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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1771 by gezelter, Fri Jul 27 17:34:10 2012 UTC vs.
Revision 1803 by gezelter, Wed Oct 3 14:20:07 2012 UTC

# Line 557 | Line 557 | namespace OpenMD {
557             atomRowData.electricField.end(), V3Zero);
558        fill(atomColData.electricField.begin(),
559             atomColData.electricField.end(), V3Zero);
560 –    }
561 –
562 –    if (storageLayout_ & DataStorage::dslFlucQForce) {    
563 –      fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(),
564 –           0.0);
565 –      fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(),
566 –           0.0);
560      }
561  
562   #endif
# Line 639 | 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 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 1132 | Line 1133 | namespace OpenMD {
1133        idat.A2 = &(atomColData.aMat[atom2]);
1134      }
1135      
1135 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1136 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1137 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1138 –    }
1139 –
1136      if (storageLayout_ & DataStorage::dslTorque) {
1137        idat.t1 = &(atomRowData.torque[atom1]);
1138        idat.t2 = &(atomColData.torque[atom2]);
1139      }
1140  
1141 +    if (storageLayout_ & DataStorage::dslDipole) {
1142 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1143 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1144 +    }
1145 +
1146 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1147 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1148 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1149 +    }
1150 +
1151      if (storageLayout_ & DataStorage::dslDensity) {
1152        idat.rho1 = &(atomRowData.density[atom1]);
1153        idat.rho2 = &(atomColData.density[atom2]);
# Line 1179 | Line 1185 | namespace OpenMD {
1185      if (storageLayout_ & DataStorage::dslAmat) {
1186        idat.A1 = &(snap_->atomData.aMat[atom1]);
1187        idat.A2 = &(snap_->atomData.aMat[atom2]);
1182 –    }
1183 –
1184 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1185 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1186 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1188      }
1189  
1190      if (storageLayout_ & DataStorage::dslTorque) {
1191        idat.t1 = &(snap_->atomData.torque[atom1]);
1192        idat.t2 = &(snap_->atomData.torque[atom2]);
1193 +    }
1194 +
1195 +    if (storageLayout_ & DataStorage::dslDipole) {
1196 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1197 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1198 +    }
1199 +
1200 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1201 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1202 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1203      }
1204  
1205      if (storageLayout_ & DataStorage::dslDensity) {    
# Line 1339 | Line 1350 | namespace OpenMD {
1350          for (int j = 0; j < 3; j++) {
1351            scaled[j] -= roundMe(scaled[j]);
1352            scaled[j] += 0.5;
1353 +          // Handle the special case when an object is exactly on the
1354 +          // boundary (a scaled coordinate of 1.0 is the same as
1355 +          // scaled coordinate of 0.0)
1356 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1357          }
1358          
1359          // find xyz-indices of cell that cutoffGroup is in.
# Line 1363 | Line 1378 | namespace OpenMD {
1378          for (int j = 0; j < 3; j++) {
1379            scaled[j] -= roundMe(scaled[j]);
1380            scaled[j] += 0.5;
1381 +          // Handle the special case when an object is exactly on the
1382 +          // boundary (a scaled coordinate of 1.0 is the same as
1383 +          // scaled coordinate of 0.0)
1384 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1385          }
1386          
1387          // find xyz-indices of cell that cutoffGroup is in.

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