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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 1821 by gezelter, Mon Jan 7 20:05:43 2013 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 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 785 | Line 787 | namespace OpenMD {
787        for (int i = 0; i < nq; i++)
788          snap_->atomData.flucQFrc[i] += fqfrc_tmp[i];
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 1187 | Line 1206 | namespace OpenMD {
1206        idat.A2 = &(snap_->atomData.aMat[atom2]);
1207      }
1208  
1190 –    RealType ct = dot(idat.A1->getColumn(2), idat.A2->getColumn(2));
1191 –
1209      if (storageLayout_ & DataStorage::dslTorque) {
1210        idat.t1 = &(snap_->atomData.torque[atom1]);
1211        idat.t2 = &(snap_->atomData.torque[atom2]);
# Line 1308 | Line 1325 | namespace OpenMD {
1325   #endif
1326  
1327      RealType rList_ = (largestRcut_ + skinThickness_);
1311 –    RealType rl2 = rList_ * rList_;
1328      Snapshot* snap_ = sman_->getCurrentSnapshot();
1329      Mat3x3d Hmat = snap_->getHmat();
1330      Vector3d Hx = Hmat.getColumn(0);

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