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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1736 by jmichalk, Tue Jun 5 17:51:31 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

# Line 35 | Line 35
35   *                                                                      
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).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
# Line 99 | Line 99 | namespace OpenMD {
99      nGroups_ = info_->getNLocalCutoffGroups();
100      // gather the information for atomtype IDs (atids):
101      idents = info_->getIdentArray();
102 +    regions = info_->getRegions();
103      AtomLocalToGlobal = info_->getGlobalAtomIndices();
104      cgLocalToGlobal = info_->getGlobalGroupIndices();
105      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
# Line 118 | Line 119 | namespace OpenMD {
119      
120   #ifdef IS_MPI
121  
122 <    MPI::Intracomm row = rowComm.getComm();
123 <    MPI::Intracomm col = colComm.getComm();
122 >    MPI_Comm row = rowComm.getComm();
123 >    MPI_Comm col = colComm.getComm();
124  
125      AtomPlanIntRow = new Plan<int>(row, nLocal_);
126      AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
# Line 163 | Line 164 | namespace OpenMD {
164      
165      AtomPlanIntRow->gather(idents, identsRow);
166      AtomPlanIntColumn->gather(idents, identsCol);
167 +
168 +    regionsRow.resize(nAtomsInRow_);
169 +    regionsCol.resize(nAtomsInCol_);
170      
171 +    AtomPlanIntRow->gather(regions, regionsRow);
172 +    AtomPlanIntColumn->gather(regions, regionsCol);
173 +    
174      // allocate memory for the parallel objects
175      atypesRow.resize(nAtomsInRow_);
176      atypesCol.resize(nAtomsInCol_);
# Line 176 | Line 183 | namespace OpenMD {
183      pot_row.resize(nAtomsInRow_);
184      pot_col.resize(nAtomsInCol_);
185  
186 +    expot_row.resize(nAtomsInRow_);
187 +    expot_col.resize(nAtomsInCol_);
188 +
189      AtomRowToGlobal.resize(nAtomsInRow_);
190      AtomColToGlobal.resize(nAtomsInCol_);
191      AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
# Line 305 | Line 315 | namespace OpenMD {
315    
316    void ForceMatrixDecomposition::createGtypeCutoffMap() {
317      
318 +    GrCut.clear();
319 +    GrCutSq.clear();
320 +    GrlistSq.clear();
321 +
322      RealType tol = 1e-6;
323      largestRcut_ = 0.0;
310 –    RealType rc;
324      int atid;
325      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
326      
# Line 392 | Line 405 | namespace OpenMD {
405        }
406        
407        bool gTypeFound = false;
408 <      for (int gt = 0; gt < gTypeCutoffs.size(); gt++) {
408 >      for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) {
409          if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) {
410            groupToGtype[cg1] = gt;
411            gTypeFound = true;
# Line 411 | Line 424 | namespace OpenMD {
424                                       gTypeCutoffs.end());
425  
426   #ifdef IS_MPI
427 <    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
428 <                              MPI::MAX);
427 >    MPI_Allreduce(&groupMax, &groupMax, 1, MPI_REALTYPE,
428 >                  MPI_MAX, MPI_COMM_WORLD);
429   #endif
430      
431      RealType tradRcut = groupMax;
432  
433 <    for (int i = 0; i < gTypeCutoffs.size();  i++) {
434 <      for (int j = 0; j < gTypeCutoffs.size();  j++) {      
433 >    GrCut.resize( gTypeCutoffs.size() );
434 >    GrCutSq.resize( gTypeCutoffs.size() );
435 >    GrlistSq.resize( gTypeCutoffs.size() );
436 >
437 >
438 >    for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
439 >      GrCut[i].resize( gTypeCutoffs.size() , 0.0);
440 >      GrCutSq[i].resize( gTypeCutoffs.size(), 0.0 );
441 >      GrlistSq[i].resize( gTypeCutoffs.size(), 0.0 );
442 >
443 >      for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {      
444          RealType thisRcut;
445          switch(cutoffPolicy_) {
446          case TRADITIONAL:
# Line 440 | Line 462 | namespace OpenMD {
462            break;
463          }
464  
465 <        pair<int,int> key = make_pair(i,j);
444 <        gTypeCutoffMap[key].first = thisRcut;
465 >        GrCut[i][j] = thisRcut;
466          if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
467 <        gTypeCutoffMap[key].second = thisRcut*thisRcut;
468 <        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
467 >        GrCutSq[i][j] = thisRcut * thisRcut;
468 >        GrlistSq[i][j] = pow(thisRcut + skinThickness_, 2);
469 >
470 >        // pair<int,int> key = make_pair(i,j);
471 >        // gTypeCutoffMap[key].first = thisRcut;
472 >        // gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
473          // sanity check
474          
475          if (userChoseCutoff_) {
476 <          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
476 >          if (abs(GrCut[i][j] - userCutoff_) > 0.0001) {
477              sprintf(painCave.errMsg,
478                      "ForceMatrixDecomposition::createGtypeCutoffMap "
479                      "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
# Line 461 | Line 486 | namespace OpenMD {
486      }
487    }
488  
489 <
465 <  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
489 >  void ForceMatrixDecomposition::getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) {
490      int i, j;  
491   #ifdef IS_MPI
492      i = groupRowToGtype[cg1];
# Line 471 | Line 495 | namespace OpenMD {
495      i = groupToGtype[cg1];
496      j = groupToGtype[cg2];
497   #endif    
498 <    return gTypeCutoffMap[make_pair(i,j)];
498 >    rcut = GrCut[i][j];
499 >    rcutsq = GrCutSq[i][j];
500 >    rlistsq = GrlistSq[i][j];
501 >    return;
502 >    //return gTypeCutoffMap[make_pair(i,j)];
503    }
504  
505    int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
506 <    for (int j = 0; j < toposForAtom[atom1].size(); j++) {
506 >    for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
507        if (toposForAtom[atom1][j] == atom2)
508          return topoDist[atom1][j];
509 <    }
509 >    }                                          
510      return 0;
511    }
512  
513    void ForceMatrixDecomposition::zeroWorkArrays() {
514      pairwisePot = 0.0;
515      embeddingPot = 0.0;
516 +    excludedPot = 0.0;
517 +    excludedSelfPot = 0.0;
518  
519   #ifdef IS_MPI
520      if (storageLayout_ & DataStorage::dslForce) {
# Line 503 | Line 533 | namespace OpenMD {
533      fill(pot_col.begin(), pot_col.end(),
534           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
535  
536 +    fill(expot_row.begin(), expot_row.end(),
537 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
538 +
539 +    fill(expot_col.begin(), expot_col.end(),
540 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
541 +
542      if (storageLayout_ & DataStorage::dslParticlePot) {    
543        fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(),
544             0.0);
# Line 550 | Line 586 | namespace OpenMD {
586             atomColData.electricField.end(), V3Zero);
587      }
588  
553 –    if (storageLayout_ & DataStorage::dslFlucQForce) {    
554 –      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
555 –           0.0);
556 –      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
557 –           0.0);
558 –    }
559 –
589   #endif
590      // even in parallel, we need to zero out the local arrays:
591  
# Line 630 | Line 659 | namespace OpenMD {
659        AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
660                                     atomColData.aMat);
661      }
662 <    
663 <    // if needed, gather the atomic eletrostatic frames
664 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
665 <      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
666 <                                atomRowData.electroFrame);
667 <      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
668 <                                   atomColData.electroFrame);
662 >
663 >    // if needed, gather the atomic eletrostatic information
664 >    if (storageLayout_ & DataStorage::dslDipole) {
665 >      AtomPlanVectorRow->gather(snap_->atomData.dipole,
666 >                                atomRowData.dipole);
667 >      AtomPlanVectorColumn->gather(snap_->atomData.dipole,
668 >                                   atomColData.dipole);
669      }
670  
671 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
672 +      AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
673 +                                atomRowData.quadrupole);
674 +      AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
675 +                                   atomColData.quadrupole);
676 +    }
677 +        
678      // if needed, gather the atomic fluctuating charge values
679      if (storageLayout_ & DataStorage::dslFlucQPosition) {
680        AtomPlanRealRow->gather(snap_->atomData.flucQPos,
# Line 670 | Line 706 | namespace OpenMD {
706          snap_->atomData.density[i] += rho_tmp[i];
707      }
708  
709 +    // this isn't necessary if we don't have polarizable atoms, but
710 +    // we'll leave it here for now.
711      if (storageLayout_ & DataStorage::dslElectricField) {
712        
713        AtomPlanVectorRow->scatter(atomRowData.electricField,
# Line 677 | Line 715 | namespace OpenMD {
715        
716        int n = snap_->atomData.electricField.size();
717        vector<Vector3d> field_tmp(n, V3Zero);
718 <      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
718 >      AtomPlanVectorColumn->scatter(atomColData.electricField,
719 >                                    field_tmp);
720        for (int i = 0; i < n; i++)
721          snap_->atomData.electricField[i] += field_tmp[i];
722      }
# Line 777 | Line 816 | namespace OpenMD {
816              
817      }
818  
819 +    if (storageLayout_ & DataStorage::dslElectricField) {
820 +
821 +      int nef = snap_->atomData.electricField.size();
822 +      vector<Vector3d> efield_tmp(nef, V3Zero);
823 +
824 +      AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
825 +      for (int i = 0; i < nef; i++) {
826 +        snap_->atomData.electricField[i] += efield_tmp[i];
827 +        efield_tmp[i] = 0.0;
828 +      }
829 +      
830 +      AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
831 +      for (int i = 0; i < nef; i++)
832 +        snap_->atomData.electricField[i] += efield_tmp[i];
833 +    }
834 +
835 +
836      nLocal_ = snap_->getNumberOfAtoms();
837  
838      vector<potVec> pot_temp(nLocal_,
839                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
840 +    vector<potVec> expot_temp(nLocal_,
841 +                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
842  
843      // scatter/gather pot_row into the members of my column
844            
845      AtomPlanPotRow->scatter(pot_row, pot_temp);
846 +    AtomPlanPotRow->scatter(expot_row, expot_temp);
847  
848 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
848 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
849        pairwisePot += pot_temp[ii];
850 +
851 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
852 +      excludedPot += expot_temp[ii];
853          
854      if (storageLayout_ & DataStorage::dslParticlePot) {
855        // This is the pairwise contribution to the particle pot.  The
# Line 805 | Line 867 | namespace OpenMD {
867  
868      fill(pot_temp.begin(), pot_temp.end(),
869           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
870 +    fill(expot_temp.begin(), expot_temp.end(),
871 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
872        
873      AtomPlanPotColumn->scatter(pot_col, pot_temp);    
874 +    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
875      
876      for (int ii = 0;  ii < pot_temp.size(); ii++ )
877        pairwisePot += pot_temp[ii];    
878  
879 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
880 +      excludedPot += expot_temp[ii];    
881 +
882      if (storageLayout_ & DataStorage::dslParticlePot) {
883        // This is the pairwise contribution to the particle pot.  The
884        // embedding contribution is added in each of the low level
# Line 848 | Line 916 | namespace OpenMD {
916      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
917        RealType ploc1 = pairwisePot[ii];
918        RealType ploc2 = 0.0;
919 <      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
919 >      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
920        pairwisePot[ii] = ploc2;
921      }
922  
923      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
924 <      RealType ploc1 = embeddingPot[ii];
924 >      RealType ploc1 = excludedPot[ii];
925        RealType ploc2 = 0.0;
926 <      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
927 <      embeddingPot[ii] = ploc2;
926 >      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
927 >      excludedPot[ii] = ploc2;
928      }
929 <    
929 >
930      // Here be dragons.
931 <    MPI::Intracomm col = colComm.getComm();
931 >    MPI_Comm col = colComm.getComm();
932  
933 <    col.Allreduce(MPI::IN_PLACE,
933 >    MPI_Allreduce(MPI_IN_PLACE,
934                    &snap_->frameData.conductiveHeatFlux[0], 3,
935 <                  MPI::REALTYPE, MPI::SUM);
935 >                  MPI_REALTYPE, MPI_SUM, col);
936  
937  
938   #endif
939  
940    }
941  
942 <  int ForceMatrixDecomposition::getNAtomsInRow() {  
942 >  /**
943 >   * Collects information obtained during the post-pair (and embedding
944 >   * functional) loops onto local data structures.
945 >   */
946 >  void ForceMatrixDecomposition::collectSelfData() {
947 >    snap_ = sman_->getCurrentSnapshot();
948 >    storageLayout_ = sman_->getStorageLayout();
949 >
950   #ifdef IS_MPI
951 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
952 +      RealType ploc1 = embeddingPot[ii];
953 +      RealType ploc2 = 0.0;
954 +      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
955 +      embeddingPot[ii] = ploc2;
956 +    }    
957 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
958 +      RealType ploc1 = excludedSelfPot[ii];
959 +      RealType ploc2 = 0.0;
960 +      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
961 +      excludedSelfPot[ii] = ploc2;
962 +    }    
963 + #endif
964 +    
965 +  }
966 +
967 +
968 +
969 +  int& ForceMatrixDecomposition::getNAtomsInRow() {  
970 + #ifdef IS_MPI
971      return nAtomsInRow_;
972   #else
973      return nLocal_;
# Line 882 | Line 977 | namespace OpenMD {
977    /**
978     * returns the list of atoms belonging to this group.  
979     */
980 <  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
980 >  vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
981   #ifdef IS_MPI
982      return groupListRow_[cg1];
983   #else
# Line 890 | Line 985 | namespace OpenMD {
985   #endif
986    }
987  
988 <  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
988 >  vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
989   #ifdef IS_MPI
990      return groupListCol_[cg2];
991   #else
# Line 907 | Line 1002 | namespace OpenMD {
1002      d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
1003   #endif
1004      
1005 <    snap_->wrapVector(d);
1005 >    if (usePeriodicBoundaryConditions_) {
1006 >      snap_->wrapVector(d);
1007 >    }
1008      return d;    
1009    }
1010  
1011 <  Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
1011 >  Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
1012   #ifdef IS_MPI
1013      return cgColData.velocity[cg2];
1014   #else
# Line 919 | Line 1016 | namespace OpenMD {
1016   #endif
1017    }
1018  
1019 <  Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
1019 >  Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
1020   #ifdef IS_MPI
1021      return atomColData.velocity[atom2];
1022   #else
# Line 937 | Line 1034 | namespace OpenMD {
1034   #else
1035      d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1036   #endif
1037 <
1038 <    snap_->wrapVector(d);
1037 >    if (usePeriodicBoundaryConditions_) {
1038 >      snap_->wrapVector(d);
1039 >    }
1040      return d;    
1041    }
1042    
# Line 950 | Line 1048 | namespace OpenMD {
1048   #else
1049      d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1050   #endif
1051 <    
1052 <    snap_->wrapVector(d);
1051 >    if (usePeriodicBoundaryConditions_) {
1052 >      snap_->wrapVector(d);
1053 >    }
1054      return d;    
1055    }
1056  
1057 <  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1057 >  RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1058   #ifdef IS_MPI
1059      return massFactorsRow[atom1];
1060   #else
# Line 963 | Line 1062 | namespace OpenMD {
1062   #endif
1063    }
1064  
1065 <  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1065 >  RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1066   #ifdef IS_MPI
1067      return massFactorsCol[atom2];
1068   #else
# Line 980 | Line 1079 | namespace OpenMD {
1079   #else
1080      d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1081   #endif
1082 <
1083 <    snap_->wrapVector(d);
1082 >    if (usePeriodicBoundaryConditions_) {
1083 >      snap_->wrapVector(d);
1084 >    }
1085      return d;    
1086    }
1087  
1088 <  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1088 >  vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1089      return excludesForAtom[atom1];
1090    }
1091  
# Line 993 | Line 1093 | namespace OpenMD {
1093     * We need to exclude some overcounted interactions that result from
1094     * the parallel decomposition.
1095     */
1096 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1096 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1097      int unique_id_1, unique_id_2;
1098          
1099   #ifdef IS_MPI
1100      // in MPI, we have to look up the unique IDs for each atom
1101      unique_id_1 = AtomRowToGlobal[atom1];
1102      unique_id_2 = AtomColToGlobal[atom2];
1103 +    // group1 = cgRowToGlobal[cg1];
1104 +    // group2 = cgColToGlobal[cg2];
1105   #else
1106      unique_id_1 = AtomLocalToGlobal[atom1];
1107      unique_id_2 = AtomLocalToGlobal[atom2];
1108 +    int group1 = cgLocalToGlobal[cg1];
1109 +    int group2 = cgLocalToGlobal[cg2];
1110   #endif  
1111  
1112      if (unique_id_1 == unique_id_2) return true;
# Line 1014 | Line 1118 | namespace OpenMD {
1118      } else {
1119        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1120      }
1121 + #endif    
1122 +
1123 + #ifndef IS_MPI
1124 +    if (group1 == group2) {
1125 +      if (unique_id_1 < unique_id_2) return true;
1126 +    }
1127   #endif
1128      
1129      return false;
# Line 1065 | Line 1175 | namespace OpenMD {
1175      idat.excluded = excludeAtomPair(atom1, atom2);
1176    
1177   #ifdef IS_MPI
1178 <    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1179 <    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1180 <    //                         ff_->getAtomType(identsCol[atom2]) );
1181 <    
1178 >    //idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1179 >    idat.atid1 = identsRow[atom1];
1180 >    idat.atid2 = identsCol[atom2];
1181 >
1182 >    if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1183 >      idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1184 >    } else {
1185 >      idat.sameRegion = false;
1186 >    }
1187 >
1188      if (storageLayout_ & DataStorage::dslAmat) {
1189        idat.A1 = &(atomRowData.aMat[atom1]);
1190        idat.A2 = &(atomColData.aMat[atom2]);
1191      }
1192      
1077 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1078 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1079 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1080 –    }
1081 –
1193      if (storageLayout_ & DataStorage::dslTorque) {
1194        idat.t1 = &(atomRowData.torque[atom1]);
1195        idat.t2 = &(atomColData.torque[atom2]);
1196      }
1197  
1198 +    if (storageLayout_ & DataStorage::dslDipole) {
1199 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1200 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1201 +    }
1202 +
1203 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1204 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1205 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1206 +    }
1207 +
1208      if (storageLayout_ & DataStorage::dslDensity) {
1209        idat.rho1 = &(atomRowData.density[atom1]);
1210        idat.rho2 = &(atomColData.density[atom2]);
# Line 1116 | Line 1237 | namespace OpenMD {
1237  
1238   #else
1239      
1240 +    //idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1241 +    idat.atid1 = idents[atom1];
1242 +    idat.atid2 = idents[atom2];
1243  
1244 <    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1245 <    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1246 <    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1244 >    if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1245 >      idat.sameRegion = (regions[atom1] == regions[atom2]);
1246 >    } else {
1247 >      idat.sameRegion = false;
1248 >    }
1249  
1124 –    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1125 –    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1126 –    //                         ff_->getAtomType(idents[atom2]) );
1127 –
1250      if (storageLayout_ & DataStorage::dslAmat) {
1251        idat.A1 = &(snap_->atomData.aMat[atom1]);
1252        idat.A2 = &(snap_->atomData.aMat[atom2]);
1253      }
1254  
1133 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1134 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1135 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1136 –    }
1137 –
1255      if (storageLayout_ & DataStorage::dslTorque) {
1256        idat.t1 = &(snap_->atomData.torque[atom1]);
1257        idat.t2 = &(snap_->atomData.torque[atom2]);
1258      }
1259  
1260 +    if (storageLayout_ & DataStorage::dslDipole) {
1261 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1262 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1263 +    }
1264 +
1265 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1266 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1267 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1268 +    }
1269 +
1270      if (storageLayout_ & DataStorage::dslDensity) {    
1271        idat.rho1 = &(snap_->atomData.density[atom1]);
1272        idat.rho2 = &(snap_->atomData.density[atom2]);
# Line 1178 | Line 1305 | namespace OpenMD {
1305   #ifdef IS_MPI
1306      pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1307      pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1308 +    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1309 +    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1310  
1311      atomRowData.force[atom1] += *(idat.f1);
1312      atomColData.force[atom2] -= *(idat.f1);
# Line 1194 | Line 1323 | namespace OpenMD {
1323  
1324   #else
1325      pairwisePot += *(idat.pot);
1326 +    excludedPot += *(idat.excludedPot);
1327  
1328      snap_->atomData.force[atom1] += *(idat.f1);
1329      snap_->atomData.force[atom2] -= *(idat.f1);
# Line 1227 | Line 1357 | namespace OpenMD {
1357     * first element of pair is row-indexed CutoffGroup
1358     * second element of pair is column-indexed CutoffGroup
1359     */
1360 <  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1361 <      
1362 <    vector<pair<int, int> > neighborList;
1360 >  void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1361 >    
1362 >    neighborList.clear();
1363      groupCutoffs cuts;
1364      bool doAllPairs = false;
1365  
1366 +    RealType rList_ = (largestRcut_ + skinThickness_);
1367 +    RealType rcut, rcutsq, rlistsq;
1368 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
1369 +    Mat3x3d box;
1370 +    Mat3x3d invBox;
1371 +
1372 +    Vector3d rs, scaled, dr;
1373 +    Vector3i whichCell;
1374 +    int cellIndex;
1375 +
1376   #ifdef IS_MPI
1377      cellListRow_.clear();
1378      cellListCol_.clear();
1379   #else
1380      cellList_.clear();
1381   #endif
1382 <
1383 <    RealType rList_ = (largestRcut_ + skinThickness_);
1384 <    RealType rl2 = rList_ * rList_;
1385 <    Snapshot* snap_ = sman_->getCurrentSnapshot();
1386 <    Mat3x3d Hmat = snap_->getHmat();
1387 <    Vector3d Hx = Hmat.getColumn(0);
1388 <    Vector3d Hy = Hmat.getColumn(1);
1389 <    Vector3d Hz = Hmat.getColumn(2);
1390 <
1391 <    nCells_.x() = (int) ( Hx.length() )/ rList_;
1392 <    nCells_.y() = (int) ( Hy.length() )/ rList_;
1393 <    nCells_.z() = (int) ( Hz.length() )/ rList_;
1394 <
1382 >    
1383 >    if (!usePeriodicBoundaryConditions_) {
1384 >      box = snap_->getBoundingBox();
1385 >      invBox = snap_->getInvBoundingBox();
1386 >    } else {
1387 >      box = snap_->getHmat();
1388 >      invBox = snap_->getInvHmat();
1389 >    }
1390 >    
1391 >    Vector3d boxX = box.getColumn(0);
1392 >    Vector3d boxY = box.getColumn(1);
1393 >    Vector3d boxZ = box.getColumn(2);
1394 >    
1395 >    nCells_.x() = int( boxX.length() / rList_ );
1396 >    nCells_.y() = int( boxY.length() / rList_ );
1397 >    nCells_.z() = int( boxZ.length() / rList_ );
1398 >    
1399      // handle small boxes where the cell offsets can end up repeating cells
1400      
1401      if (nCells_.x() < 3) doAllPairs = true;
1402      if (nCells_.y() < 3) doAllPairs = true;
1403      if (nCells_.z() < 3) doAllPairs = true;
1404 <
1261 <    Mat3x3d invHmat = snap_->getInvHmat();
1262 <    Vector3d rs, scaled, dr;
1263 <    Vector3i whichCell;
1264 <    int cellIndex;
1404 >    
1405      int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1406 <
1406 >    
1407   #ifdef IS_MPI
1408      cellListRow_.resize(nCtot);
1409      cellListCol_.resize(nCtot);
1410   #else
1411      cellList_.resize(nCtot);
1412   #endif
1413 <
1413 >    
1414      if (!doAllPairs) {
1415   #ifdef IS_MPI
1416 <
1416 >      
1417        for (int i = 0; i < nGroupsInRow_; i++) {
1418          rs = cgRowData.position[i];
1419          
1420          // scaled positions relative to the box vectors
1421 <        scaled = invHmat * rs;
1421 >        scaled = invBox * rs;
1422          
1423          // wrap the vector back into the unit box by subtracting integer box
1424          // numbers
1425          for (int j = 0; j < 3; j++) {
1426            scaled[j] -= roundMe(scaled[j]);
1427            scaled[j] += 0.5;
1428 +          // Handle the special case when an object is exactly on the
1429 +          // boundary (a scaled coordinate of 1.0 is the same as
1430 +          // scaled coordinate of 0.0)
1431 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1432          }
1433          
1434          // find xyz-indices of cell that cutoffGroup is in.
# Line 1302 | Line 1446 | namespace OpenMD {
1446          rs = cgColData.position[i];
1447          
1448          // scaled positions relative to the box vectors
1449 <        scaled = invHmat * rs;
1449 >        scaled = invBox * rs;
1450          
1451          // wrap the vector back into the unit box by subtracting integer box
1452          // numbers
1453          for (int j = 0; j < 3; j++) {
1454            scaled[j] -= roundMe(scaled[j]);
1455            scaled[j] += 0.5;
1456 +          // Handle the special case when an object is exactly on the
1457 +          // boundary (a scaled coordinate of 1.0 is the same as
1458 +          // scaled coordinate of 0.0)
1459 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1460          }
1461          
1462          // find xyz-indices of cell that cutoffGroup is in.
# Line 1322 | Line 1470 | namespace OpenMD {
1470          // add this cutoff group to the list of groups in this cell;
1471          cellListCol_[cellIndex].push_back(i);
1472        }
1473 <    
1473 >      
1474   #else
1475        for (int i = 0; i < nGroups_; i++) {
1476          rs = snap_->cgData.position[i];
1477          
1478          // scaled positions relative to the box vectors
1479 <        scaled = invHmat * rs;
1479 >        scaled = invBox * rs;
1480          
1481          // wrap the vector back into the unit box by subtracting integer box
1482          // numbers
1483          for (int j = 0; j < 3; j++) {
1484            scaled[j] -= roundMe(scaled[j]);
1485            scaled[j] += 0.5;
1486 +          // Handle the special case when an object is exactly on the
1487 +          // boundary (a scaled coordinate of 1.0 is the same as
1488 +          // scaled coordinate of 0.0)
1489 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1490          }
1491          
1492          // find xyz-indices of cell that cutoffGroup is in.
1493 <        whichCell.x() = nCells_.x() * scaled.x();
1494 <        whichCell.y() = nCells_.y() * scaled.y();
1495 <        whichCell.z() = nCells_.z() * scaled.z();
1493 >        whichCell.x() = int(nCells_.x() * scaled.x());
1494 >        whichCell.y() = int(nCells_.y() * scaled.y());
1495 >        whichCell.z() = int(nCells_.z() * scaled.z());
1496          
1497          // find single index of this cell:
1498          cellIndex = Vlinear(whichCell, nCells_);
# Line 1393 | Line 1545 | namespace OpenMD {
1545                    // & column indicies and will divide labor in the
1546                    // force evaluation later.
1547                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1548 <                  snap_->wrapVector(dr);
1549 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1550 <                  if (dr.lengthSquare() < cuts.third) {
1548 >                  if (usePeriodicBoundaryConditions_) {
1549 >                    snap_->wrapVector(dr);
1550 >                  }
1551 >                  getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1552 >                  if (dr.lengthSquare() < rlistsq) {
1553                      neighborList.push_back(make_pair((*j1), (*j2)));
1554                    }                  
1555                  }
# Line 1415 | Line 1569 | namespace OpenMD {
1569                    // allows atoms within a single cutoff group to
1570                    // interact with each other.
1571  
1418 –
1419 –
1572                    if (m2 != m1 || (*j2) >= (*j1) ) {
1573  
1574                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1575 <                    snap_->wrapVector(dr);
1576 <                    cuts = getGroupCutoffs( (*j1), (*j2) );
1577 <                    if (dr.lengthSquare() < cuts.third) {
1575 >                    if (usePeriodicBoundaryConditions_) {
1576 >                      snap_->wrapVector(dr);
1577 >                    }
1578 >                    getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1579 >                    if (dr.lengthSquare() < rlistsq) {
1580                        neighborList.push_back(make_pair((*j1), (*j2)));
1581                      }
1582                    }
# Line 1439 | Line 1593 | namespace OpenMD {
1593        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1594          for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1595            dr = cgColData.position[j2] - cgRowData.position[j1];
1596 <          snap_->wrapVector(dr);
1597 <          cuts = getGroupCutoffs( j1, j2 );
1598 <          if (dr.lengthSquare() < cuts.third) {
1596 >          if (usePeriodicBoundaryConditions_) {
1597 >            snap_->wrapVector(dr);
1598 >          }
1599 >          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1600 >          if (dr.lengthSquare() < rlistsq) {
1601              neighborList.push_back(make_pair(j1, j2));
1602            }
1603          }
# Line 1452 | Line 1608 | namespace OpenMD {
1608          // include self group interactions j2 == j1
1609          for (int j2 = j1; j2 < nGroups_; j2++) {
1610            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1611 <          snap_->wrapVector(dr);
1612 <          cuts = getGroupCutoffs( j1, j2 );
1613 <          if (dr.lengthSquare() < cuts.third) {
1611 >          if (usePeriodicBoundaryConditions_) {
1612 >            snap_->wrapVector(dr);
1613 >          }
1614 >          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1615 >          if (dr.lengthSquare() < rlistsq) {
1616              neighborList.push_back(make_pair(j1, j2));
1617            }
1618          }    
# Line 1467 | Line 1625 | namespace OpenMD {
1625      saved_CG_positions_.clear();
1626      for (int i = 0; i < nGroups_; i++)
1627        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1470 –    
1471 –    return neighborList;
1628    }
1629   } //end namespace OpenMD

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