStorage::dslDensity) {      
# Line 450 | Line 515 | namespace OpenMD {
515      }
516  
517      if (storageLayout_ & DataStorage::dslFunctional) {  
518 <      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
519 <      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
518 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
519 >           0.0);
520 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
521 >           0.0);
522      }
523  
524      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
# Line 468 | Line 535 | namespace OpenMD {
535             atomColData.skippedCharge.end(), 0.0);
536      }
537  
538 < #else
539 <    
538 > #endif
539 >    // even in parallel, we need to zero out the local arrays:
540 >
541      if (storageLayout_ & DataStorage::dslParticlePot) {      
542        fill(snap_->atomData.particlePot.begin(),
543             snap_->atomData.particlePot.end(), 0.0);
# Line 491 | Line 559 | namespace OpenMD {
559        fill(snap_->atomData.skippedCharge.begin(),
560             snap_->atomData.skippedCharge.end(), 0.0);
561      }
494 – #endif
562      
563    }
564  
# Line 502 | Line 569 | namespace OpenMD {
569   #ifdef IS_MPI
570      
571      // gather up the atomic positions
572 <    AtomCommVectorRow->gather(snap_->atomData.position,
572 >    AtomPlanVectorRow->gather(snap_->atomData.position,
573                                atomRowData.position);
574 <    AtomCommVectorColumn->gather(snap_->atomData.position,
574 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
575                                   atomColData.position);
576      
577      // gather up the cutoff group positions
578 <    cgCommVectorRow->gather(snap_->cgData.position,
578 >
579 >    cerr  << "before gather\n";
580 >    for (int i = 0; i < snap_->cgData.position.size(); i++) {
581 >      cerr << "cgpos = " << snap_->cgData.position[i] << "\n";
582 >    }
583 >
584 >    cgPlanVectorRow->gather(snap_->cgData.position,
585                              cgRowData.position);
586 <    cgCommVectorColumn->gather(snap_->cgData.position,
586 >
587 >    cerr  << "after gather\n";
588 >    for (int i = 0; i < cgRowData.position.size(); i++) {
589 >      cerr << "cgRpos = " << cgRowData.position[i] << "\n";
590 >    }
591 >
592 >    cgPlanVectorColumn->gather(snap_->cgData.position,
593                                 cgColData.position);
594 +    for (int i = 0; i < cgColData.position.size(); i++) {
595 +      cerr << "cgCpos = " << cgColData.position[i] << "\n";
596 +    }
597 +
598      
599      // if needed, gather the atomic rotation matrices
600      if (storageLayout_ & DataStorage::dslAmat) {
601 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
601 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
602                                  atomRowData.aMat);
603 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
603 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
604                                     atomColData.aMat);
605      }
606      
607      // if needed, gather the atomic eletrostatic frames
608      if (storageLayout_ & DataStorage::dslElectroFrame) {
609 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
609 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
610                                  atomRowData.electroFrame);
611 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
611 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
612                                     atomColData.electroFrame);
613      }
614 +
615   #endif      
616    }
617    
# Line 541 | Line 625 | namespace OpenMD {
625      
626      if (storageLayout_ & DataStorage::dslDensity) {
627        
628 <      AtomCommRealRow->scatter(atomRowData.density,
628 >      AtomPlanRealRow->scatter(atomRowData.density,
629                                 snap_->atomData.density);
630        
631        int n = snap_->atomData.density.size();
632        vector<RealType> rho_tmp(n, 0.0);
633 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
633 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
634        for (int i = 0; i < n; i++)
635          snap_->atomData.density[i] += rho_tmp[i];
636      }
# Line 562 | Line 646 | namespace OpenMD {
646      storageLayout_ = sman_->getStorageLayout();
647   #ifdef IS_MPI
648      if (storageLayout_ & DataStorage::dslFunctional) {
649 <      AtomCommRealRow->gather(snap_->atomData.functional,
649 >      AtomPlanRealRow->gather(snap_->atomData.functional,
650                                atomRowData.functional);
651 <      AtomCommRealColumn->gather(snap_->atomData.functional,
651 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
652                                   atomColData.functional);
653      }
654      
655      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
656 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
656 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
657                                atomRowData.functionalDerivative);
658 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
658 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
659                                   atomColData.functionalDerivative);
660      }
661   #endif
# Line 585 | Line 669 | namespace OpenMD {
669      int n = snap_->atomData.force.size();
670      vector<Vector3d> frc_tmp(n, V3Zero);
671      
672 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
672 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
673      for (int i = 0; i < n; i++) {
674        snap_->atomData.force[i] += frc_tmp[i];
675        frc_tmp[i] = 0.0;
676      }
677      
678 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
679 <    for (int i = 0; i < n; i++)
678 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
679 >    for (int i = 0; i < n; i++) {
680        snap_->atomData.force[i] += frc_tmp[i];
681 <    
682 <    
681 >    }
682 >        
683      if (storageLayout_ & DataStorage::dslTorque) {
684  
685        int nt = snap_->atomData.torque.size();
686        vector<Vector3d> trq_tmp(nt, V3Zero);
687  
688 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
688 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
689        for (int i = 0; i < nt; i++) {
690          snap_->atomData.torque[i] += trq_tmp[i];
691          trq_tmp[i] = 0.0;
692        }
693        
694 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
694 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
695        for (int i = 0; i < nt; i++)
696          snap_->atomData.torque[i] += trq_tmp[i];
697      }
# Line 617 | Line 701 | namespace OpenMD {
701        int ns = snap_->atomData.skippedCharge.size();
702        vector<RealType> skch_tmp(ns, 0.0);
703  
704 <      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
704 >      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
705        for (int i = 0; i < ns; i++) {
706 <        snap_->atomData.skippedCharge[i] = skch_tmp[i];
706 >        snap_->atomData.skippedCharge[i] += skch_tmp[i];
707          skch_tmp[i] = 0.0;
708        }
709        
710 <      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
710 >      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
711        for (int i = 0; i < ns; i++)
712          snap_->atomData.skippedCharge[i] += skch_tmp[i];
713      }
# Line 635 | Line 719 | namespace OpenMD {
719  
720      // scatter/gather pot_row into the members of my column
721            
722 <    AtomCommPotRow->scatter(pot_row, pot_temp);
722 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
723  
724      for (int ii = 0;  ii < pot_temp.size(); ii++ )
725        pairwisePot += pot_temp[ii];
# Line 643 | Line 727 | namespace OpenMD {
727      fill(pot_temp.begin(), pot_temp.end(),
728           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
729        
730 <    AtomCommPotColumn->scatter(pot_col, pot_temp);    
730 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
731      
732      for (int ii = 0;  ii < pot_temp.size(); ii++ )
733        pairwisePot += pot_temp[ii];    
734   #endif
735  
736 +    cerr << "pairwisePot = " <<  pairwisePot << "\n";
737    }
738  
739    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 683 | Line 768 | namespace OpenMD {
768      
769   #ifdef IS_MPI
770      d = cgColData.position[cg2] - cgRowData.position[cg1];
771 +    cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n";
772 +    cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n";
773   #else
774      d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
775 +    cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n";
776 +    cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n";
777   #endif
778      
779      snap_->wrapVector(d);
# Line 759 | Line 848 | namespace OpenMD {
848     */
849    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
850      int unique_id_1, unique_id_2;
851 +    
852  
853 +    cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
854   #ifdef IS_MPI
855      // in MPI, we have to look up the unique IDs for each atom
856      unique_id_1 = AtomRowToGlobal[atom1];
857      unique_id_2 = AtomColToGlobal[atom2];
858  
859 +    cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
860      // this situation should only arise in MPI simulations
861      if (unique_id_1 == unique_id_2) return true;
862      
# Line 789 | Line 881 | namespace OpenMD {
881     */
882    bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
883      int unique_id_2;
792 –    
884   #ifdef IS_MPI
885      // in MPI, we have to look up the unique IDs for the row atom.
886      unique_id_2 = AtomColToGlobal[atom2];
# Line 830 | Line 921 | namespace OpenMD {
921      idat.excluded = excludeAtomPair(atom1, atom2);
922    
923   #ifdef IS_MPI
924 <    
925 <    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
926 <                             ff_->getAtomType(identsCol[atom2]) );
924 >    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
925 >    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
926 >    //                         ff_->getAtomType(identsCol[atom2]) );
927      
928      if (storageLayout_ & DataStorage::dslAmat) {
929        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 876 | Line 967 | namespace OpenMD {
967  
968   #else
969  
970 <    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
971 <                             ff_->getAtomType(idents[atom2]) );
970 >    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
971 >    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
972 >    //                         ff_->getAtomType(idents[atom2]) );
973  
974      if (storageLayout_ & DataStorage::dslAmat) {
975        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 1015 | Line 1107 | namespace OpenMD {
1107          // add this cutoff group to the list of groups in this cell;
1108          cellListRow_[cellIndex].push_back(i);
1109        }
1018 –      
1110        for (int i = 0; i < nGroupsInCol_; i++) {
1111          rs = cgColData.position[i];
1112          
# Line 1060 | Line 1151 | namespace OpenMD {
1151          whichCell.z() = nCells_.z() * scaled.z();
1152          
1153          // find single index of this cell:
1154 <        cellIndex = Vlinear(whichCell, nCells_);      
1154 >        cellIndex = Vlinear(whichCell, nCells_);
1155          
1156          // add this cutoff group to the list of groups in this cell;
1157          cellList_[cellIndex].push_back(i);
# Line 1104 | Line 1195 | namespace OpenMD {
1195                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1196                       j2 != cellListCol_[m2].end(); ++j2) {
1197                    
1198 <                  // Always do this if we're in different cells or if
1199 <                  // we're in the same cell and the global index of the
1200 <                  // j2 cutoff group is less than the j1 cutoff group
1201 <                  
1202 <                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1203 <                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1204 <                    snap_->wrapVector(dr);
1205 <                    cuts = getGroupCutoffs( (*j1), (*j2) );
1115 <                    if (dr.lengthSquare() < cuts.third) {
1116 <                      neighborList.push_back(make_pair((*j1), (*j2)));
1117 <                    }
1118 <                  }
1198 >                  // In parallel, we need to visit *all* pairs of row &
1199 >                  // column indicies and will truncate later on.
1200 >                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1201 >                  snap_->wrapVector(dr);
1202 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1203 >                  if (dr.lengthSquare() < cuts.third) {
1204 >                    neighborList.push_back(make_pair((*j1), (*j2)));
1205 >                  }                  
1206                  }
1207                }
1208   #else

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