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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 1593 by gezelter, Fri Jul 15 21:35:14 2011 UTC vs.
Revision 1756 by gezelter, Mon Jun 18 18:23:20 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 53 | Line 54 | namespace OpenMD {
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_.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) );
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) );
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) );
66 –    cellOffsets_.push_back( Vector3i( 1, 1,-1) );
67 –    cellOffsets_.push_back( Vector3i( 0, 1,-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  
# Line 79 | Line 95 | namespace OpenMD {
95      storageLayout_ = sman_->getStorageLayout();
96      ff_ = info_->getForceField();
97      nLocal_ = snap_->getNumberOfAtoms();
98 <    
98 >  
99      nGroups_ = info_->getNLocalCutoffGroups();
100      // gather the information for atomtype IDs (atids):
101      idents = info_->getIdentArray();
# Line 93 | Line 109 | namespace OpenMD {
109      PairList* oneTwo = info_->getOneTwoInteractions();
110      PairList* oneThree = info_->getOneThreeInteractions();
111      PairList* oneFour = info_->getOneFourInteractions();
112 <
112 >    
113 >    if (needVelocities_)
114 >      snap_->cgData.setStorageLayout(DataStorage::dslPosition |
115 >                                     DataStorage::dslVelocity);
116 >    else
117 >      snap_->cgData.setStorageLayout(DataStorage::dslPosition);
118 >    
119   #ifdef IS_MPI
120  
121      MPI::Intracomm row = rowComm.getComm();
# Line 129 | Line 151 | namespace OpenMD {
151      cgRowData.resize(nGroupsInRow_);
152      cgRowData.setStorageLayout(DataStorage::dslPosition);
153      cgColData.resize(nGroupsInCol_);
154 <    cgColData.setStorageLayout(DataStorage::dslPosition);
155 <        
154 >    if (needVelocities_)
155 >      // we only need column velocities if we need them.
156 >      cgColData.setStorageLayout(DataStorage::dslPosition |
157 >                                 DataStorage::dslVelocity);
158 >    else    
159 >      cgColData.setStorageLayout(DataStorage::dslPosition);
160 >      
161      identsRow.resize(nAtomsInRow_);
162      identsCol.resize(nAtomsInCol_);
163      
# Line 153 | Line 180 | namespace OpenMD {
180      AtomColToGlobal.resize(nAtomsInCol_);
181      AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
182      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 –    }
183  
184      cgRowToGlobal.resize(nGroupsInRow_);
185      cgColToGlobal.resize(nGroupsInCol_);
186      cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
187      cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
188  
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      massFactorsRow.resize(nAtomsInRow_);
190      massFactorsCol.resize(nAtomsInCol_);
191      AtomPlanRealRow->gather(massFactors, massFactorsRow);
# Line 245 | Line 245 | namespace OpenMD {
245        }      
246      }
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++) {
259 <      int gid = cgLocalToGlobal[i];
260 <      for (int j = 0; j < nLocal_; j++) {
261 <        int aid = AtomLocalToGlobal[j];
262 <        if (globalGroupMembership[aid] == gid) {
263 <          groupList_[i].push_back(j);
264 <        }
265 <      }      
266 <    }
267 <
248 > #else
249      excludesForAtom.clear();
250      excludesForAtom.resize(nLocal_);
251      toposForAtom.clear();
# Line 297 | Line 278 | namespace OpenMD {
278          }
279        }      
280      }
281 <    
281 > #endif
282 >
283 >    // allocate memory for the parallel objects
284 >    atypesLocal.resize(nLocal_);
285 >
286 >    for (int i = 0; i < nLocal_; i++)
287 >      atypesLocal[i] = ff_->getAtomType(idents[i]);
288 >
289 >    groupList_.clear();
290 >    groupList_.resize(nGroups_);
291 >    for (int i = 0; i < nGroups_; i++) {
292 >      int gid = cgLocalToGlobal[i];
293 >      for (int j = 0; j < nLocal_; j++) {
294 >        int aid = AtomLocalToGlobal[j];
295 >        if (globalGroupMembership[aid] == gid) {
296 >          groupList_[i].push_back(j);
297 >        }
298 >      }      
299 >    }
300 >
301 >
302      createGtypeCutoffMap();
303  
304    }
# Line 460 | Line 461 | namespace OpenMD {
461      }
462    }
463  
463 –
464    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
465      int i, j;  
466   #ifdef IS_MPI
# Line 533 | Line 533 | namespace OpenMD {
533             atomRowData.skippedCharge.end(), 0.0);
534        fill(atomColData.skippedCharge.begin(),
535             atomColData.skippedCharge.end(), 0.0);
536 +    }
537 +
538 +    if (storageLayout_ & DataStorage::dslFlucQForce) {      
539 +      fill(atomRowData.flucQFrc.begin(),
540 +           atomRowData.flucQFrc.end(), 0.0);
541 +      fill(atomColData.flucQFrc.begin(),
542 +           atomColData.flucQFrc.end(), 0.0);
543 +    }
544 +
545 +    if (storageLayout_ & DataStorage::dslElectricField) {    
546 +      fill(atomRowData.electricField.begin(),
547 +           atomRowData.electricField.end(), V3Zero);
548 +      fill(atomColData.electricField.begin(),
549 +           atomColData.electricField.end(), V3Zero);
550      }
551  
552 +    if (storageLayout_ & DataStorage::dslFlucQForce) {    
553 +      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
554 +           0.0);
555 +      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
556 +           0.0);
557 +    }
558 +
559   #endif
560      // even in parallel, we need to zero out the local arrays:
561  
# Line 547 | Line 568 | namespace OpenMD {
568        fill(snap_->atomData.density.begin(),
569             snap_->atomData.density.end(), 0.0);
570      }
571 +
572      if (storageLayout_ & DataStorage::dslFunctional) {
573        fill(snap_->atomData.functional.begin(),
574             snap_->atomData.functional.end(), 0.0);
575      }
576 +
577      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
578        fill(snap_->atomData.functionalDerivative.begin(),
579             snap_->atomData.functionalDerivative.end(), 0.0);
580      }
581 +
582      if (storageLayout_ & DataStorage::dslSkippedCharge) {      
583        fill(snap_->atomData.skippedCharge.begin(),
584             snap_->atomData.skippedCharge.end(), 0.0);
585      }
586 <    
586 >
587 >    if (storageLayout_ & DataStorage::dslElectricField) {      
588 >      fill(snap_->atomData.electricField.begin(),
589 >           snap_->atomData.electricField.end(), V3Zero);
590 >    }
591    }
592  
593  
# Line 576 | Line 604 | namespace OpenMD {
604      
605      // gather up the cutoff group positions
606  
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 –
607      cgPlanVectorRow->gather(snap_->cgData.position,
608                              cgRowData.position);
609  
587 –    cerr  << "after gather\n";
588 –    for (int i = 0; i < cgRowData.position.size(); i++) {
589 –      cerr << "cgRpos = " << cgRowData.position[i] << "\n";
590 –    }
591 –
610      cgPlanVectorColumn->gather(snap_->cgData.position,
611                                 cgColData.position);
612 <    for (int i = 0; i < cgColData.position.size(); i++) {
613 <      cerr << "cgCpos = " << cgColData.position[i] << "\n";
612 >
613 >
614 >
615 >    if (needVelocities_) {
616 >      // gather up the atomic velocities
617 >      AtomPlanVectorColumn->gather(snap_->atomData.velocity,
618 >                                   atomColData.velocity);
619 >      
620 >      cgPlanVectorColumn->gather(snap_->cgData.velocity,
621 >                                 cgColData.velocity);
622      }
623  
624      
# Line 612 | Line 638 | namespace OpenMD {
638                                     atomColData.electroFrame);
639      }
640  
641 +    // if needed, gather the atomic fluctuating charge values
642 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {
643 +      AtomPlanRealRow->gather(snap_->atomData.flucQPos,
644 +                              atomRowData.flucQPos);
645 +      AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
646 +                                 atomColData.flucQPos);
647 +    }
648 +
649   #endif      
650    }
651    
# Line 634 | Line 668 | namespace OpenMD {
668        for (int i = 0; i < n; i++)
669          snap_->atomData.density[i] += rho_tmp[i];
670      }
671 +
672 +    if (storageLayout_ & DataStorage::dslElectricField) {
673 +      
674 +      AtomPlanVectorRow->scatter(atomRowData.electricField,
675 +                                 snap_->atomData.electricField);
676 +      
677 +      int n = snap_->atomData.electricField.size();
678 +      vector<Vector3d> field_tmp(n, V3Zero);
679 +      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
680 +      for (int i = 0; i < n; i++)
681 +        snap_->atomData.electricField[i] += field_tmp[i];
682 +    }
683   #endif
684    }
685  
# Line 708 | Line 754 | namespace OpenMD {
754        }
755        
756        AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp);
757 <      for (int i = 0; i < ns; i++)
757 >      for (int i = 0; i < ns; i++)
758          snap_->atomData.skippedCharge[i] += skch_tmp[i];
759 +            
760      }
761      
762 +    if (storageLayout_ & DataStorage::dslFlucQForce) {
763 +
764 +      int nq = snap_->atomData.flucQFrc.size();
765 +      vector<RealType> fqfrc_tmp(nq, 0.0);
766 +
767 +      AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
768 +      for (int i = 0; i < nq; i++) {
769 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
770 +        fqfrc_tmp[i] = 0.0;
771 +      }
772 +      
773 +      AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
774 +      for (int i = 0; i < nq; i++)
775 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
776 +            
777 +    }
778 +
779      nLocal_ = snap_->getNumberOfAtoms();
780  
781      vector<potVec> pot_temp(nLocal_,
# Line 723 | Line 787 | namespace OpenMD {
787  
788      for (int ii = 0;  ii < pot_temp.size(); ii++ )
789        pairwisePot += pot_temp[ii];
790 <    
790 >        
791 >    if (storageLayout_ & DataStorage::dslParticlePot) {
792 >      // This is the pairwise contribution to the particle pot.  The
793 >      // embedding contribution is added in each of the low level
794 >      // non-bonded routines.  In single processor, this is done in
795 >      // unpackInteractionData, not in collectData.
796 >      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
797 >        for (int i = 0; i < nLocal_; i++) {
798 >          // factor of two is because the total potential terms are divided
799 >          // by 2 in parallel due to row/ column scatter      
800 >          snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
801 >        }
802 >      }
803 >    }
804 >
805      fill(pot_temp.begin(), pot_temp.end(),
806           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
807        
# Line 731 | Line 809 | namespace OpenMD {
809      
810      for (int ii = 0;  ii < pot_temp.size(); ii++ )
811        pairwisePot += pot_temp[ii];    
734 – #endif
812  
813 <    cerr << "pairwisePot = " <<  pairwisePot << "\n";
813 >    if (storageLayout_ & DataStorage::dslParticlePot) {
814 >      // This is the pairwise contribution to the particle pot.  The
815 >      // embedding contribution is added in each of the low level
816 >      // non-bonded routines.  In single processor, this is done in
817 >      // unpackInteractionData, not in collectData.
818 >      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
819 >        for (int i = 0; i < nLocal_; i++) {
820 >          // factor of two is because the total potential terms are divided
821 >          // by 2 in parallel due to row/ column scatter      
822 >          snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
823 >        }
824 >      }
825 >    }
826 >    
827 >    if (storageLayout_ & DataStorage::dslParticlePot) {
828 >      int npp = snap_->atomData.particlePot.size();
829 >      vector<RealType> ppot_temp(npp, 0.0);
830 >
831 >      // This is the direct or embedding contribution to the particle
832 >      // pot.
833 >      
834 >      AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
835 >      for (int i = 0; i < npp; i++) {
836 >        snap_->atomData.particlePot[i] += ppot_temp[i];
837 >      }
838 >
839 >      fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
840 >      
841 >      AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
842 >      for (int i = 0; i < npp; i++) {
843 >        snap_->atomData.particlePot[i] += ppot_temp[i];
844 >      }
845 >    }
846 >
847 >    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
848 >      RealType ploc1 = pairwisePot[ii];
849 >      RealType ploc2 = 0.0;
850 >      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
851 >      pairwisePot[ii] = ploc2;
852 >    }
853 >
854 >    // Here be dragons.
855 >    MPI::Intracomm col = colComm.getComm();
856 >
857 >    col.Allreduce(MPI::IN_PLACE,
858 >                  &snap_->frameData.conductiveHeatFlux[0], 3,
859 >                  MPI::REALTYPE, MPI::SUM);
860 >
861 >
862 > #endif
863 >
864    }
865  
866 +  /**
867 +   * Collects information obtained during the post-pair (and embedding
868 +   * functional) loops onto local data structures.
869 +   */
870 +  void ForceMatrixDecomposition::collectSelfData() {
871 +    snap_ = sman_->getCurrentSnapshot();
872 +    storageLayout_ = sman_->getStorageLayout();
873 +
874 + #ifdef IS_MPI
875 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
876 +      RealType ploc1 = embeddingPot[ii];
877 +      RealType ploc2 = 0.0;
878 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
879 +      embeddingPot[ii] = ploc2;
880 +    }    
881 + #endif
882 +    
883 +  }
884 +
885 +
886 +
887    int ForceMatrixDecomposition::getNAtomsInRow() {  
888   #ifdef IS_MPI
889      return nAtomsInRow_;
# Line 768 | Line 916 | namespace OpenMD {
916      
917   #ifdef IS_MPI
918      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";
919   #else
920      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";
921   #endif
922      
923      snap_->wrapVector(d);
924      return d;    
925    }
926  
927 +  Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
928 + #ifdef IS_MPI
929 +    return cgColData.velocity[cg2];
930 + #else
931 +    return snap_->cgData.velocity[cg2];
932 + #endif
933 +  }
934  
935 +  Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
936 + #ifdef IS_MPI
937 +    return atomColData.velocity[atom2];
938 + #else
939 +    return snap_->atomData.velocity[atom2];
940 + #endif
941 +  }
942 +
943 +
944    Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
945  
946      Vector3d d;
# Line 846 | Line 1006 | namespace OpenMD {
1006     * We need to exclude some overcounted interactions that result from
1007     * the parallel decomposition.
1008     */
1009 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1010 <    int unique_id_1, unique_id_2;
1011 <    
852 <
853 <    cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n";
1009 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1010 >    int unique_id_1, unique_id_2, group1, group2;
1011 >        
1012   #ifdef IS_MPI
1013      // in MPI, we have to look up the unique IDs for each atom
1014      unique_id_1 = AtomRowToGlobal[atom1];
1015      unique_id_2 = AtomColToGlobal[atom2];
1016 +    group1 = cgRowToGlobal[cg1];
1017 +    group2 = cgColToGlobal[cg2];
1018 + #else
1019 +    unique_id_1 = AtomLocalToGlobal[atom1];
1020 +    unique_id_2 = AtomLocalToGlobal[atom2];
1021 +    group1 = cgLocalToGlobal[cg1];
1022 +    group2 = cgLocalToGlobal[cg2];
1023 + #endif  
1024  
859 –    cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n";
860 –    // this situation should only arise in MPI simulations
1025      if (unique_id_1 == unique_id_2) return true;
1026 <    
1026 >
1027 > #ifdef IS_MPI
1028      // this prevents us from doing the pair on multiple processors
1029      if (unique_id_1 < unique_id_2) {
1030        if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1031      } else {
1032 <      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1032 >      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1033      }
1034 + #endif    
1035 +
1036 + #ifndef IS_MPI
1037 +    if (group1 == group2) {
1038 +      if (unique_id_1 < unique_id_2) return true;
1039 +    }
1040   #endif
1041 +    
1042      return false;
1043    }
1044  
# Line 880 | Line 1052 | namespace OpenMD {
1052     * field) must still be handled for these pairs.
1053     */
1054    bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) {
1055 <    int unique_id_2;
1056 < #ifdef IS_MPI
1057 <    // in MPI, we have to look up the unique IDs for the row atom.
886 <    unique_id_2 = AtomColToGlobal[atom2];
887 < #else
888 <    // in the normal loop, the atom numbers are unique
889 <    unique_id_2 = atom2;
890 < #endif
1055 >
1056 >    // excludesForAtom was constructed to use row/column indices in the MPI
1057 >    // version, and to use local IDs in the non-MPI version:
1058      
1059      for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1060           i != excludesForAtom[atom1].end(); ++i) {
1061 <      if ( (*i) == unique_id_2 ) return true;
1061 >      if ( (*i) == atom2 ) return true;
1062      }
1063  
1064      return false;
# Line 965 | Line 1132 | namespace OpenMD {
1132        idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1133      }
1134  
1135 < #else
1135 >    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
1136 >      idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1137 >      idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1138 >    }
1139  
1140 + #else
1141 +    
1142      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
971 –    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
972 –    //                         ff_->getAtomType(idents[atom2]) );
1143  
1144      if (storageLayout_ & DataStorage::dslAmat) {
1145        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 1010 | Line 1180 | namespace OpenMD {
1180        idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1181        idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1182      }
1183 +
1184 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
1185 +      idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1186 +      idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1187 +    }
1188 +
1189   #endif
1190    }
1191  
1192    
1193    void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1194   #ifdef IS_MPI
1195 <    pot_row[atom1] += 0.5 *  *(idat.pot);
1196 <    pot_col[atom2] += 0.5 *  *(idat.pot);
1195 >    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1196 >    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1197  
1198      atomRowData.force[atom1] += *(idat.f1);
1199      atomColData.force[atom2] -= *(idat.f1);
1200 +
1201 +    if (storageLayout_ & DataStorage::dslFlucQForce) {              
1202 +      atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1203 +      atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1204 +    }
1205 +
1206 +    if (storageLayout_ & DataStorage::dslElectricField) {              
1207 +      atomRowData.electricField[atom1] += *(idat.eField1);
1208 +      atomColData.electricField[atom2] += *(idat.eField2);
1209 +    }
1210 +
1211   #else
1212      pairwisePot += *(idat.pot);
1213  
1214      snap_->atomData.force[atom1] += *(idat.f1);
1215      snap_->atomData.force[atom2] -= *(idat.f1);
1216 +
1217 +    if (idat.doParticlePot) {
1218 +      // This is the pairwise contribution to the particle pot.  The
1219 +      // embedding contribution is added in each of the low level
1220 +      // non-bonded routines.  In parallel, this calculation is done
1221 +      // in collectData, not in unpackInteractionData.
1222 +      snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1223 +      snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1224 +    }
1225 +    
1226 +    if (storageLayout_ & DataStorage::dslFlucQForce) {              
1227 +      snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1228 +      snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1229 +    }
1230 +
1231 +    if (storageLayout_ & DataStorage::dslElectricField) {              
1232 +      snap_->atomData.electricField[atom1] += *(idat.eField1);
1233 +      snap_->atomData.electricField[atom2] += *(idat.eField2);
1234 +    }
1235 +
1236   #endif
1237      
1238    }
# Line 1131 | Line 1338 | namespace OpenMD {
1338          // add this cutoff group to the list of groups in this cell;
1339          cellListCol_[cellIndex].push_back(i);
1340        }
1341 +    
1342   #else
1343        for (int i = 0; i < nGroups_; i++) {
1344          rs = snap_->cgData.position[i];
# Line 1156 | Line 1364 | namespace OpenMD {
1364          // add this cutoff group to the list of groups in this cell;
1365          cellList_[cellIndex].push_back(i);
1366        }
1367 +
1368   #endif
1369  
1370        for (int m1z = 0; m1z < nCells_.z(); m1z++) {
# Line 1168 | Line 1377 | namespace OpenMD {
1377                   os != cellOffsets_.end(); ++os) {
1378                
1379                Vector3i m2v = m1v + (*os);
1380 <              
1380 >            
1381 >
1382                if (m2v.x() >= nCells_.x()) {
1383                  m2v.x() = 0;          
1384                } else if (m2v.x() < 0) {
# Line 1186 | Line 1396 | namespace OpenMD {
1396                } else if (m2v.z() < 0) {
1397                  m2v.z() = nCells_.z() - 1;
1398                }
1399 <              
1399 >
1400                int m2 = Vlinear (m2v, nCells_);
1401                
1402   #ifdef IS_MPI
# Line 1195 | Line 1405 | namespace OpenMD {
1405                  for (vector<int>::iterator j2 = cellListCol_[m2].begin();
1406                       j2 != cellListCol_[m2].end(); ++j2) {
1407                    
1408 <                  // In parallel, we need to visit *all* pairs of row &
1409 <                  // column indicies and will truncate later on.
1408 >                  // In parallel, we need to visit *all* pairs of row
1409 >                  // & column indicies and will divide labor in the
1410 >                  // force evaluation later.
1411                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1412                    snap_->wrapVector(dr);
1413                    cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1206 | Line 1417 | namespace OpenMD {
1417                  }
1418                }
1419   #else
1209 –              
1420                for (vector<int>::iterator j1 = cellList_[m1].begin();
1421                     j1 != cellList_[m1].end(); ++j1) {
1422                  for (vector<int>::iterator j2 = cellList_[m2].begin();
1423                       j2 != cellList_[m2].end(); ++j2) {
1424 <                  
1424 >    
1425                    // Always do this if we're in different cells or if
1426 <                  // we're in the same cell and the global index of the
1427 <                  // j2 cutoff group is less than the j1 cutoff group
1428 <                  
1429 <                  if (m2 != m1 || (*j2) < (*j1)) {
1426 >                  // we're in the same cell and the global index of
1427 >                  // the j2 cutoff group is greater than or equal to
1428 >                  // the j1 cutoff group.  Note that Rappaport's code
1429 >                  // has a "less than" conditional here, but that
1430 >                  // deals with atom-by-atom computation.  OpenMD
1431 >                  // allows atoms within a single cutoff group to
1432 >                  // interact with each other.
1433 >
1434 >
1435 >
1436 >                  if (m2 != m1 || (*j2) >= (*j1) ) {
1437 >
1438                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1439                      snap_->wrapVector(dr);
1440                      cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1235 | Line 1453 | namespace OpenMD {
1453        // branch to do all cutoff group pairs
1454   #ifdef IS_MPI
1455        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1456 <        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1456 >        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1457            dr = cgColData.position[j2] - cgRowData.position[j1];
1458            snap_->wrapVector(dr);
1459            cuts = getGroupCutoffs( j1, j2 );
# Line 1243 | Line 1461 | namespace OpenMD {
1461              neighborList.push_back(make_pair(j1, j2));
1462            }
1463          }
1464 <      }
1464 >      }      
1465   #else
1466 <      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1467 <        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1466 >      // include all groups here.
1467 >      for (int j1 = 0; j1 < nGroups_; j1++) {
1468 >        // include self group interactions j2 == j1
1469 >        for (int j2 = j1; j2 < nGroups_; j2++) {
1470            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1471            snap_->wrapVector(dr);
1472            cuts = getGroupCutoffs( j1, j2 );
1473            if (dr.lengthSquare() < cuts.third) {
1474              neighborList.push_back(make_pair(j1, j2));
1475            }
1476 <        }
1477 <      }        
1476 >        }    
1477 >      }
1478   #endif
1479      }
1480        

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