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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1993 by gezelter, Tue Apr 29 17:32:31 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_);
# Line 308 | 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;
324      int atid;
# Line 413 | 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(MPI_IN_PLACE, &groupMax, 1, MPI_REALTYPE,
428 >                  MPI_MAX, MPI_COMM_WORLD);
429   #endif
430      
431      RealType tradRcut = groupMax;
432  
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_) {
# Line 442 | Line 462 | namespace OpenMD {
462            break;
463          }
464  
465 <        pair<int,int> key = make_pair(i,j);
446 <        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 463 | Line 486 | namespace OpenMD {
486      }
487    }
488  
489 <  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 472 | 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 (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  
# Line 559 | Line 586 | namespace OpenMD {
586             atomColData.electricField.end(), V3Zero);
587      }
588  
589 <    if (storageLayout_ & DataStorage::dslFlucQForce) {    
590 <      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
591 <           0.0);
592 <      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
593 <           0.0);
589 >    if (storageLayout_ & DataStorage::dslSitePotential) {    
590 >      fill(atomRowData.sitePotential.begin(),
591 >           atomRowData.sitePotential.end(), 0.0);
592 >      fill(atomColData.sitePotential.begin(),
593 >           atomColData.sitePotential.end(), 0.0);
594      }
595  
596   #endif
# Line 598 | Line 625 | namespace OpenMD {
625        fill(snap_->atomData.electricField.begin(),
626             snap_->atomData.electricField.end(), V3Zero);
627      }
628 +    if (storageLayout_ & DataStorage::dslSitePotential) {      
629 +      fill(snap_->atomData.sitePotential.begin(),
630 +           snap_->atomData.sitePotential.end(), 0.0);
631 +    }
632    }
633  
634  
# Line 639 | Line 670 | namespace OpenMD {
670        AtomPlanMatrixColumn->gather(snap_->atomData.aMat,
671                                     atomColData.aMat);
672      }
673 <    
674 <    // if needed, gather the atomic eletrostatic frames
675 <    if (storageLayout_ & DataStorage::dslElectroFrame) {
676 <      AtomPlanMatrixRow->gather(snap_->atomData.electroFrame,
677 <                                atomRowData.electroFrame);
678 <      AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame,
679 <                                   atomColData.electroFrame);
673 >
674 >    // if needed, gather the atomic eletrostatic information
675 >    if (storageLayout_ & DataStorage::dslDipole) {
676 >      AtomPlanVectorRow->gather(snap_->atomData.dipole,
677 >                                atomRowData.dipole);
678 >      AtomPlanVectorColumn->gather(snap_->atomData.dipole,
679 >                                   atomColData.dipole);
680      }
681  
682 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
683 +      AtomPlanMatrixRow->gather(snap_->atomData.quadrupole,
684 +                                atomRowData.quadrupole);
685 +      AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole,
686 +                                   atomColData.quadrupole);
687 +    }
688 +        
689      // if needed, gather the atomic fluctuating charge values
690      if (storageLayout_ & DataStorage::dslFlucQPosition) {
691        AtomPlanRealRow->gather(snap_->atomData.flucQPos,
# Line 679 | Line 717 | namespace OpenMD {
717          snap_->atomData.density[i] += rho_tmp[i];
718      }
719  
720 +    // this isn't necessary if we don't have polarizable atoms, but
721 +    // we'll leave it here for now.
722      if (storageLayout_ & DataStorage::dslElectricField) {
723        
724        AtomPlanVectorRow->scatter(atomRowData.electricField,
# Line 686 | Line 726 | namespace OpenMD {
726        
727        int n = snap_->atomData.electricField.size();
728        vector<Vector3d> field_tmp(n, V3Zero);
729 <      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
729 >      AtomPlanVectorColumn->scatter(atomColData.electricField,
730 >                                    field_tmp);
731        for (int i = 0; i < n; i++)
732          snap_->atomData.electricField[i] += field_tmp[i];
733      }
# Line 784 | Line 825 | namespace OpenMD {
825        for (int i = 0; i < nq; i++)
826          snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
827              
828 +    }
829 +
830 +    if (storageLayout_ & DataStorage::dslElectricField) {
831 +
832 +      int nef = snap_->atomData.electricField.size();
833 +      vector<Vector3d> efield_tmp(nef, V3Zero);
834 +
835 +      AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
836 +      for (int i = 0; i < nef; i++) {
837 +        snap_->atomData.electricField[i] += efield_tmp[i];
838 +        efield_tmp[i] = 0.0;
839 +      }
840 +      
841 +      AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
842 +      for (int i = 0; i < nef; i++)
843 +        snap_->atomData.electricField[i] += efield_tmp[i];
844      }
845  
846 +    if (storageLayout_ & DataStorage::dslSitePotential) {
847 +
848 +      int nsp = snap_->atomData.sitePotential.size();
849 +      vector<RealType> sp_tmp(nsp, 0.0);
850 +
851 +      AtomPlanRealRow->scatter(atomRowData.sitePotential, sp_tmp);
852 +      for (int i = 0; i < nsp; i++) {
853 +        snap_->atomData.sitePotential[i] += sp_tmp[i];
854 +        sp_tmp[i] = 0.0;
855 +      }
856 +      
857 +      AtomPlanRealColumn->scatter(atomColData.sitePotential, sp_tmp);
858 +      for (int i = 0; i < nsp; i++)
859 +        snap_->atomData.sitePotential[i] += sp_tmp[i];
860 +    }
861 +
862      nLocal_ = snap_->getNumberOfAtoms();
863  
864      vector<potVec> pot_temp(nLocal_,
# Line 869 | Line 942 | namespace OpenMD {
942      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
943        RealType ploc1 = pairwisePot[ii];
944        RealType ploc2 = 0.0;
945 <      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
945 >      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
946        pairwisePot[ii] = ploc2;
947      }
948  
949      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
950        RealType ploc1 = excludedPot[ii];
951        RealType ploc2 = 0.0;
952 <      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
952 >      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
953        excludedPot[ii] = ploc2;
954      }
955  
956      // Here be dragons.
957 <    MPI::Intracomm col = colComm.getComm();
957 >    MPI_Comm col = colComm.getComm();
958  
959 <    col.Allreduce(MPI::IN_PLACE,
959 >    MPI_Allreduce(MPI_IN_PLACE,
960                    &snap_->frameData.conductiveHeatFlux[0], 3,
961 <                  MPI::REALTYPE, MPI::SUM);
961 >                  MPI_REALTYPE, MPI_SUM, col);
962  
963  
964   #endif
# Line 904 | Line 977 | namespace OpenMD {
977      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
978        RealType ploc1 = embeddingPot[ii];
979        RealType ploc2 = 0.0;
980 <      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
980 >      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
981        embeddingPot[ii] = ploc2;
982      }    
983      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
984        RealType ploc1 = excludedSelfPot[ii];
985        RealType ploc2 = 0.0;
986 <      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
986 >      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
987        excludedSelfPot[ii] = ploc2;
988      }    
989   #endif
# Line 919 | Line 992 | namespace OpenMD {
992  
993  
994  
995 <  int ForceMatrixDecomposition::getNAtomsInRow() {  
995 >  int& ForceMatrixDecomposition::getNAtomsInRow() {  
996   #ifdef IS_MPI
997      return nAtomsInRow_;
998   #else
# Line 930 | Line 1003 | namespace OpenMD {
1003    /**
1004     * returns the list of atoms belonging to this group.  
1005     */
1006 <  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
1006 >  vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
1007   #ifdef IS_MPI
1008      return groupListRow_[cg1];
1009   #else
# Line 938 | Line 1011 | namespace OpenMD {
1011   #endif
1012    }
1013  
1014 <  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
1014 >  vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
1015   #ifdef IS_MPI
1016      return groupListCol_[cg2];
1017   #else
# Line 955 | Line 1028 | namespace OpenMD {
1028      d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
1029   #endif
1030      
1031 <    snap_->wrapVector(d);
1031 >    if (usePeriodicBoundaryConditions_) {
1032 >      snap_->wrapVector(d);
1033 >    }
1034      return d;    
1035    }
1036  
1037 <  Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
1037 >  Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
1038   #ifdef IS_MPI
1039      return cgColData.velocity[cg2];
1040   #else
# Line 967 | Line 1042 | namespace OpenMD {
1042   #endif
1043    }
1044  
1045 <  Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
1045 >  Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
1046   #ifdef IS_MPI
1047      return atomColData.velocity[atom2];
1048   #else
# Line 985 | Line 1060 | namespace OpenMD {
1060   #else
1061      d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1062   #endif
1063 <
1064 <    snap_->wrapVector(d);
1063 >    if (usePeriodicBoundaryConditions_) {
1064 >      snap_->wrapVector(d);
1065 >    }
1066      return d;    
1067    }
1068    
# Line 998 | Line 1074 | namespace OpenMD {
1074   #else
1075      d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1076   #endif
1077 <    
1078 <    snap_->wrapVector(d);
1077 >    if (usePeriodicBoundaryConditions_) {
1078 >      snap_->wrapVector(d);
1079 >    }
1080      return d;    
1081    }
1082  
1083 <  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1083 >  RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1084   #ifdef IS_MPI
1085      return massFactorsRow[atom1];
1086   #else
# Line 1011 | Line 1088 | namespace OpenMD {
1088   #endif
1089    }
1090  
1091 <  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1091 >  RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1092   #ifdef IS_MPI
1093      return massFactorsCol[atom2];
1094   #else
# Line 1028 | Line 1105 | namespace OpenMD {
1105   #else
1106      d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1107   #endif
1108 <
1109 <    snap_->wrapVector(d);
1108 >    if (usePeriodicBoundaryConditions_) {
1109 >      snap_->wrapVector(d);
1110 >    }
1111      return d;    
1112    }
1113  
1114 <  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1114 >  vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1115      return excludesForAtom[atom1];
1116    }
1117  
# Line 1042 | Line 1120 | namespace OpenMD {
1120     * the parallel decomposition.
1121     */
1122    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1123 <    int unique_id_1, unique_id_2, group1, group2;
1123 >    int unique_id_1, unique_id_2;
1124          
1125   #ifdef IS_MPI
1126      // in MPI, we have to look up the unique IDs for each atom
1127      unique_id_1 = AtomRowToGlobal[atom1];
1128      unique_id_2 = AtomColToGlobal[atom2];
1129 <    group1 = cgRowToGlobal[cg1];
1130 <    group2 = cgColToGlobal[cg2];
1129 >    // group1 = cgRowToGlobal[cg1];
1130 >    // group2 = cgColToGlobal[cg2];
1131   #else
1132      unique_id_1 = AtomLocalToGlobal[atom1];
1133      unique_id_2 = AtomLocalToGlobal[atom2];
1134 <    group1 = cgLocalToGlobal[cg1];
1135 <    group2 = cgLocalToGlobal[cg2];
1134 >    int group1 = cgLocalToGlobal[cg1];
1135 >    int group2 = cgLocalToGlobal[cg2];
1136   #endif  
1137  
1138      if (unique_id_1 == unique_id_2) return true;
# Line 1123 | Line 1201 | namespace OpenMD {
1201      idat.excluded = excludeAtomPair(atom1, atom2);
1202    
1203   #ifdef IS_MPI
1204 <    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1205 <    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1206 <    //                         ff_->getAtomType(identsCol[atom2]) );
1207 <    
1204 >    //idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1205 >    idat.atid1 = identsRow[atom1];
1206 >    idat.atid2 = identsCol[atom2];
1207 >
1208 >    if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1209 >      idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1210 >    } else {
1211 >      idat.sameRegion = false;
1212 >    }
1213 >
1214      if (storageLayout_ & DataStorage::dslAmat) {
1215        idat.A1 = &(atomRowData.aMat[atom1]);
1216        idat.A2 = &(atomColData.aMat[atom2]);
1217      }
1218      
1135 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1136 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1137 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1138 –    }
1139 –
1219      if (storageLayout_ & DataStorage::dslTorque) {
1220        idat.t1 = &(atomRowData.torque[atom1]);
1221        idat.t2 = &(atomColData.torque[atom2]);
1222      }
1223  
1224 +    if (storageLayout_ & DataStorage::dslDipole) {
1225 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1226 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1227 +    }
1228 +
1229 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1230 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1231 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1232 +    }
1233 +
1234      if (storageLayout_ & DataStorage::dslDensity) {
1235        idat.rho1 = &(atomRowData.density[atom1]);
1236        idat.rho2 = &(atomColData.density[atom2]);
# Line 1174 | Line 1263 | namespace OpenMD {
1263  
1264   #else
1265      
1266 <    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1266 >    //idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1267 >    idat.atid1 = idents[atom1];
1268 >    idat.atid2 = idents[atom2];
1269  
1270 +    if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1271 +      idat.sameRegion = (regions[atom1] == regions[atom2]);
1272 +    } else {
1273 +      idat.sameRegion = false;
1274 +    }
1275 +
1276      if (storageLayout_ & DataStorage::dslAmat) {
1277        idat.A1 = &(snap_->atomData.aMat[atom1]);
1278        idat.A2 = &(snap_->atomData.aMat[atom2]);
1279      }
1280  
1184 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1185 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1186 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1187 –    }
1188 –
1281      if (storageLayout_ & DataStorage::dslTorque) {
1282        idat.t1 = &(snap_->atomData.torque[atom1]);
1283        idat.t2 = &(snap_->atomData.torque[atom2]);
1284      }
1285  
1286 +    if (storageLayout_ & DataStorage::dslDipole) {
1287 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1288 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1289 +    }
1290 +
1291 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1292 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1293 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1294 +    }
1295 +
1296      if (storageLayout_ & DataStorage::dslDensity) {    
1297        idat.rho1 = &(snap_->atomData.density[atom1]);
1298        idat.rho2 = &(snap_->atomData.density[atom2]);
# Line 1245 | Line 1347 | namespace OpenMD {
1347        atomColData.electricField[atom2] += *(idat.eField2);
1348      }
1349  
1350 +    if (storageLayout_ & DataStorage::dslSitePotential) {              
1351 +      atomRowData.sitePotential[atom1] += *(idat.sPot1);
1352 +      atomColData.sitePotential[atom2] += *(idat.sPot2);
1353 +    }
1354 +
1355   #else
1356      pairwisePot += *(idat.pot);
1357      excludedPot += *(idat.excludedPot);
# Line 1271 | Line 1378 | namespace OpenMD {
1378        snap_->atomData.electricField[atom2] += *(idat.eField2);
1379      }
1380  
1381 +    if (storageLayout_ & DataStorage::dslSitePotential) {              
1382 +      snap_->atomData.sitePotential[atom1] += *(idat.sPot1);
1383 +      snap_->atomData.sitePotential[atom2] += *(idat.sPot2);
1384 +    }
1385 +
1386   #endif
1387      
1388    }
# Line 1281 | Line 1393 | namespace OpenMD {
1393     * first element of pair is row-indexed CutoffGroup
1394     * second element of pair is column-indexed CutoffGroup
1395     */
1396 <  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1397 <      
1398 <    vector<pair<int, int> > neighborList;
1396 >  void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1397 >    
1398 >    neighborList.clear();
1399      groupCutoffs cuts;
1400      bool doAllPairs = false;
1401  
1402 +    RealType rList_ = (largestRcut_ + skinThickness_);
1403 +    RealType rcut, rcutsq, rlistsq;
1404 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
1405 +    Mat3x3d box;
1406 +    Mat3x3d invBox;
1407 +
1408 +    Vector3d rs, scaled, dr;
1409 +    Vector3i whichCell;
1410 +    int cellIndex;
1411 +
1412   #ifdef IS_MPI
1413      cellListRow_.clear();
1414      cellListCol_.clear();
1415   #else
1416      cellList_.clear();
1417   #endif
1418 <
1419 <    RealType rList_ = (largestRcut_ + skinThickness_);
1420 <    RealType rl2 = rList_ * rList_;
1421 <    Snapshot* snap_ = sman_->getCurrentSnapshot();
1422 <    Mat3x3d Hmat = snap_->getHmat();
1423 <    Vector3d Hx = Hmat.getColumn(0);
1424 <    Vector3d Hy = Hmat.getColumn(1);
1425 <    Vector3d Hz = Hmat.getColumn(2);
1426 <
1427 <    nCells_.x() = (int) ( Hx.length() )/ rList_;
1428 <    nCells_.y() = (int) ( Hy.length() )/ rList_;
1429 <    nCells_.z() = (int) ( Hz.length() )/ rList_;
1430 <
1418 >    
1419 >    if (!usePeriodicBoundaryConditions_) {
1420 >      box = snap_->getBoundingBox();
1421 >      invBox = snap_->getInvBoundingBox();
1422 >    } else {
1423 >      box = snap_->getHmat();
1424 >      invBox = snap_->getInvHmat();
1425 >    }
1426 >    
1427 >    Vector3d boxX = box.getColumn(0);
1428 >    Vector3d boxY = box.getColumn(1);
1429 >    Vector3d boxZ = box.getColumn(2);
1430 >    
1431 >    nCells_.x() = int( boxX.length() / rList_ );
1432 >    nCells_.y() = int( boxY.length() / rList_ );
1433 >    nCells_.z() = int( boxZ.length() / rList_ );
1434 >    
1435      // handle small boxes where the cell offsets can end up repeating cells
1436      
1437      if (nCells_.x() < 3) doAllPairs = true;
1438      if (nCells_.y() < 3) doAllPairs = true;
1439      if (nCells_.z() < 3) doAllPairs = true;
1440 <
1315 <    Mat3x3d invHmat = snap_->getInvHmat();
1316 <    Vector3d rs, scaled, dr;
1317 <    Vector3i whichCell;
1318 <    int cellIndex;
1440 >    
1441      int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1442 <
1442 >    
1443   #ifdef IS_MPI
1444      cellListRow_.resize(nCtot);
1445      cellListCol_.resize(nCtot);
1446   #else
1447      cellList_.resize(nCtot);
1448   #endif
1449 <
1449 >    
1450      if (!doAllPairs) {
1451   #ifdef IS_MPI
1452 <
1452 >      
1453        for (int i = 0; i < nGroupsInRow_; i++) {
1454          rs = cgRowData.position[i];
1455          
1456          // scaled positions relative to the box vectors
1457 <        scaled = invHmat * rs;
1457 >        scaled = invBox * rs;
1458          
1459          // wrap the vector back into the unit box by subtracting integer box
1460          // numbers
1461          for (int j = 0; j < 3; j++) {
1462            scaled[j] -= roundMe(scaled[j]);
1463            scaled[j] += 0.5;
1464 +          // Handle the special case when an object is exactly on the
1465 +          // boundary (a scaled coordinate of 1.0 is the same as
1466 +          // scaled coordinate of 0.0)
1467 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1468          }
1469          
1470          // find xyz-indices of cell that cutoffGroup is in.
# Line 1356 | Line 1482 | namespace OpenMD {
1482          rs = cgColData.position[i];
1483          
1484          // scaled positions relative to the box vectors
1485 <        scaled = invHmat * rs;
1485 >        scaled = invBox * rs;
1486          
1487          // wrap the vector back into the unit box by subtracting integer box
1488          // numbers
1489          for (int j = 0; j < 3; j++) {
1490            scaled[j] -= roundMe(scaled[j]);
1491            scaled[j] += 0.5;
1492 +          // Handle the special case when an object is exactly on the
1493 +          // boundary (a scaled coordinate of 1.0 is the same as
1494 +          // scaled coordinate of 0.0)
1495 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1496          }
1497          
1498          // find xyz-indices of cell that cutoffGroup is in.
# Line 1376 | Line 1506 | namespace OpenMD {
1506          // add this cutoff group to the list of groups in this cell;
1507          cellListCol_[cellIndex].push_back(i);
1508        }
1509 <    
1509 >      
1510   #else
1511        for (int i = 0; i < nGroups_; i++) {
1512          rs = snap_->cgData.position[i];
1513          
1514          // scaled positions relative to the box vectors
1515 <        scaled = invHmat * rs;
1515 >        scaled = invBox * rs;
1516          
1517          // wrap the vector back into the unit box by subtracting integer box
1518          // numbers
1519          for (int j = 0; j < 3; j++) {
1520            scaled[j] -= roundMe(scaled[j]);
1521            scaled[j] += 0.5;
1522 +          // Handle the special case when an object is exactly on the
1523 +          // boundary (a scaled coordinate of 1.0 is the same as
1524 +          // scaled coordinate of 0.0)
1525 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1526          }
1527          
1528          // find xyz-indices of cell that cutoffGroup is in.
1529 <        whichCell.x() = nCells_.x() * scaled.x();
1530 <        whichCell.y() = nCells_.y() * scaled.y();
1531 <        whichCell.z() = nCells_.z() * scaled.z();
1529 >        whichCell.x() = int(nCells_.x() * scaled.x());
1530 >        whichCell.y() = int(nCells_.y() * scaled.y());
1531 >        whichCell.z() = int(nCells_.z() * scaled.z());
1532          
1533          // find single index of this cell:
1534          cellIndex = Vlinear(whichCell, nCells_);
# Line 1447 | Line 1581 | namespace OpenMD {
1581                    // & column indicies and will divide labor in the
1582                    // force evaluation later.
1583                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1584 <                  snap_->wrapVector(dr);
1585 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1586 <                  if (dr.lengthSquare() < cuts.third) {
1584 >                  if (usePeriodicBoundaryConditions_) {
1585 >                    snap_->wrapVector(dr);
1586 >                  }
1587 >                  getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1588 >                  if (dr.lengthSquare() < rlistsq) {
1589                      neighborList.push_back(make_pair((*j1), (*j2)));
1590                    }                  
1591                  }
# Line 1469 | Line 1605 | namespace OpenMD {
1605                    // allows atoms within a single cutoff group to
1606                    // interact with each other.
1607  
1472 –
1473 –
1608                    if (m2 != m1 || (*j2) >= (*j1) ) {
1609  
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 1493 | Line 1629 | namespace OpenMD {
1629        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1630          for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1631            dr = cgColData.position[j2] - cgRowData.position[j1];
1632 <          snap_->wrapVector(dr);
1633 <          cuts = getGroupCutoffs( j1, j2 );
1634 <          if (dr.lengthSquare() < cuts.third) {
1632 >          if (usePeriodicBoundaryConditions_) {
1633 >            snap_->wrapVector(dr);
1634 >          }
1635 >          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1636 >          if (dr.lengthSquare() < rlistsq) {
1637              neighborList.push_back(make_pair(j1, j2));
1638            }
1639          }
# Line 1506 | Line 1644 | namespace OpenMD {
1644          // include self group interactions j2 == j1
1645          for (int j2 = j1; j2 < nGroups_; j2++) {
1646            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1647 <          snap_->wrapVector(dr);
1648 <          cuts = getGroupCutoffs( j1, j2 );
1649 <          if (dr.lengthSquare() < cuts.third) {
1647 >          if (usePeriodicBoundaryConditions_) {
1648 >            snap_->wrapVector(dr);
1649 >          }
1650 >          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1651 >          if (dr.lengthSquare() < rlistsq) {
1652              neighborList.push_back(make_pair(j1, j2));
1653            }
1654          }    
# Line 1521 | Line 1661 | namespace OpenMD {
1661      saved_CG_positions_.clear();
1662      for (int i = 0; i < nGroups_; i++)
1663        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1524 –    
1525 –    return neighborList;
1664    }
1665   } //end namespace OpenMD

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