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root/OpenMD/branches/development/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC vs.
Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

# Line 686 | Line 686 | namespace OpenMD {
686        
687        int n = snap_->atomData.electricField.size();
688        vector<Vector3d> field_tmp(n, V3Zero);
689 <      AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp);
689 >      AtomPlanVectorColumn->scatter(atomColData.electricField,
690 >                                    field_tmp);
691        for (int i = 0; i < n; i++)
692          snap_->atomData.electricField[i] += field_tmp[i];
693      }
# Line 1042 | Line 1043 | namespace OpenMD {
1043     * the parallel decomposition.
1044     */
1045    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1046 <    int unique_id_1, unique_id_2, group1, group2;
1046 >    int unique_id_1, unique_id_2;
1047          
1048   #ifdef IS_MPI
1049      // in MPI, we have to look up the unique IDs for each atom
1050      unique_id_1 = AtomRowToGlobal[atom1];
1051      unique_id_2 = AtomColToGlobal[atom2];
1052 <    group1 = cgRowToGlobal[cg1];
1053 <    group2 = cgColToGlobal[cg2];
1052 >    // group1 = cgRowToGlobal[cg1];
1053 >    // group2 = cgColToGlobal[cg2];
1054   #else
1055      unique_id_1 = AtomLocalToGlobal[atom1];
1056      unique_id_2 = AtomLocalToGlobal[atom2];
1057 <    group1 = cgLocalToGlobal[cg1];
1058 <    group2 = cgLocalToGlobal[cg2];
1057 >    int group1 = cgLocalToGlobal[cg1];
1058 >    int group2 = cgLocalToGlobal[cg2];
1059   #endif  
1060  
1061      if (unique_id_1 == unique_id_2) return true;
# Line 1186 | Line 1187 | namespace OpenMD {
1187        idat.A2 = &(snap_->atomData.aMat[atom2]);
1188      }
1189  
1190 +    RealType ct = dot(idat.A1->getColumn(2), idat.A2->getColumn(2));
1191 +
1192      if (storageLayout_ & DataStorage::dslTorque) {
1193        idat.t1 = &(snap_->atomData.torque[atom1]);
1194        idat.t2 = &(snap_->atomData.torque[atom2]);
# Line 1305 | Line 1308 | namespace OpenMD {
1308   #endif
1309  
1310      RealType rList_ = (largestRcut_ + skinThickness_);
1308 –    RealType rl2 = rList_ * rList_;
1311      Snapshot* snap_ = sman_->getCurrentSnapshot();
1312      Mat3x3d Hmat = snap_->getHmat();
1313      Vector3d Hx = Hmat.getColumn(0);

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