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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1755 by gezelter, Thu Jun 14 01:58:35 2012 UTC vs.
trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents), Revision 1895 by gezelter, Mon Jul 1 21:09:37 2013 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 176 | 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 307 | Line 310 | namespace OpenMD {
310      
311      RealType tol = 1e-6;
312      largestRcut_ = 0.0;
310 –    RealType rc;
313      int atid;
314      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
315      
# Line 392 | 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 417 | 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 461 | Line 463 | namespace OpenMD {
463      }
464    }
465  
464 –
466    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
467      int i, j;  
468   #ifdef IS_MPI
# Line 475 | 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 <    }
482 >    }                                          
483      return 0;
484    }
485  
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 503 | 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 550 | Line 559 | namespace OpenMD {
559             atomColData.electricField.end(), V3Zero);
560      }
561  
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 –
562   #endif
563      // even in parallel, we need to zero out the local arrays:
564  
# Line 630 | 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,
# Line 670 | Line 679 | namespace OpenMD {
679          snap_->atomData.density[i] += rho_tmp[i];
680      }
681  
682 +    // this isn't necessary if we don't have polarizable atoms, but
683 +    // we'll leave it here for now.
684      if (storageLayout_ & DataStorage::dslElectricField) {
685        
686        AtomPlanVectorRow->scatter(atomRowData.electricField,
# Line 677 | Line 688 | namespace OpenMD {
688        
689        int n = snap_->atomData.electricField.size();
690        vector<Vector3d> field_tmp(n, V3Zero);
691 <      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
691 >      AtomPlanVectorColumn->scatter(atomColData.electricField,
692 >                                    field_tmp);
693        for (int i = 0; i < n; i++)
694          snap_->atomData.electricField[i] += field_tmp[i];
695      }
# Line 777 | Line 789 | namespace OpenMD {
789              
790      }
791  
792 +    if (storageLayout_ & DataStorage::dslElectricField) {
793 +
794 +      int nef = snap_->atomData.electricField.size();
795 +      vector<Vector3d> efield_tmp(nef, V3Zero);
796 +
797 +      AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp);
798 +      for (int i = 0; i < nef; i++) {
799 +        snap_->atomData.electricField[i] += efield_tmp[i];
800 +        efield_tmp[i] = 0.0;
801 +      }
802 +      
803 +      AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp);
804 +      for (int i = 0; i < nef; i++)
805 +        snap_->atomData.electricField[i] += efield_tmp[i];
806 +    }
807 +
808 +
809      nLocal_ = snap_->getNumberOfAtoms();
810  
811      vector<potVec> pot_temp(nLocal_,
812                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
813 +    vector<potVec> expot_temp(nLocal_,
814 +                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
815  
816      // scatter/gather pot_row into the members of my column
817            
818      AtomPlanPotRow->scatter(pot_row, pot_temp);
819 <
820 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
819 >    AtomPlanPotRow->scatter(expot_row, expot_temp);
820 >
821 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
822        pairwisePot += pot_temp[ii];
823 +
824 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
825 +      excludedPot += expot_temp[ii];
826          
827      if (storageLayout_ & DataStorage::dslParticlePot) {
828        // This is the pairwise contribution to the particle pot.  The
# Line 805 | Line 840 | namespace OpenMD {
840  
841      fill(pot_temp.begin(), pot_temp.end(),
842           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
843 +    fill(expot_temp.begin(), expot_temp.end(),
844 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
845        
846      AtomPlanPotColumn->scatter(pot_col, pot_temp);    
847 +    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
848      
849      for (int ii = 0;  ii < pot_temp.size(); ii++ )
850        pairwisePot += pot_temp[ii];    
851  
852 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
853 +      excludedPot += expot_temp[ii];    
854 +
855      if (storageLayout_ & DataStorage::dslParticlePot) {
856        // This is the pairwise contribution to the particle pot.  The
857        // embedding contribution is added in each of the low level
# Line 853 | Line 894 | namespace OpenMD {
894      }
895  
896      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
897 <      RealType ploc1 = embeddingPot[ii];
897 >      RealType ploc1 = excludedPot[ii];
898        RealType ploc2 = 0.0;
899        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
900 <      embeddingPot[ii] = ploc2;
900 >      excludedPot[ii] = ploc2;
901      }
902 <    
902 >
903      // Here be dragons.
904      MPI::Intracomm col = colComm.getComm();
905  
# Line 871 | Line 912 | namespace OpenMD {
912  
913    }
914  
915 <  int ForceMatrixDecomposition::getNAtomsInRow() {  
915 >  /**
916 >   * Collects information obtained during the post-pair (and embedding
917 >   * functional) loops onto local data structures.
918 >   */
919 >  void ForceMatrixDecomposition::collectSelfData() {
920 >    snap_ = sman_->getCurrentSnapshot();
921 >    storageLayout_ = sman_->getStorageLayout();
922 >
923   #ifdef IS_MPI
924 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
925 +      RealType ploc1 = embeddingPot[ii];
926 +      RealType ploc2 = 0.0;
927 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
928 +      embeddingPot[ii] = ploc2;
929 +    }    
930 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
931 +      RealType ploc1 = excludedSelfPot[ii];
932 +      RealType ploc2 = 0.0;
933 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
934 +      excludedSelfPot[ii] = ploc2;
935 +    }    
936 + #endif
937 +    
938 +  }
939 +
940 +
941 +
942 +  int& ForceMatrixDecomposition::getNAtomsInRow() {  
943 + #ifdef IS_MPI
944      return nAtomsInRow_;
945   #else
946      return nLocal_;
# Line 882 | Line 950 | namespace OpenMD {
950    /**
951     * returns the list of atoms belonging to this group.  
952     */
953 <  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
953 >  vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
954   #ifdef IS_MPI
955      return groupListRow_[cg1];
956   #else
# Line 890 | Line 958 | namespace OpenMD {
958   #endif
959    }
960  
961 <  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
961 >  vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
962   #ifdef IS_MPI
963      return groupListCol_[cg2];
964   #else
# Line 907 | Line 975 | namespace OpenMD {
975      d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1];
976   #endif
977      
978 <    snap_->wrapVector(d);
978 >    if (usePeriodicBoundaryConditions_) {
979 >      snap_->wrapVector(d);
980 >    }
981      return d;    
982    }
983  
984 <  Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
984 >  Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
985   #ifdef IS_MPI
986      return cgColData.velocity[cg2];
987   #else
# Line 919 | Line 989 | namespace OpenMD {
989   #endif
990    }
991  
992 <  Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
992 >  Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
993   #ifdef IS_MPI
994      return atomColData.velocity[atom2];
995   #else
# Line 937 | Line 1007 | namespace OpenMD {
1007   #else
1008      d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1];
1009   #endif
1010 <
1011 <    snap_->wrapVector(d);
1010 >    if (usePeriodicBoundaryConditions_) {
1011 >      snap_->wrapVector(d);
1012 >    }
1013      return d;    
1014    }
1015    
# Line 950 | Line 1021 | namespace OpenMD {
1021   #else
1022      d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2];
1023   #endif
1024 <    
1025 <    snap_->wrapVector(d);
1024 >    if (usePeriodicBoundaryConditions_) {
1025 >      snap_->wrapVector(d);
1026 >    }
1027      return d;    
1028    }
1029  
1030 <  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1030 >  RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1031   #ifdef IS_MPI
1032      return massFactorsRow[atom1];
1033   #else
# Line 963 | Line 1035 | namespace OpenMD {
1035   #endif
1036    }
1037  
1038 <  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1038 >  RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1039   #ifdef IS_MPI
1040      return massFactorsCol[atom2];
1041   #else
# Line 980 | Line 1052 | namespace OpenMD {
1052   #else
1053      d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1];
1054   #endif
1055 <
1056 <    snap_->wrapVector(d);
1055 >    if (usePeriodicBoundaryConditions_) {
1056 >      snap_->wrapVector(d);
1057 >    }
1058      return d;    
1059    }
1060  
1061 <  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1061 >  vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1062      return excludesForAtom[atom1];
1063    }
1064  
# Line 993 | Line 1066 | namespace OpenMD {
1066     * We need to exclude some overcounted interactions that result from
1067     * the parallel decomposition.
1068     */
1069 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1069 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1070      int unique_id_1, unique_id_2;
1071          
1072   #ifdef IS_MPI
1073      // in MPI, we have to look up the unique IDs for each atom
1074      unique_id_1 = AtomRowToGlobal[atom1];
1075      unique_id_2 = AtomColToGlobal[atom2];
1076 +    // group1 = cgRowToGlobal[cg1];
1077 +    // group2 = cgColToGlobal[cg2];
1078   #else
1079      unique_id_1 = AtomLocalToGlobal[atom1];
1080      unique_id_2 = AtomLocalToGlobal[atom2];
1081 +    int group1 = cgLocalToGlobal[cg1];
1082 +    int group2 = cgLocalToGlobal[cg2];
1083   #endif  
1084  
1085      if (unique_id_1 == unique_id_2) return true;
# Line 1014 | Line 1091 | namespace OpenMD {
1091      } else {
1092        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1093      }
1094 + #endif    
1095 +
1096 + #ifndef IS_MPI
1097 +    if (group1 == group2) {
1098 +      if (unique_id_1 < unique_id_2) return true;
1099 +    }
1100   #endif
1101      
1102      return false;
# Line 1066 | Line 1149 | namespace OpenMD {
1149    
1150   #ifdef IS_MPI
1151      idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1152 +    idat.atid1 = identsRow[atom1];
1153 +    idat.atid2 = identsCol[atom2];
1154      //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1155      //                         ff_->getAtomType(identsCol[atom2]) );
1156      
# Line 1074 | Line 1159 | namespace OpenMD {
1159        idat.A2 = &(atomColData.aMat[atom2]);
1160      }
1161      
1077 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1078 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1079 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1080 –    }
1081 –
1162      if (storageLayout_ & DataStorage::dslTorque) {
1163        idat.t1 = &(atomRowData.torque[atom1]);
1164        idat.t2 = &(atomColData.torque[atom2]);
1165      }
1166  
1167 +    if (storageLayout_ & DataStorage::dslDipole) {
1168 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1169 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1170 +    }
1171 +
1172 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1173 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1174 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1175 +    }
1176 +
1177      if (storageLayout_ & DataStorage::dslDensity) {
1178        idat.rho1 = &(atomRowData.density[atom1]);
1179        idat.rho2 = &(atomColData.density[atom2]);
# Line 1117 | Line 1207 | namespace OpenMD {
1207   #else
1208      
1209      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1210 +    idat.atid1 = idents[atom1];
1211 +    idat.atid2 = idents[atom2];
1212  
1213      if (storageLayout_ & DataStorage::dslAmat) {
1214        idat.A1 = &(snap_->atomData.aMat[atom1]);
1215        idat.A2 = &(snap_->atomData.aMat[atom2]);
1216      }
1217  
1126 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1127 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1128 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1129 –    }
1130 –
1218      if (storageLayout_ & DataStorage::dslTorque) {
1219        idat.t1 = &(snap_->atomData.torque[atom1]);
1220        idat.t2 = &(snap_->atomData.torque[atom2]);
1221      }
1222  
1223 +    if (storageLayout_ & DataStorage::dslDipole) {
1224 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1225 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1226 +    }
1227 +
1228 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1229 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1230 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1231 +    }
1232 +
1233      if (storageLayout_ & DataStorage::dslDensity) {    
1234        idat.rho1 = &(snap_->atomData.density[atom1]);
1235        idat.rho2 = &(snap_->atomData.density[atom2]);
# Line 1171 | Line 1268 | namespace OpenMD {
1268   #ifdef IS_MPI
1269      pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1270      pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1271 +    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1272 +    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1273  
1274      atomRowData.force[atom1] += *(idat.f1);
1275      atomColData.force[atom2] -= *(idat.f1);
# Line 1187 | Line 1286 | namespace OpenMD {
1286  
1287   #else
1288      pairwisePot += *(idat.pot);
1289 +    excludedPot += *(idat.excludedPot);
1290  
1291      snap_->atomData.force[atom1] += *(idat.f1);
1292      snap_->atomData.force[atom2] -= *(idat.f1);
# Line 1220 | Line 1320 | namespace OpenMD {
1320     * first element of pair is row-indexed CutoffGroup
1321     * second element of pair is column-indexed CutoffGroup
1322     */
1323 <  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1324 <      
1325 <    vector<pair<int, int> > neighborList;
1323 >  void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1324 >    
1325 >    neighborList.clear();
1326      groupCutoffs cuts;
1327      bool doAllPairs = false;
1328  
1329 +    RealType rList_ = (largestRcut_ + skinThickness_);
1330 +    Snapshot* snap_ = sman_->getCurrentSnapshot();
1331 +    Mat3x3d box;
1332 +    Mat3x3d invBox;
1333 +
1334 +    Vector3d rs, scaled, dr;
1335 +    Vector3i whichCell;
1336 +    int cellIndex;
1337 +
1338   #ifdef IS_MPI
1339      cellListRow_.clear();
1340      cellListCol_.clear();
1341   #else
1342      cellList_.clear();
1343   #endif
1344 <
1345 <    RealType rList_ = (largestRcut_ + skinThickness_);
1346 <    RealType rl2 = rList_ * rList_;
1347 <    Snapshot* snap_ = sman_->getCurrentSnapshot();
1348 <    Mat3x3d Hmat = snap_->getHmat();
1349 <    Vector3d Hx = Hmat.getColumn(0);
1350 <    Vector3d Hy = Hmat.getColumn(1);
1351 <    Vector3d Hz = Hmat.getColumn(2);
1352 <
1353 <    nCells_.x() = (int) ( Hx.length() )/ rList_;
1354 <    nCells_.y() = (int) ( Hy.length() )/ rList_;
1355 <    nCells_.z() = (int) ( Hz.length() )/ rList_;
1356 <
1344 >    
1345 >    if (!usePeriodicBoundaryConditions_) {
1346 >      box = snap_->getBoundingBox();
1347 >      invBox = snap_->getInvBoundingBox();
1348 >    } else {
1349 >      box = snap_->getHmat();
1350 >      invBox = snap_->getInvHmat();
1351 >    }
1352 >    
1353 >    Vector3d boxX = box.getColumn(0);
1354 >    Vector3d boxY = box.getColumn(1);
1355 >    Vector3d boxZ = box.getColumn(2);
1356 >    
1357 >    nCells_.x() = (int) ( boxX.length() )/ rList_;
1358 >    nCells_.y() = (int) ( boxY.length() )/ rList_;
1359 >    nCells_.z() = (int) ( boxZ.length() )/ rList_;
1360 >    
1361      // handle small boxes where the cell offsets can end up repeating cells
1362      
1363      if (nCells_.x() < 3) doAllPairs = true;
1364      if (nCells_.y() < 3) doAllPairs = true;
1365      if (nCells_.z() < 3) doAllPairs = true;
1366 <
1254 <    Mat3x3d invHmat = snap_->getInvHmat();
1255 <    Vector3d rs, scaled, dr;
1256 <    Vector3i whichCell;
1257 <    int cellIndex;
1366 >    
1367      int nCtot = nCells_.x() * nCells_.y() * nCells_.z();
1368 <
1368 >    
1369   #ifdef IS_MPI
1370      cellListRow_.resize(nCtot);
1371      cellListCol_.resize(nCtot);
1372   #else
1373      cellList_.resize(nCtot);
1374   #endif
1375 <
1375 >    
1376      if (!doAllPairs) {
1377   #ifdef IS_MPI
1378 <
1378 >      
1379        for (int i = 0; i < nGroupsInRow_; i++) {
1380          rs = cgRowData.position[i];
1381          
1382          // scaled positions relative to the box vectors
1383 <        scaled = invHmat * rs;
1383 >        scaled = invBox * rs;
1384          
1385          // wrap the vector back into the unit box by subtracting integer box
1386          // numbers
1387          for (int j = 0; j < 3; j++) {
1388            scaled[j] -= roundMe(scaled[j]);
1389            scaled[j] += 0.5;
1390 +          // Handle the special case when an object is exactly on the
1391 +          // boundary (a scaled coordinate of 1.0 is the same as
1392 +          // scaled coordinate of 0.0)
1393 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1394          }
1395          
1396          // find xyz-indices of cell that cutoffGroup is in.
# Line 1295 | Line 1408 | namespace OpenMD {
1408          rs = cgColData.position[i];
1409          
1410          // scaled positions relative to the box vectors
1411 <        scaled = invHmat * rs;
1411 >        scaled = invBox * rs;
1412          
1413          // wrap the vector back into the unit box by subtracting integer box
1414          // numbers
1415          for (int j = 0; j < 3; j++) {
1416            scaled[j] -= roundMe(scaled[j]);
1417            scaled[j] += 0.5;
1418 +          // Handle the special case when an object is exactly on the
1419 +          // boundary (a scaled coordinate of 1.0 is the same as
1420 +          // scaled coordinate of 0.0)
1421 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1422          }
1423          
1424          // find xyz-indices of cell that cutoffGroup is in.
# Line 1315 | Line 1432 | namespace OpenMD {
1432          // add this cutoff group to the list of groups in this cell;
1433          cellListCol_[cellIndex].push_back(i);
1434        }
1435 <    
1435 >      
1436   #else
1437        for (int i = 0; i < nGroups_; i++) {
1438          rs = snap_->cgData.position[i];
1439          
1440          // scaled positions relative to the box vectors
1441 <        scaled = invHmat * rs;
1441 >        scaled = invBox * rs;
1442          
1443          // wrap the vector back into the unit box by subtracting integer box
1444          // numbers
1445          for (int j = 0; j < 3; j++) {
1446            scaled[j] -= roundMe(scaled[j]);
1447            scaled[j] += 0.5;
1448 +          // Handle the special case when an object is exactly on the
1449 +          // boundary (a scaled coordinate of 1.0 is the same as
1450 +          // scaled coordinate of 0.0)
1451 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1452          }
1453          
1454          // find xyz-indices of cell that cutoffGroup is in.
# Line 1386 | Line 1507 | namespace OpenMD {
1507                    // & column indicies and will divide labor in the
1508                    // force evaluation later.
1509                    dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)];
1510 <                  snap_->wrapVector(dr);
1510 >                  if (usePeriodicBoundaryConditions_) {
1511 >                    snap_->wrapVector(dr);
1512 >                  }
1513                    cuts = getGroupCutoffs( (*j1), (*j2) );
1514                    if (dr.lengthSquare() < cuts.third) {
1515                      neighborList.push_back(make_pair((*j1), (*j2)));
# Line 1408 | Line 1531 | namespace OpenMD {
1531                    // allows atoms within a single cutoff group to
1532                    // interact with each other.
1533  
1411 –
1412 –
1534                    if (m2 != m1 || (*j2) >= (*j1) ) {
1535  
1536                      dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)];
1537 <                    snap_->wrapVector(dr);
1537 >                    if (usePeriodicBoundaryConditions_) {
1538 >                      snap_->wrapVector(dr);
1539 >                    }
1540                      cuts = getGroupCutoffs( (*j1), (*j2) );
1541                      if (dr.lengthSquare() < cuts.third) {
1542                        neighborList.push_back(make_pair((*j1), (*j2)));
# Line 1432 | Line 1555 | namespace OpenMD {
1555        for (int j1 = 0; j1 < nGroupsInRow_; j1++) {
1556          for (int j2 = 0; j2 < nGroupsInCol_; j2++) {    
1557            dr = cgColData.position[j2] - cgRowData.position[j1];
1558 <          snap_->wrapVector(dr);
1558 >          if (usePeriodicBoundaryConditions_) {
1559 >            snap_->wrapVector(dr);
1560 >          }
1561            cuts = getGroupCutoffs( j1, j2 );
1562            if (dr.lengthSquare() < cuts.third) {
1563              neighborList.push_back(make_pair(j1, j2));
# Line 1445 | Line 1570 | namespace OpenMD {
1570          // include self group interactions j2 == j1
1571          for (int j2 = j1; j2 < nGroups_; j2++) {
1572            dr = snap_->cgData.position[j2] - snap_->cgData.position[j1];
1573 <          snap_->wrapVector(dr);
1573 >          if (usePeriodicBoundaryConditions_) {
1574 >            snap_->wrapVector(dr);
1575 >          }
1576            cuts = getGroupCutoffs( j1, j2 );
1577            if (dr.lengthSquare() < cuts.third) {
1578              neighborList.push_back(make_pair(j1, j2));
# Line 1460 | Line 1587 | namespace OpenMD {
1587      saved_CG_positions_.clear();
1588      for (int i = 0; i < nGroups_; i++)
1589        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1463 –    
1464 –    return neighborList;
1590    }
1591   } //end namespace OpenMD

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