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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 1713 by gezelter, Sat May 19 14:21:02 2012 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 <    vector<int>::iterator it;
157 <    for (it = AtomLocalToGlobal.begin(); it != AtomLocalToGlobal.end(); ++it) {
158 <      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);
156 >    // allocate memory for the parallel objects
157 >    atypesRow.resize(nAtomsInRow_);
158 >    atypesCol.resize(nAtomsInCol_);
159  
160 <    AtomCommRealRow->gather(massFactors, massFactorsRow);
161 <    AtomCommRealColumn->gather(massFactors, massFactorsCol);
160 >    for (int i = 0; i < nAtomsInRow_; i++)
161 >      atypesRow[i] = ff_->getAtomType(identsRow[i]);
162 >    for (int i = 0; i < nAtomsInCol_; i++)
163 >      atypesCol[i] = ff_->getAtomType(identsCol[i]);        
164  
165 +    pot_row.resize(nAtomsInRow_);
166 +    pot_col.resize(nAtomsInCol_);
167 +
168 +    AtomRowToGlobal.resize(nAtomsInRow_);
169 +    AtomColToGlobal.resize(nAtomsInCol_);
170 +    AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
171 +    AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
172 +
173 +    cgRowToGlobal.resize(nGroupsInRow_);
174 +    cgColToGlobal.resize(nGroupsInCol_);
175 +    cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
176 +    cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
177 +
178 +    massFactorsRow.resize(nAtomsInRow_);
179 +    massFactorsCol.resize(nAtomsInCol_);
180 +    AtomPlanRealRow->gather(massFactors, massFactorsRow);
181 +    AtomPlanRealColumn->gather(massFactors, massFactorsCol);
182 +
183      groupListRow_.clear();
184      groupListRow_.resize(nGroupsInRow_);
185      for (int i = 0; i < nGroupsInRow_; i++) {
# Line 175 | Line 230 | namespace OpenMD {
230                topoDist[i].push_back(3);
231              }
232            }
178 –        }
179 –      }      
180 –    }
181 –
182 – #endif
183 –
184 –    groupList_.clear();
185 –    groupList_.resize(nGroups_);
186 –    for (int i = 0; i < nGroups_; i++) {
187 –      int gid = cgLocalToGlobal[i];
188 –      for (int j = 0; j < nLocal_; j++) {
189 –        int aid = AtomLocalToGlobal[j];
190 –        if (globalGroupMembership[aid] == gid) {
191 –          groupList_[i].push_back(j);
233          }
234        }      
235      }
236  
237 + #else
238      excludesForAtom.clear();
239      excludesForAtom.resize(nLocal_);
240      toposForAtom.clear();
# Line 225 | 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 233 | Line 295 | namespace OpenMD {
295    void ForceMatrixDecomposition::createGtypeCutoffMap() {
296      
297      RealType tol = 1e-6;
298 +    largestRcut_ = 0.0;
299      RealType rc;
300      int atid;
301      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
302 +    
303      map<int, RealType> atypeCutoff;
304        
305      for (set<AtomType*>::iterator at = atypes.begin();
# Line 243 | Line 307 | namespace OpenMD {
307        atid = (*at)->getIdent();
308        if (userChoseCutoff_)
309          atypeCutoff[atid] = userCutoff_;
310 <      else
310 >      else
311          atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
312      }
313 <
313 >    
314      vector<RealType> gTypeCutoffs;
315      // first we do a single loop over the cutoff groups to find the
316      // largest cutoff for any atypes present in this group.
# Line 306 | Line 370 | namespace OpenMD {
370      vector<RealType> groupCutoff(nGroups_, 0.0);
371      groupToGtype.resize(nGroups_);
372      for (int cg1 = 0; cg1 < nGroups_; cg1++) {
309 –
373        groupCutoff[cg1] = 0.0;
374        vector<int> atomList = getAtomsInGroupRow(cg1);
312 –
375        for (vector<int>::iterator ia = atomList.begin();
376             ia != atomList.end(); ++ia) {            
377          int atom1 = (*ia);
378          atid = idents[atom1];
379 <        if (atypeCutoff[atid] > groupCutoff[cg1]) {
379 >        if (atypeCutoff[atid] > groupCutoff[cg1])
380            groupCutoff[cg1] = atypeCutoff[atid];
319 –        }
381        }
382 <
382 >      
383        bool gTypeFound = false;
384        for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
385          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
# Line 326 | Line 387 | namespace OpenMD {
387            gTypeFound = true;
388          }
389        }
390 <      if (!gTypeFound) {
390 >      if (!gTypeFound) {      
391          gTypeCutoffs.push_back( groupCutoff[cg1] );
392          groupToGtype[cg1] = gTypeCutoffs.size() - 1;
393        }      
# Line 335 | Line 396 | namespace OpenMD {
396  
397      // Now we find the maximum group cutoff value present in the simulation
398  
399 <    RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end());
399 >    RealType groupMax = *max_element(gTypeCutoffs.begin(),
400 >                                     gTypeCutoffs.end());
401  
402   #ifdef IS_MPI
403 <    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, MPI::MAX);
403 >    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
404 >                              MPI::MAX);
405   #endif
406      
407      RealType tradRcut = groupMax;
# Line 368 | Line 431 | namespace OpenMD {
431  
432          pair<int,int> key = make_pair(i,j);
433          gTypeCutoffMap[key].first = thisRcut;
371 –
434          if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
373 –
435          gTypeCutoffMap[key].second = thisRcut*thisRcut;
375 –        
436          gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
377 –
437          // sanity check
438          
439          if (userChoseCutoff_) {
# Line 434 | Line 493 | namespace OpenMD {
493           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
494  
495      if (storageLayout_ & DataStorage::dslParticlePot) {    
496 <      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
497 <      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), 0.0);
496 >      fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
497 >           0.0);
498 >      fill(atomColData.particlePot.begin(), atomColData.particlePot.end(),
499 >           0.0);
500      }
501  
502      if (storageLayout_ & DataStorage::dslDensity) {      
# Line 444 | Line 505 | namespace OpenMD {
505      }
506  
507      if (storageLayout_ & DataStorage::dslFunctional) {  
508 <      fill(atomRowData.functional.begin(), atomRowData.functional.end(), 0.0);
509 <      fill(atomColData.functional.begin(), atomColData.functional.end(), 0.0);
508 >      fill(atomRowData.functional.begin(), atomRowData.functional.end(),
509 >           0.0);
510 >      fill(atomColData.functional.begin(), atomColData.functional.end(),
511 >           0.0);
512      }
513  
514      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
# Line 462 | Line 525 | namespace OpenMD {
525             atomColData.skippedCharge.end(), 0.0);
526      }
527  
528 < #else
529 <    
528 >    if (storageLayout_ & DataStorage::dslElectricField) {    
529 >      fill(atomRowData.electricField.begin(),
530 >           atomRowData.electricField.end(), V3Zero);
531 >      fill(atomColData.electricField.begin(),
532 >           atomColData.electricField.end(), V3Zero);
533 >    }
534 >    if (storageLayout_ & DataStorage::dslFlucQForce) {    
535 >      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
536 >           0.0);
537 >      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
538 >           0.0);
539 >    }
540 >
541 > #endif
542 >    // even in parallel, we need to zero out the local arrays:
543 >
544      if (storageLayout_ & DataStorage::dslParticlePot) {      
545        fill(snap_->atomData.particlePot.begin(),
546             snap_->atomData.particlePot.end(), 0.0);
# Line 473 | Line 550 | namespace OpenMD {
550        fill(snap_->atomData.density.begin(),
551             snap_->atomData.density.end(), 0.0);
552      }
553 +
554      if (storageLayout_ & DataStorage::dslFunctional) {
555        fill(snap_->atomData.functional.begin(),
556             snap_->atomData.functional.end(), 0.0);
557      }
558 +
559      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
560        fill(snap_->atomData.functionalDerivative.begin(),
561             snap_->atomData.functionalDerivative.end(), 0.0);
562      }
563 +
564      if (storageLayout_ & DataStorage::dslSkippedCharge) {      
565        fill(snap_->atomData.skippedCharge.begin(),
566             snap_->atomData.skippedCharge.end(), 0.0);
567      }
568 < #endif
569 <    
568 >
569 >    if (storageLayout_ & DataStorage::dslElectricField) {      
570 >      fill(snap_->atomData.electricField.begin(),
571 >           snap_->atomData.electricField.end(), V3Zero);
572 >    }
573    }
574  
575  
# Line 496 | Line 579 | namespace OpenMD {
579   #ifdef IS_MPI
580      
581      // gather up the atomic positions
582 <    AtomCommVectorRow->gather(snap_->atomData.position,
582 >    AtomPlanVectorRow->gather(snap_->atomData.position,
583                                atomRowData.position);
584 <    AtomCommVectorColumn->gather(snap_->atomData.position,
584 >    AtomPlanVectorColumn->gather(snap_->atomData.position,
585                                   atomColData.position);
586      
587      // gather up the cutoff group positions
588 <    cgCommVectorRow->gather(snap_->cgData.position,
588 >
589 >    cgPlanVectorRow->gather(snap_->cgData.position,
590                              cgRowData.position);
591 <    cgCommVectorColumn->gather(snap_->cgData.position,
591 >
592 >    cgPlanVectorColumn->gather(snap_->cgData.position,
593                                 cgColData.position);
594 +
595      
596      // if needed, gather the atomic rotation matrices
597      if (storageLayout_ & DataStorage::dslAmat) {
598 <      AtomCommMatrixRow->gather(snap_->atomData.aMat,
598 >      AtomPlanMatrixRow->gather(snap_->atomData.aMat,
599                                  atomRowData.aMat);
600 <      AtomCommMatrixColumn->gather(snap_->atomData.aMat,
600 >      AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
601                                     atomColData.aMat);
602      }
603      
604      // if needed, gather the atomic eletrostatic frames
605      if (storageLayout_ & DataStorage::dslElectroFrame) {
606 <      AtomCommMatrixRow->gather(snap_->atomData.electroFrame,
606 >      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
607                                  atomRowData.electroFrame);
608 <      AtomCommMatrixColumn->gather(snap_->atomData.electroFrame,
608 >      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
609                                     atomColData.electroFrame);
610      }
611 +
612 +    // if needed, gather the atomic fluctuating charge values
613 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {
614 +      AtomPlanRealRow->gather(snap_->atomData.flucQPos,
615 +                              atomRowData.flucQPos);
616 +      AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
617 +                                 atomColData.flucQPos);
618 +    }
619 +
620   #endif      
621    }
622    
# Line 535 | Line 630 | namespace OpenMD {
630      
631      if (storageLayout_ & DataStorage::dslDensity) {
632        
633 <      AtomCommRealRow->scatter(atomRowData.density,
633 >      AtomPlanRealRow->scatter(atomRowData.density,
634                                 snap_->atomData.density);
635        
636        int n = snap_->atomData.density.size();
637        vector<RealType> rho_tmp(n, 0.0);
638 <      AtomCommRealColumn->scatter(atomColData.density, rho_tmp);
638 >      AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
639        for (int i = 0; i < n; i++)
640          snap_->atomData.density[i] += rho_tmp[i];
641      }
642 +
643 +    if (storageLayout_ & DataStorage::dslElectricField) {
644 +      
645 +      AtomPlanVectorRow->scatter(atomRowData.electricField,
646 +                                 snap_->atomData.electricField);
647 +      
648 +      int n = snap_->atomData.electricField.size();
649 +      vector<Vector3d> field_tmp(n, V3Zero);
650 +      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
651 +      for (int i = 0; i < n; i++)
652 +        snap_->atomData.electricField[i] += field_tmp[i];
653 +    }
654   #endif
655    }
656  
# Line 556 | Line 663 | namespace OpenMD {
663      storageLayout_ = sman_->getStorageLayout();
664   #ifdef IS_MPI
665      if (storageLayout_ & DataStorage::dslFunctional) {
666 <      AtomCommRealRow->gather(snap_->atomData.functional,
666 >      AtomPlanRealRow->gather(snap_->atomData.functional,
667                                atomRowData.functional);
668 <      AtomCommRealColumn->gather(snap_->atomData.functional,
668 >      AtomPlanRealColumn->gather(snap_->atomData.functional,
669                                   atomColData.functional);
670      }
671      
672      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
673 <      AtomCommRealRow->gather(snap_->atomData.functionalDerivative,
673 >      AtomPlanRealRow->gather(snap_->atomData.functionalDerivative,
674                                atomRowData.functionalDerivative);
675 <      AtomCommRealColumn->gather(snap_->atomData.functionalDerivative,
675 >      AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative,
676                                   atomColData.functionalDerivative);
677      }
678   #endif
# Line 579 | Line 686 | namespace OpenMD {
686      int n = snap_->atomData.force.size();
687      vector<Vector3d> frc_tmp(n, V3Zero);
688      
689 <    AtomCommVectorRow->scatter(atomRowData.force, frc_tmp);
689 >    AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp);
690      for (int i = 0; i < n; i++) {
691        snap_->atomData.force[i] += frc_tmp[i];
692        frc_tmp[i] = 0.0;
693      }
694      
695 <    AtomCommVectorColumn->scatter(atomColData.force, frc_tmp);
696 <    for (int i = 0; i < n; i++)
695 >    AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp);
696 >    for (int i = 0; i < n; i++) {
697        snap_->atomData.force[i] += frc_tmp[i];
698 <    
699 <    
698 >    }
699 >        
700      if (storageLayout_ & DataStorage::dslTorque) {
701  
702        int nt = snap_->atomData.torque.size();
703        vector<Vector3d> trq_tmp(nt, V3Zero);
704  
705 <      AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp);
705 >      AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp);
706        for (int i = 0; i < nt; i++) {
707          snap_->atomData.torque[i] += trq_tmp[i];
708          trq_tmp[i] = 0.0;
709        }
710        
711 <      AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp);
711 >      AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp);
712        for (int i = 0; i < nt; i++)
713          snap_->atomData.torque[i] += trq_tmp[i];
714      }
# Line 611 | Line 718 | namespace OpenMD {
718        int ns = snap_->atomData.skippedCharge.size();
719        vector<RealType> skch_tmp(ns, 0.0);
720  
721 <      AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
721 >      AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp);
722        for (int i = 0; i < ns; i++) {
723 <        snap_->atomData.skippedCharge[i] = skch_tmp[i];
723 >        snap_->atomData.skippedCharge[i] += skch_tmp[i];
724          skch_tmp[i] = 0.0;
725        }
726        
727 <      AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
728 <      for (int i = 0; i < ns; i++)
727 >      AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
728 >      for (int i = 0; i < ns; i++)
729          snap_->atomData.skippedCharge[i] += skch_tmp[i];
730 +            
731      }
732      
733 +    if (storageLayout_ & DataStorage::dslFlucQForce) {
734 +
735 +      int nq = snap_->atomData.flucQFrc.size();
736 +      vector<RealType> fqfrc_tmp(nq, 0.0);
737 +
738 +      AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
739 +      for (int i = 0; i < nq; i++) {
740 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
741 +        fqfrc_tmp[i] = 0.0;
742 +      }
743 +      
744 +      AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
745 +      for (int i = 0; i < nq; i++)
746 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
747 +            
748 +    }
749 +
750      nLocal_ = snap_->getNumberOfAtoms();
751  
752      vector<potVec> pot_temp(nLocal_,
# Line 629 | Line 754 | namespace OpenMD {
754  
755      // scatter/gather pot_row into the members of my column
756            
757 <    AtomCommPotRow->scatter(pot_row, pot_temp);
757 >    AtomPlanPotRow->scatter(pot_row, pot_temp);
758  
759      for (int ii = 0;  ii < pot_temp.size(); ii++ )
760        pairwisePot += pot_temp[ii];
# Line 637 | Line 762 | namespace OpenMD {
762      fill(pot_temp.begin(), pot_temp.end(),
763           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
764        
765 <    AtomCommPotColumn->scatter(pot_col, pot_temp);    
765 >    AtomPlanPotColumn->scatter(pot_col, pot_temp);    
766      
767      for (int ii = 0;  ii < pot_temp.size(); ii++ )
768        pairwisePot += pot_temp[ii];    
769 +    
770 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
771 +      RealType ploc1 = pairwisePot[ii];
772 +      RealType ploc2 = 0.0;
773 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
774 +      pairwisePot[ii] = ploc2;
775 +    }
776 +
777 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
778 +      RealType ploc1 = embeddingPot[ii];
779 +      RealType ploc2 = 0.0;
780 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
781 +      embeddingPot[ii] = ploc2;
782 +    }
783 +
784   #endif
785  
786    }
# Line 753 | Line 893 | namespace OpenMD {
893     */
894    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
895      int unique_id_1, unique_id_2;
896 <
896 >        
897   #ifdef IS_MPI
898      // in MPI, we have to look up the unique IDs for each atom
899      unique_id_1 = AtomRowToGlobal[atom1];
900      unique_id_2 = AtomColToGlobal[atom2];
901 + #else
902 +    unique_id_1 = AtomLocalToGlobal[atom1];
903 +    unique_id_2 = AtomLocalToGlobal[atom2];
904 + #endif  
905  
762 –    // this situation should only arise in MPI simulations
906      if (unique_id_1 == unique_id_2) return true;
907 <    
907 >
908 > #ifdef IS_MPI
909      // this prevents us from doing the pair on multiple processors
910      if (unique_id_1 < unique_id_2) {
911        if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
912      } else {
913 <      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
913 >      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
914      }
915   #endif
916 +    
917      return false;
918    }
919  
# Line 782 | Line 927 | namespace OpenMD {
927     * field) must still be handled for these pairs.
928     */
929    bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
930 <    int unique_id_2;
930 >
931 >    // excludesForAtom was constructed to use row/column indices in the MPI
932 >    // version, and to use local IDs in the non-MPI version:
933      
787 – #ifdef IS_MPI
788 –    // in MPI, we have to look up the unique IDs for the row atom.
789 –    unique_id_2 = AtomColToGlobal[atom2];
790 – #else
791 –    // in the normal loop, the atom numbers are unique
792 –    unique_id_2 = atom2;
793 – #endif
794 –    
934      for (vector<int>::iterator i = excludesForAtom[atom1].begin();
935           i != excludesForAtom[atom1].end(); ++i) {
936 <      if ( (*i) == unique_id_2 ) return true;
936 >      if ( (*i) == atom2 ) return true;
937      }
938  
939      return false;
# Line 824 | Line 963 | namespace OpenMD {
963      idat.excluded = excludeAtomPair(atom1, atom2);
964    
965   #ifdef IS_MPI
966 +    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
967 +    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
968 +    //                         ff_->getAtomType(identsCol[atom2]) );
969      
828 –    idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
829 –                             ff_->getAtomType(identsCol[atom2]) );
830 –    
970      if (storageLayout_ & DataStorage::dslAmat) {
971        idat.A1 = &(atomRowData.aMat[atom1]);
972        idat.A2 = &(atomColData.aMat[atom2]);
# Line 869 | Line 1008 | namespace OpenMD {
1008      }
1009  
1010   #else
1011 +    
1012  
1013 <    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1014 <                             ff_->getAtomType(idents[atom2]) );
1013 >    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1014 >    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1015 >    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1016  
1017 +    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1018 +    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1019 +    //                         ff_->getAtomType(idents[atom2]) );
1020 +
1021      if (storageLayout_ & DataStorage::dslAmat) {
1022        idat.A1 = &(snap_->atomData.aMat[atom1]);
1023        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 918 | Line 1063 | namespace OpenMD {
1063    
1064    void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1065   #ifdef IS_MPI
1066 <    pot_row[atom1] += 0.5 *  *(idat.pot);
1067 <    pot_col[atom2] += 0.5 *  *(idat.pot);
1066 >    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1067 >    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1068  
1069      atomRowData.force[atom1] += *(idat.f1);
1070      atomColData.force[atom2] -= *(idat.f1);
1071 +
1072 +    // should particle pot be done here also?
1073   #else
1074      pairwisePot += *(idat.pot);
1075  
1076      snap_->atomData.force[atom1] += *(idat.f1);
1077      snap_->atomData.force[atom2] -= *(idat.f1);
1078 +
1079 +    if (idat.doParticlePot) {
1080 +      snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1081 +      snap_->atomData.particlePot[atom2] -= *(idat.vpair) * *(idat.sw);
1082 +    }
1083 +      
1084   #endif
1085      
1086    }
# Line 1009 | Line 1162 | namespace OpenMD {
1162          // add this cutoff group to the list of groups in this cell;
1163          cellListRow_[cellIndex].push_back(i);
1164        }
1012 –      
1165        for (int i = 0; i < nGroupsInCol_; i++) {
1166          rs = cgColData.position[i];
1167          
# Line 1034 | Line 1186 | namespace OpenMD {
1186          // add this cutoff group to the list of groups in this cell;
1187          cellListCol_[cellIndex].push_back(i);
1188        }
1189 +    
1190   #else
1191        for (int i = 0; i < nGroups_; i++) {
1192          rs = snap_->cgData.position[i];
# Line 1054 | Line 1207 | namespace OpenMD {
1207          whichCell.z() = nCells_.z() * scaled.z();
1208          
1209          // find single index of this cell:
1210 <        cellIndex = Vlinear(whichCell, nCells_);      
1210 >        cellIndex = Vlinear(whichCell, nCells_);
1211          
1212          // add this cutoff group to the list of groups in this cell;
1213          cellList_[cellIndex].push_back(i);
1214        }
1215 +
1216   #endif
1217  
1218        for (int m1z = 0; m1z < nCells_.z(); m1z++) {
# Line 1071 | Line 1225 | namespace OpenMD {
1225                   os != cellOffsets_.end(); ++os) {
1226                
1227                Vector3i m2v = m1v + (*os);
1228 <              
1228 >            
1229 >
1230                if (m2v.x() >= nCells_.x()) {
1231                  m2v.x() = 0;          
1232                } else if (m2v.x() < 0) {
# Line 1089 | Line 1244 | namespace OpenMD {
1244                } else if (m2v.z() < 0) {
1245                  m2v.z() = nCells_.z() - 1;
1246                }
1247 <              
1247 >
1248                int m2 = Vlinear (m2v, nCells_);
1249                
1250   #ifdef IS_MPI
# Line 1098 | Line 1253 | namespace OpenMD {
1253                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1254                       j2 != cellListCol_[m2].end(); ++j2) {
1255                    
1256 <                  // Always do this if we're in different cells or if
1257 <                  // we're in the same cell and the global index of the
1258 <                  // j2 cutoff group is less than the j1 cutoff group
1259 <                  
1260 <                  if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) {
1261 <                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1262 <                    snap_->wrapVector(dr);
1263 <                    cuts = getGroupCutoffs( (*j1), (*j2) );
1264 <                    if (dr.lengthSquare() < cuts.third) {
1110 <                      neighborList.push_back(make_pair((*j1), (*j2)));
1111 <                    }
1112 <                  }
1256 >                  // In parallel, we need to visit *all* pairs of row
1257 >                  // & column indicies and will divide labor in the
1258 >                  // force evaluation later.
1259 >                  dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1260 >                  snap_->wrapVector(dr);
1261 >                  cuts = getGroupCutoffs( (*j1), (*j2) );
1262 >                  if (dr.lengthSquare() < cuts.third) {
1263 >                    neighborList.push_back(make_pair((*j1), (*j2)));
1264 >                  }                  
1265                  }
1266                }
1267   #else
1116 –              
1268                for (vector<int>::iterator j1 = cellList_[m1].begin();
1269                     j1 != cellList_[m1].end(); ++j1) {
1270                  for (vector<int>::iterator j2 = cellList_[m2].begin();
1271                       j2 != cellList_[m2].end(); ++j2) {
1272 <                  
1272 >    
1273                    // Always do this if we're in different cells or if
1274 <                  // we're in the same cell and the global index of the
1275 <                  // j2 cutoff group is less than the j1 cutoff group
1276 <                  
1277 <                  if (m2 != m1 || (*j2) < (*j1)) {
1274 >                  // we're in the same cell and the global index of
1275 >                  // the j2 cutoff group is greater than or equal to
1276 >                  // the j1 cutoff group.  Note that Rappaport's code
1277 >                  // has a "less than" conditional here, but that
1278 >                  // deals with atom-by-atom computation.  OpenMD
1279 >                  // allows atoms within a single cutoff group to
1280 >                  // interact with each other.
1281 >
1282 >
1283 >
1284 >                  if (m2 != m1 || (*j2) >= (*j1) ) {
1285 >
1286                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1287                      snap_->wrapVector(dr);
1288                      cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1142 | Line 1301 | namespace OpenMD {
1301        // branch to do all cutoff group pairs
1302   #ifdef IS_MPI
1303        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1304 <        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1304 >        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1305            dr = cgColData.position[j2] - cgRowData.position[j1];
1306            snap_->wrapVector(dr);
1307            cuts = getGroupCutoffs( j1, j2 );
# Line 1150 | Line 1309 | namespace OpenMD {
1309              neighborList.push_back(make_pair(j1, j2));
1310            }
1311          }
1312 <      }
1312 >      }      
1313   #else
1314 <      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1315 <        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1314 >      // include all groups here.
1315 >      for (int j1 = 0; j1 < nGroups_; j1++) {
1316 >        // include self group interactions j2 == j1
1317 >        for (int j2 = j1; j2 < nGroups_; j2++) {
1318            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1319            snap_->wrapVector(dr);
1320            cuts = getGroupCutoffs( j1, j2 );
1321            if (dr.lengthSquare() < cuts.third) {
1322              neighborList.push_back(make_pair(j1, j2));
1323            }
1324 <        }
1325 <      }        
1324 >        }    
1325 >      }
1326   #endif
1327      }
1328        

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