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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC vs.
Revision 1895 by gezelter, Mon Jul 1 21:09:37 2013 UTC

# Line 479 | Line 479 | namespace OpenMD {
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  
# Line 939 | Line 939 | namespace OpenMD {
939  
940  
941  
942 <  int ForceMatrixDecomposition::getNAtomsInRow() {  
942 >  int& ForceMatrixDecomposition::getNAtomsInRow() {  
943   #ifdef IS_MPI
944      return nAtomsInRow_;
945   #else
# Line 950 | 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 958 | 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 981 | Line 981 | namespace OpenMD {
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 989 | 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 1027 | Line 1027 | namespace OpenMD {
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 1035 | 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 1058 | Line 1058 | namespace OpenMD {
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 1149 | 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 1205 | 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]);
# Line 1316 | 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  
# Line 1583 | 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]);
1586 –    
1587 –    return neighborList;
1590    }
1591   } //end namespace OpenMD

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