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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 1855 by gezelter, Tue Apr 2 18:31:51 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 559 | Line 559 | namespace OpenMD {
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);
567 –    }
568 –
562   #endif
563      // even in parallel, we need to zero out the local arrays:
564  
# 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 679 | 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 686 | 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 786 | 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_,
# Line 1042 | Line 1062 | namespace OpenMD {
1062     * the parallel decomposition.
1063     */
1064    bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1065 <    int unique_id_1, unique_id_2, group1, group2;
1065 >    int unique_id_1, unique_id_2;
1066          
1067   #ifdef IS_MPI
1068      // in MPI, we have to look up the unique IDs for each atom
1069      unique_id_1 = AtomRowToGlobal[atom1];
1070      unique_id_2 = AtomColToGlobal[atom2];
1071 <    group1 = cgRowToGlobal[cg1];
1072 <    group2 = cgColToGlobal[cg2];
1071 >    // group1 = cgRowToGlobal[cg1];
1072 >    // group2 = cgColToGlobal[cg2];
1073   #else
1074      unique_id_1 = AtomLocalToGlobal[atom1];
1075      unique_id_2 = AtomLocalToGlobal[atom2];
1076 <    group1 = cgLocalToGlobal[cg1];
1077 <    group2 = cgLocalToGlobal[cg2];
1076 >    int group1 = cgLocalToGlobal[cg1];
1077 >    int group2 = cgLocalToGlobal[cg2];
1078   #endif  
1079  
1080      if (unique_id_1 == unique_id_2) return true;
# Line 1132 | Line 1152 | namespace OpenMD {
1152        idat.A2 = &(atomColData.aMat[atom2]);
1153      }
1154      
1135 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1136 –      idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
1137 –      idat.eFrame2 = &(atomColData.electroFrame[atom2]);
1138 –    }
1139 –
1155      if (storageLayout_ & DataStorage::dslTorque) {
1156        idat.t1 = &(atomRowData.torque[atom1]);
1157        idat.t2 = &(atomColData.torque[atom2]);
1158      }
1159  
1160 +    if (storageLayout_ & DataStorage::dslDipole) {
1161 +      idat.dipole1 = &(atomRowData.dipole[atom1]);
1162 +      idat.dipole2 = &(atomColData.dipole[atom2]);
1163 +    }
1164 +
1165 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1166 +      idat.quadrupole1 = &(atomRowData.quadrupole[atom1]);
1167 +      idat.quadrupole2 = &(atomColData.quadrupole[atom2]);
1168 +    }
1169 +
1170      if (storageLayout_ & DataStorage::dslDensity) {
1171        idat.rho1 = &(atomRowData.density[atom1]);
1172        idat.rho2 = &(atomColData.density[atom2]);
# Line 1181 | Line 1206 | namespace OpenMD {
1206        idat.A2 = &(snap_->atomData.aMat[atom2]);
1207      }
1208  
1184 –    if (storageLayout_ & DataStorage::dslElectroFrame) {
1185 –      idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
1186 –      idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
1187 –    }
1188 –
1209      if (storageLayout_ & DataStorage::dslTorque) {
1210        idat.t1 = &(snap_->atomData.torque[atom1]);
1211        idat.t2 = &(snap_->atomData.torque[atom2]);
1212 +    }
1213 +
1214 +    if (storageLayout_ & DataStorage::dslDipole) {
1215 +      idat.dipole1 = &(snap_->atomData.dipole[atom1]);
1216 +      idat.dipole2 = &(snap_->atomData.dipole[atom2]);
1217 +    }
1218 +
1219 +    if (storageLayout_ & DataStorage::dslQuadrupole) {
1220 +      idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]);
1221 +      idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]);
1222      }
1223  
1224      if (storageLayout_ & DataStorage::dslDensity) {    
# Line 1295 | Line 1325 | namespace OpenMD {
1325   #endif
1326  
1327      RealType rList_ = (largestRcut_ + skinThickness_);
1298 –    RealType rl2 = rList_ * rList_;
1328      Snapshot* snap_ = sman_->getCurrentSnapshot();
1329      Mat3x3d Hmat = snap_->getHmat();
1330      Vector3d Hx = Hmat.getColumn(0);
# Line 1339 | Line 1368 | namespace OpenMD {
1368          for (int j = 0; j < 3; j++) {
1369            scaled[j] -= roundMe(scaled[j]);
1370            scaled[j] += 0.5;
1371 +          // Handle the special case when an object is exactly on the
1372 +          // boundary (a scaled coordinate of 1.0 is the same as
1373 +          // scaled coordinate of 0.0)
1374 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1375          }
1376          
1377          // find xyz-indices of cell that cutoffGroup is in.
# Line 1363 | Line 1396 | namespace OpenMD {
1396          for (int j = 0; j < 3; j++) {
1397            scaled[j] -= roundMe(scaled[j]);
1398            scaled[j] += 0.5;
1399 +          // Handle the special case when an object is exactly on the
1400 +          // boundary (a scaled coordinate of 1.0 is the same as
1401 +          // scaled coordinate of 0.0)
1402 +          if (scaled[j] >= 1.0) scaled[j] -= 1.0;
1403          }
1404          
1405          // find xyz-indices of cell that cutoffGroup is in.

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