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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1613 by gezelter, Thu Aug 18 20:18:19 2011 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1796 by gezelter, Mon Sep 10 18:38:44 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 94 | 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 108 | 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 144 | 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 163 | Line 175 | namespace OpenMD {
175  
176      pot_row.resize(nAtomsInRow_);
177      pot_col.resize(nAtomsInCol_);
178 +
179 +    expot_row.resize(nAtomsInRow_);
180 +    expot_col.resize(nAtomsInCol_);
181  
182      AtomRowToGlobal.resize(nAtomsInRow_);
183      AtomColToGlobal.resize(nAtomsInCol_);
# Line 247 | Line 262 | namespace OpenMD {
262        for (int j = 0; j < nLocal_; j++) {
263          int jglob = AtomLocalToGlobal[j];
264  
265 <        if (excludes->hasPair(iglob, jglob))          
265 >        if (excludes->hasPair(iglob, jglob))
266            excludesForAtom[i].push_back(j);              
267          
253 –        
268          if (oneTwo->hasPair(iglob, jglob)) {
269            toposForAtom[i].push_back(j);
270            topoDist[i].push_back(1);
# Line 296 | Line 310 | namespace OpenMD {
310      
311      RealType tol = 1e-6;
312      largestRcut_ = 0.0;
299 –    RealType rc;
313      int atid;
314      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315      
# Line 381 | Line 394 | namespace OpenMD {
394        }
395        
396        bool gTypeFound = false;
397 <      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
397 >      for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
398          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
399            groupToGtype[cg1] = gt;
400            gTypeFound = true;
# Line 406 | Line 419 | namespace OpenMD {
419      
420      RealType tradRcut = groupMax;
421  
422 <    for (int i = 0; i < gTypeCutoffs.size();  i++) {
423 <      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
422 >    for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
423 >      for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {      
424          RealType thisRcut;
425          switch(cutoffPolicy_) {
426          case TRADITIONAL:
# Line 450 | Line 463 | namespace OpenMD {
463      }
464    }
465  
453 –
466    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467      int i, j;  
468   #ifdef IS_MPI
# Line 464 | Line 476 | namespace OpenMD {
476    }
477  
478    int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
479 <    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
479 >    for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
480        if (toposForAtom[atom1][j] == atom2)
481          return topoDist[atom1][j];
482      }
# Line 474 | Line 486 | namespace OpenMD {
486    void ForceMatrixDecomposition::zeroWorkArrays() {
487      pairwisePot = 0.0;
488      embeddingPot = 0.0;
489 +    excludedPot = 0.0;
490 +    excludedSelfPot = 0.0;
491  
492   #ifdef IS_MPI
493      if (storageLayout_ & DataStorage::dslForce) {
# Line 492 | Line 506 | namespace OpenMD {
506      fill(pot_col.begin(), pot_col.end(),
507           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
508  
509 +    fill(expot_row.begin(), expot_row.end(),
510 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
511 +
512 +    fill(expot_col.begin(), expot_col.end(),
513 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
514 +
515      if (storageLayout_ & DataStorage::dslParticlePot) {    
516        fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
517             0.0);
# Line 523 | Line 543 | namespace OpenMD {
543             atomRowData.skippedCharge.end(), 0.0);
544        fill(atomColData.skippedCharge.begin(),
545             atomColData.skippedCharge.end(), 0.0);
546 +    }
547 +
548 +    if (storageLayout_ & DataStorage::dslFlucQForce) {      
549 +      fill(atomRowData.flucQFrc.begin(),
550 +           atomRowData.flucQFrc.end(), 0.0);
551 +      fill(atomColData.flucQFrc.begin(),
552 +           atomColData.flucQFrc.end(), 0.0);
553      }
554  
555 +    if (storageLayout_ & DataStorage::dslElectricField) {    
556 +      fill(atomRowData.electricField.begin(),
557 +           atomRowData.electricField.end(), V3Zero);
558 +      fill(atomColData.electricField.begin(),
559 +           atomColData.electricField.end(), V3Zero);
560 +    }
561 +
562 +    if (storageLayout_ & DataStorage::dslFlucQForce) {    
563 +      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
564 +           0.0);
565 +      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
566 +           0.0);
567 +    }
568 +
569   #endif
570      // even in parallel, we need to zero out the local arrays:
571  
# Line 537 | Line 578 | namespace OpenMD {
578        fill(snap_->atomData.density.begin(),
579             snap_->atomData.density.end(), 0.0);
580      }
581 +
582      if (storageLayout_ & DataStorage::dslFunctional) {
583        fill(snap_->atomData.functional.begin(),
584             snap_->atomData.functional.end(), 0.0);
585      }
586 +
587      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
588        fill(snap_->atomData.functionalDerivative.begin(),
589             snap_->atomData.functionalDerivative.end(), 0.0);
590      }
591 +
592      if (storageLayout_ & DataStorage::dslSkippedCharge) {      
593        fill(snap_->atomData.skippedCharge.begin(),
594             snap_->atomData.skippedCharge.end(), 0.0);
595      }
596 <    
596 >
597 >    if (storageLayout_ & DataStorage::dslElectricField) {      
598 >      fill(snap_->atomData.electricField.begin(),
599 >           snap_->atomData.electricField.end(), V3Zero);
600 >    }
601    }
602  
603  
# Line 572 | Line 620 | namespace OpenMD {
620      cgPlanVectorColumn->gather(snap_->cgData.position,
621                                 cgColData.position);
622  
623 +
624 +
625 +    if (needVelocities_) {
626 +      // gather up the atomic velocities
627 +      AtomPlanVectorColumn->gather(snap_->atomData.velocity,
628 +                                   atomColData.velocity);
629 +      
630 +      cgPlanVectorColumn->gather(snap_->cgData.velocity,
631 +                                 cgColData.velocity);
632 +    }
633 +
634      
635      // if needed, gather the atomic rotation matrices
636      if (storageLayout_ & DataStorage::dslAmat) {
# Line 589 | Line 648 | namespace OpenMD {
648                                     atomColData.electroFrame);
649      }
650  
651 +    // if needed, gather the atomic fluctuating charge values
652 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {
653 +      AtomPlanRealRow->gather(snap_->atomData.flucQPos,
654 +                              atomRowData.flucQPos);
655 +      AtomPlanRealColumn->gather(snap_->atomData.flucQPos,
656 +                                 atomColData.flucQPos);
657 +    }
658 +
659   #endif      
660    }
661    
# Line 610 | Line 677 | namespace OpenMD {
677        AtomPlanRealColumn->scatter(atomColData.density, rho_tmp);
678        for (int i = 0; i < n; i++)
679          snap_->atomData.density[i] += rho_tmp[i];
680 +    }
681 +
682 +    if (storageLayout_ & DataStorage::dslElectricField) {
683 +      
684 +      AtomPlanVectorRow->scatter(atomRowData.electricField,
685 +                                 snap_->atomData.electricField);
686 +      
687 +      int n = snap_->atomData.electricField.size();
688 +      vector<Vector3d> field_tmp(n, V3Zero);
689 +      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
690 +      for (int i = 0; i < n; i++)
691 +        snap_->atomData.electricField[i] += field_tmp[i];
692      }
693   #endif
694    }
# Line 690 | Line 769 | namespace OpenMD {
769              
770      }
771      
772 +    if (storageLayout_ & DataStorage::dslFlucQForce) {
773 +
774 +      int nq = snap_->atomData.flucQFrc.size();
775 +      vector<RealType> fqfrc_tmp(nq, 0.0);
776 +
777 +      AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp);
778 +      for (int i = 0; i < nq; i++) {
779 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
780 +        fqfrc_tmp[i] = 0.0;
781 +      }
782 +      
783 +      AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp);
784 +      for (int i = 0; i < nq; i++)
785 +        snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
786 +            
787 +    }
788 +
789      nLocal_ = snap_->getNumberOfAtoms();
790  
791      vector<potVec> pot_temp(nLocal_,
792                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
793 +    vector<potVec> expot_temp(nLocal_,
794 +                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
795  
796      // scatter/gather pot_row into the members of my column
797            
798      AtomPlanPotRow->scatter(pot_row, pot_temp);
799 +    AtomPlanPotRow->scatter(expot_row, expot_temp);
800  
801 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
801 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
802        pairwisePot += pot_temp[ii];
803 <    
803 >
804 >    for (int ii = 0;  ii < expot_temp.size(); ii++ )
805 >      excludedPot += expot_temp[ii];
806 >        
807 >    if (storageLayout_ & DataStorage::dslParticlePot) {
808 >      // This is the pairwise contribution to the particle pot.  The
809 >      // embedding contribution is added in each of the low level
810 >      // non-bonded routines.  In single processor, this is done in
811 >      // unpackInteractionData, not in collectData.
812 >      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
813 >        for (int i = 0; i < nLocal_; i++) {
814 >          // factor of two is because the total potential terms are divided
815 >          // by 2 in parallel due to row/ column scatter      
816 >          snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
817 >        }
818 >      }
819 >    }
820 >
821      fill(pot_temp.begin(), pot_temp.end(),
822           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
823 +    fill(expot_temp.begin(), expot_temp.end(),
824 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
825        
826      AtomPlanPotColumn->scatter(pot_col, pot_temp);    
827 +    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
828      
829      for (int ii = 0;  ii < pot_temp.size(); ii++ )
830        pairwisePot += pot_temp[ii];    
831 +
832 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
833 +      excludedPot += expot_temp[ii];    
834 +
835 +    if (storageLayout_ & DataStorage::dslParticlePot) {
836 +      // This is the pairwise contribution to the particle pot.  The
837 +      // embedding contribution is added in each of the low level
838 +      // non-bonded routines.  In single processor, this is done in
839 +      // unpackInteractionData, not in collectData.
840 +      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
841 +        for (int i = 0; i < nLocal_; i++) {
842 +          // factor of two is because the total potential terms are divided
843 +          // by 2 in parallel due to row/ column scatter      
844 +          snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii);
845 +        }
846 +      }
847 +    }
848      
849 +    if (storageLayout_ & DataStorage::dslParticlePot) {
850 +      int npp = snap_->atomData.particlePot.size();
851 +      vector<RealType> ppot_temp(npp, 0.0);
852 +
853 +      // This is the direct or embedding contribution to the particle
854 +      // pot.
855 +      
856 +      AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp);
857 +      for (int i = 0; i < npp; i++) {
858 +        snap_->atomData.particlePot[i] += ppot_temp[i];
859 +      }
860 +
861 +      fill(ppot_temp.begin(), ppot_temp.end(), 0.0);
862 +      
863 +      AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp);
864 +      for (int i = 0; i < npp; i++) {
865 +        snap_->atomData.particlePot[i] += ppot_temp[i];
866 +      }
867 +    }
868 +
869      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
870        RealType ploc1 = pairwisePot[ii];
871        RealType ploc2 = 0.0;
# Line 718 | Line 874 | namespace OpenMD {
874      }
875  
876      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
877 <      RealType ploc1 = embeddingPot[ii];
877 >      RealType ploc1 = excludedPot[ii];
878        RealType ploc2 = 0.0;
879        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
880 <      embeddingPot[ii] = ploc2;
880 >      excludedPot[ii] = ploc2;
881      }
882  
883 +    // Here be dragons.
884 +    MPI::Intracomm col = colComm.getComm();
885 +
886 +    col.Allreduce(MPI::IN_PLACE,
887 +                  &snap_->frameData.conductiveHeatFlux[0], 3,
888 +                  MPI::REALTYPE, MPI::SUM);
889 +
890 +
891   #endif
892  
893    }
894  
895 +  /**
896 +   * Collects information obtained during the post-pair (and embedding
897 +   * functional) loops onto local data structures.
898 +   */
899 +  void ForceMatrixDecomposition::collectSelfData() {
900 +    snap_ = sman_->getCurrentSnapshot();
901 +    storageLayout_ = sman_->getStorageLayout();
902 +
903 + #ifdef IS_MPI
904 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
905 +      RealType ploc1 = embeddingPot[ii];
906 +      RealType ploc2 = 0.0;
907 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
908 +      embeddingPot[ii] = ploc2;
909 +    }    
910 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
911 +      RealType ploc1 = excludedSelfPot[ii];
912 +      RealType ploc2 = 0.0;
913 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
914 +      excludedSelfPot[ii] = ploc2;
915 +    }    
916 + #endif
917 +    
918 +  }
919 +
920 +
921 +
922    int ForceMatrixDecomposition::getNAtomsInRow() {  
923   #ifdef IS_MPI
924      return nAtomsInRow_;
# Line 766 | Line 957 | namespace OpenMD {
957      
958      snap_->wrapVector(d);
959      return d;    
960 +  }
961 +
962 +  Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
963 + #ifdef IS_MPI
964 +    return cgColData.velocity[cg2];
965 + #else
966 +    return snap_->cgData.velocity[cg2];
967 + #endif
968 +  }
969 +
970 +  Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
971 + #ifdef IS_MPI
972 +    return atomColData.velocity[atom2];
973 + #else
974 +    return snap_->atomData.velocity[atom2];
975 + #endif
976    }
977  
978  
# Line 834 | Line 1041 | namespace OpenMD {
1041     * We need to exclude some overcounted interactions that result from
1042     * the parallel decomposition.
1043     */
1044 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1044 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1045      int unique_id_1, unique_id_2;
1046 <    
1046 >        
1047   #ifdef IS_MPI
1048      // in MPI, we have to look up the unique IDs for each atom
1049      unique_id_1 = AtomRowToGlobal[atom1];
1050      unique_id_2 = AtomColToGlobal[atom2];
1051 +    // group1 = cgRowToGlobal[cg1];
1052 +    // group2 = cgColToGlobal[cg2];
1053 + #else
1054 +    unique_id_1 = AtomLocalToGlobal[atom1];
1055 +    unique_id_2 = AtomLocalToGlobal[atom2];
1056 +    int group1 = cgLocalToGlobal[cg1];
1057 +    int group2 = cgLocalToGlobal[cg2];
1058 + #endif  
1059  
845 –    // this situation should only arise in MPI simulations
1060      if (unique_id_1 == unique_id_2) return true;
1061 <    
1061 >
1062 > #ifdef IS_MPI
1063      // this prevents us from doing the pair on multiple processors
1064      if (unique_id_1 < unique_id_2) {
1065        if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1066      } else {
1067 <      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1067 >      if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1068      }
1069 + #endif    
1070 +
1071 + #ifndef IS_MPI
1072 +    if (group1 == group2) {
1073 +      if (unique_id_1 < unique_id_2) return true;
1074 +    }
1075   #endif
1076 +    
1077      return false;
1078    }
1079  
# Line 871 | Line 1093 | namespace OpenMD {
1093      
1094      for (vector<int>::iterator i = excludesForAtom[atom1].begin();
1095           i != excludesForAtom[atom1].end(); ++i) {
1096 <      if ( (*i) == atom2 )  return true;
1096 >      if ( (*i) == atom2 ) return true;
1097      }
1098  
1099      return false;
# Line 945 | Line 1167 | namespace OpenMD {
1167        idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1168      }
1169  
1170 < #else
1170 >    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
1171 >      idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1172 >      idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1173 >    }
1174  
1175 + #else
1176 +    
1177      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
951 –    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
952 –    //                         ff_->getAtomType(idents[atom2]) );
1178  
1179      if (storageLayout_ & DataStorage::dslAmat) {
1180        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 989 | Line 1214 | namespace OpenMD {
1214      if (storageLayout_ & DataStorage::dslSkippedCharge) {
1215        idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1216        idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1217 +    }
1218 +
1219 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
1220 +      idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1221 +      idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1222      }
1223 +
1224   #endif
1225    }
1226  
1227    
1228    void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
1229   #ifdef IS_MPI
1230 <    pot_row[atom1] += 0.5 *  *(idat.pot);
1231 <    pot_col[atom2] += 0.5 *  *(idat.pot);
1230 >    pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1231 >    pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1232 >    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1233 >    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1234  
1235      atomRowData.force[atom1] += *(idat.f1);
1236      atomColData.force[atom2] -= *(idat.f1);
1237 +
1238 +    if (storageLayout_ & DataStorage::dslFlucQForce) {              
1239 +      atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1240 +      atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1241 +    }
1242 +
1243 +    if (storageLayout_ & DataStorage::dslElectricField) {              
1244 +      atomRowData.electricField[atom1] += *(idat.eField1);
1245 +      atomColData.electricField[atom2] += *(idat.eField2);
1246 +    }
1247 +
1248   #else
1249      pairwisePot += *(idat.pot);
1250 +    excludedPot += *(idat.excludedPot);
1251  
1252      snap_->atomData.force[atom1] += *(idat.f1);
1253      snap_->atomData.force[atom2] -= *(idat.f1);
1254 +
1255 +    if (idat.doParticlePot) {
1256 +      // This is the pairwise contribution to the particle pot.  The
1257 +      // embedding contribution is added in each of the low level
1258 +      // non-bonded routines.  In parallel, this calculation is done
1259 +      // in collectData, not in unpackInteractionData.
1260 +      snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1261 +      snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1262 +    }
1263 +    
1264 +    if (storageLayout_ & DataStorage::dslFlucQForce) {              
1265 +      snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1266 +      snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1267 +    }
1268 +
1269 +    if (storageLayout_ & DataStorage::dslElectricField) {              
1270 +      snap_->atomData.electricField[atom1] += *(idat.eField1);
1271 +      snap_->atomData.electricField[atom2] += *(idat.eField2);
1272 +    }
1273 +
1274   #endif
1275      
1276    }
# Line 1030 | Line 1295 | namespace OpenMD {
1295   #endif
1296  
1297      RealType rList_ = (largestRcut_ + skinThickness_);
1033 –    RealType rl2 = rList_ * rList_;
1298      Snapshot* snap_ = sman_->getCurrentSnapshot();
1299      Mat3x3d Hmat = snap_->getHmat();
1300      Vector3d Hx = Hmat.getColumn(0);
# Line 1074 | Line 1338 | namespace OpenMD {
1338          for (int j = 0; j < 3; j++) {
1339            scaled[j] -= roundMe(scaled[j]);
1340            scaled[j] += 0.5;
1341 +          // Handle the special case when an object is exactly on the
1342 +          // boundary (a scaled coordinate of 1.0 is the same as
1343 +          // scaled coordinate of 0.0)
1344 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1345          }
1346          
1347          // find xyz-indices of cell that cutoffGroup is in.
# Line 1098 | Line 1366 | namespace OpenMD {
1366          for (int j = 0; j < 3; j++) {
1367            scaled[j] -= roundMe(scaled[j]);
1368            scaled[j] += 0.5;
1369 +          // Handle the special case when an object is exactly on the
1370 +          // boundary (a scaled coordinate of 1.0 is the same as
1371 +          // scaled coordinate of 0.0)
1372 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1373          }
1374          
1375          // find xyz-indices of cell that cutoffGroup is in.
# Line 1124 | Line 1396 | namespace OpenMD {
1396          for (int j = 0; j < 3; j++) {
1397            scaled[j] -= roundMe(scaled[j]);
1398            scaled[j] += 0.5;
1399 +          // Handle the special case when an object is exactly on the
1400 +          // boundary (a scaled coordinate of 1.0 is the same as
1401 +          // scaled coordinate of 0.0)
1402 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1403          }
1404          
1405          // find xyz-indices of cell that cutoffGroup is in.
# Line 1190 | Line 1466 | namespace OpenMD {
1466                  }
1467                }
1468   #else
1193 –              
1469                for (vector<int>::iterator j1 = cellList_[m1].begin();
1470                     j1 != cellList_[m1].end(); ++j1) {
1471                  for (vector<int>::iterator j2 = cellList_[m2].begin();
1472                       j2 != cellList_[m2].end(); ++j2) {
1473 <                  
1473 >    
1474                    // Always do this if we're in different cells or if
1475 <                  // we're in the same cell and the global index of the
1476 <                  // j2 cutoff group is less than the j1 cutoff group
1477 <                  
1478 <                  if (m2 != m1 || (*j2) < (*j1)) {
1475 >                  // we're in the same cell and the global index of
1476 >                  // the j2 cutoff group is greater than or equal to
1477 >                  // the j1 cutoff group.  Note that Rappaport's code
1478 >                  // has a "less than" conditional here, but that
1479 >                  // deals with atom-by-atom computation.  OpenMD
1480 >                  // allows atoms within a single cutoff group to
1481 >                  // interact with each other.
1482 >
1483 >
1484 >
1485 >                  if (m2 != m1 || (*j2) >= (*j1) ) {
1486 >
1487                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1488                      snap_->wrapVector(dr);
1489                      cuts = getGroupCutoffs( (*j1), (*j2) );
# Line 1219 | Line 1502 | namespace OpenMD {
1502        // branch to do all cutoff group pairs
1503   #ifdef IS_MPI
1504        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1505 <        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {      
1505 >        for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1506            dr = cgColData.position[j2] - cgRowData.position[j1];
1507            snap_->wrapVector(dr);
1508            cuts = getGroupCutoffs( j1, j2 );
# Line 1227 | Line 1510 | namespace OpenMD {
1510              neighborList.push_back(make_pair(j1, j2));
1511            }
1512          }
1513 <      }
1513 >      }      
1514   #else
1515 <      for (int j1 = 0; j1 < nGroups_ - 1; j1++) {
1516 <        for (int j2 = j1 + 1; j2 < nGroups_; j2++) {
1515 >      // include all groups here.
1516 >      for (int j1 = 0; j1 < nGroups_; j1++) {
1517 >        // include self group interactions j2 == j1
1518 >        for (int j2 = j1; j2 < nGroups_; j2++) {
1519            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1520            snap_->wrapVector(dr);
1521            cuts = getGroupCutoffs( j1, j2 );
1522            if (dr.lengthSquare() < cuts.third) {
1523              neighborList.push_back(make_pair(j1, j2));
1524            }
1525 <        }
1526 <      }        
1525 >        }    
1526 >      }
1527   #endif
1528      }
1529        

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