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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1688 by gezelter, Wed Mar 14 17:56:01 2012 UTC vs.
Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

# Line 95 | 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 109 | 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 145 | 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 165 | Line 176 | namespace OpenMD {
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_);
184      AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
# 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   #endif
563      // even in parallel, we need to zero out the local arrays:
564  
# Line 537 | Line 571 | namespace OpenMD {
571        fill(snap_->atomData.density.begin(),
572             snap_->atomData.density.end(), 0.0);
573      }
574 +
575      if (storageLayout_ & DataStorage::dslFunctional) {
576        fill(snap_->atomData.functional.begin(),
577             snap_->atomData.functional.end(), 0.0);
578      }
579 +
580      if (storageLayout_ & DataStorage::dslFunctionalDerivative) {      
581        fill(snap_->atomData.functionalDerivative.begin(),
582             snap_->atomData.functionalDerivative.end(), 0.0);
583      }
584 +
585      if (storageLayout_ & DataStorage::dslSkippedCharge) {      
586        fill(snap_->atomData.skippedCharge.begin(),
587             snap_->atomData.skippedCharge.end(), 0.0);
588      }
589 <    
589 >
590 >    if (storageLayout_ & DataStorage::dslElectricField) {      
591 >      fill(snap_->atomData.electricField.begin(),
592 >           snap_->atomData.electricField.end(), V3Zero);
593 >    }
594    }
595  
596  
# Line 572 | Line 613 | namespace OpenMD {
613      cgPlanVectorColumn->gather(snap_->cgData.position,
614                                 cgColData.position);
615  
616 +
617 +
618 +    if (needVelocities_) {
619 +      // gather up the atomic velocities
620 +      AtomPlanVectorColumn->gather(snap_->atomData.velocity,
621 +                                   atomColData.velocity);
622 +      
623 +      cgPlanVectorColumn->gather(snap_->cgData.velocity,
624 +                                 cgColData.velocity);
625 +    }
626 +
627      
628      // if needed, gather the atomic rotation matrices
629      if (storageLayout_ & DataStorage::dslAmat) {
# Line 580 | Line 632 | namespace OpenMD {
632        AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
633                                     atomColData.aMat);
634      }
635 <    
636 <    // if needed, gather the atomic eletrostatic frames
637 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
638 <      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
639 <                                atomRowData.electroFrame);
640 <      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
641 <                                   atomColData.electroFrame);
635 >
636 >    // if needed, gather the atomic eletrostatic information
637 >    if (storageLayout_ & DataStorage::dslDipole) {
638 >      AtomPlanVectorRow->gather(snap_->atomData.dipole,
639 >                                atomRowData.dipole);
640 >      AtomPlanVectorColumn->gather(snap_->atomData.dipole,
641 >                                   atomColData.dipole);
642 >    }
643 >
644 >    if (storageLayout_ & DataStorage::dslQuadrupole) {
645 >      AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
646 >                                atomRowData.quadrupole);
647 >      AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
648 >                                   atomColData.quadrupole);
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    }
# Line 611 | Line 678 | namespace OpenMD {
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    }
695  
# 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 768 | Line 959 | namespace OpenMD {
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 +
979    Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){
980  
981      Vector3d d;
# 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) {
1045 <    int unique_id_1, unique_id_2;
1044 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1045 >    int unique_id_1, unique_id_2, group1, group2;
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 +    group1 = cgLocalToGlobal[cg1];
1057 +    group2 = cgLocalToGlobal[cg2];
1058   #endif  
1059  
1060      if (unique_id_1 == unique_id_2) return true;
# Line 855 | Line 1066 | namespace OpenMD {
1066      } else {
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;
# Line 915 | Line 1132 | namespace OpenMD {
1132        idat.A2 = &(atomColData.aMat[atom2]);
1133      }
1134      
918 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
919 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
920 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
921 –    }
922 –
1135      if (storageLayout_ & DataStorage::dslTorque) {
1136        idat.t1 = &(atomRowData.torque[atom1]);
1137        idat.t2 = &(atomColData.torque[atom2]);
1138      }
1139  
1140 +    if (storageLayout_ & DataStorage::dslDipole) {
1141 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1142 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1143 +    }
1144 +
1145 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1146 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1147 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1148 +    }
1149 +
1150      if (storageLayout_ & DataStorage::dslDensity) {
1151        idat.rho1 = &(atomRowData.density[atom1]);
1152        idat.rho2 = &(atomColData.density[atom2]);
# Line 950 | Line 1172 | namespace OpenMD {
1172        idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
1173      }
1174  
1175 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
1176 +      idat.flucQ1 = &(atomRowData.flucQPos[atom1]);
1177 +      idat.flucQ2 = &(atomColData.flucQPos[atom2]);
1178 +    }
1179 +
1180   #else
1181      
955 –
956 –    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
957 –    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
958 –    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
959 –
1182      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
961 –    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
962 –    //                         ff_->getAtomType(idents[atom2]) );
1183  
1184      if (storageLayout_ & DataStorage::dslAmat) {
1185        idat.A1 = &(snap_->atomData.aMat[atom1]);
1186        idat.A2 = &(snap_->atomData.aMat[atom2]);
1187      }
1188  
969 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
970 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
971 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
972 –    }
973 –
1189      if (storageLayout_ & DataStorage::dslTorque) {
1190        idat.t1 = &(snap_->atomData.torque[atom1]);
1191        idat.t2 = &(snap_->atomData.torque[atom2]);
1192      }
1193  
1194 +    if (storageLayout_ & DataStorage::dslDipole) {
1195 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1196 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1197 +    }
1198 +
1199 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1200 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1201 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1202 +    }
1203 +
1204      if (storageLayout_ & DataStorage::dslDensity) {    
1205        idat.rho1 = &(snap_->atomData.density[atom1]);
1206        idat.rho2 = &(snap_->atomData.density[atom2]);
# Line 1000 | Line 1225 | namespace OpenMD {
1225        idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
1226        idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
1227      }
1228 +
1229 +    if (storageLayout_ & DataStorage::dslFlucQPosition) {              
1230 +      idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]);
1231 +      idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]);
1232 +    }
1233 +
1234   #endif
1235    }
1236  
# Line 1008 | Line 1239 | namespace OpenMD {
1239   #ifdef IS_MPI
1240      pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1241      pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1242 +    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1243 +    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1244  
1245      atomRowData.force[atom1] += *(idat.f1);
1246      atomColData.force[atom2] -= *(idat.f1);
1247 +
1248 +    if (storageLayout_ & DataStorage::dslFlucQForce) {              
1249 +      atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1250 +      atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1251 +    }
1252 +
1253 +    if (storageLayout_ & DataStorage::dslElectricField) {              
1254 +      atomRowData.electricField[atom1] += *(idat.eField1);
1255 +      atomColData.electricField[atom2] += *(idat.eField2);
1256 +    }
1257 +
1258   #else
1259      pairwisePot += *(idat.pot);
1260 +    excludedPot += *(idat.excludedPot);
1261  
1262      snap_->atomData.force[atom1] += *(idat.f1);
1263      snap_->atomData.force[atom2] -= *(idat.f1);
1264 +
1265 +    if (idat.doParticlePot) {
1266 +      // This is the pairwise contribution to the particle pot.  The
1267 +      // embedding contribution is added in each of the low level
1268 +      // non-bonded routines.  In parallel, this calculation is done
1269 +      // in collectData, not in unpackInteractionData.
1270 +      snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw);
1271 +      snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw);
1272 +    }
1273 +    
1274 +    if (storageLayout_ & DataStorage::dslFlucQForce) {              
1275 +      snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1276 +      snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1277 +    }
1278 +
1279 +    if (storageLayout_ & DataStorage::dslElectricField) {              
1280 +      snap_->atomData.electricField[atom1] += *(idat.eField1);
1281 +      snap_->atomData.electricField[atom2] += *(idat.eField2);
1282 +    }
1283 +
1284   #endif
1285      
1286    }
# Line 1084 | Line 1349 | namespace OpenMD {
1349          for (int j = 0; j < 3; j++) {
1350            scaled[j] -= roundMe(scaled[j]);
1351            scaled[j] += 0.5;
1352 +          // Handle the special case when an object is exactly on the
1353 +          // boundary (a scaled coordinate of 1.0 is the same as
1354 +          // scaled coordinate of 0.0)
1355 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1356          }
1357          
1358          // find xyz-indices of cell that cutoffGroup is in.
# Line 1108 | Line 1377 | namespace OpenMD {
1377          for (int j = 0; j < 3; j++) {
1378            scaled[j] -= roundMe(scaled[j]);
1379            scaled[j] += 0.5;
1380 +          // Handle the special case when an object is exactly on the
1381 +          // boundary (a scaled coordinate of 1.0 is the same as
1382 +          // scaled coordinate of 0.0)
1383 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1384          }
1385          
1386          // find xyz-indices of cell that cutoffGroup is in.
# Line 1134 | Line 1407 | namespace OpenMD {
1407          for (int j = 0; j < 3; j++) {
1408            scaled[j] -= roundMe(scaled[j]);
1409            scaled[j] += 0.5;
1410 +          // Handle the special case when an object is exactly on the
1411 +          // boundary (a scaled coordinate of 1.0 is the same as
1412 +          // scaled coordinate of 0.0)
1413 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1414          }
1415          
1416          // find xyz-indices of cell that cutoffGroup is in.

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