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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing branches/development/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1756 by gezelter, Mon Jun 18 18:23:20 2012 UTC vs.
Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

# Line 176 | Line 176 | namespace OpenMD {
176      pot_row.resize(nAtomsInRow_);
177      pot_col.resize(nAtomsInCol_);
178  
179 +    expot_row.resize(nAtomsInRow_);
180 +    expot_col.resize(nAtomsInCol_);
181 +
182      AtomRowToGlobal.resize(nAtomsInRow_);
183      AtomColToGlobal.resize(nAtomsInCol_);
184      AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
# Line 484 | Line 487 | namespace OpenMD {
487    void ForceMatrixDecomposition::zeroWorkArrays() {
488      pairwisePot = 0.0;
489      embeddingPot = 0.0;
490 +    excludedPot = 0.0;
491  
492   #ifdef IS_MPI
493      if (storageLayout_ & DataStorage::dslForce) {
# Line 500 | Line 504 | namespace OpenMD {
504           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
505  
506      fill(pot_col.begin(), pot_col.end(),
507 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
508 +
509 +    fill(expot_row.begin(), expot_row.end(),
510 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
511 +
512 +    fill(expot_col.begin(), expot_col.end(),
513           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
514  
515      if (storageLayout_ & DataStorage::dslParticlePot) {    
# Line 780 | Line 790 | namespace OpenMD {
790  
791      vector<potVec> pot_temp(nLocal_,
792                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
793 +    vector<potVec> expot_temp(nLocal_,
794 +                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
795  
796      // scatter/gather pot_row into the members of my column
797            
798      AtomPlanPotRow->scatter(pot_row, pot_temp);
799 +    AtomPlanPotRow->scatter(expot_row, expot_temp);
800  
801 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
801 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
802        pairwisePot += pot_temp[ii];
803 +
804 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
805 +      excludedPot += expot_temp[ii];
806          
807      if (storageLayout_ & DataStorage::dslParticlePot) {
808        // This is the pairwise contribution to the particle pot.  The
# Line 804 | Line 820 | namespace OpenMD {
820  
821      fill(pot_temp.begin(), pot_temp.end(),
822           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
823 +    fill(expot_temp.begin(), expot_temp.end(),
824 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
825        
826      AtomPlanPotColumn->scatter(pot_col, pot_temp);    
827 +    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
828      
829      for (int ii = 0;  ii < pot_temp.size(); ii++ )
830        pairwisePot += pot_temp[ii];    
831  
832 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
833 +      excludedPot += expot_temp[ii];    
834 +
835      if (storageLayout_ & DataStorage::dslParticlePot) {
836        // This is the pairwise contribution to the particle pot.  The
837        // embedding contribution is added in each of the low level
# Line 849 | Line 871 | namespace OpenMD {
871        RealType ploc2 = 0.0;
872        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
873        pairwisePot[ii] = ploc2;
874 +    }
875 +
876 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
877 +      RealType ploc1 = excludedPot[ii];
878 +      RealType ploc2 = 0.0;
879 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
880 +      excludedPot[ii] = ploc2;
881      }
882  
883      // Here be dragons.
# Line 1194 | Line 1223 | namespace OpenMD {
1223   #ifdef IS_MPI
1224      pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1225      pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1226 +    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1227 +    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1228  
1229      atomRowData.force[atom1] += *(idat.f1);
1230      atomColData.force[atom2] -= *(idat.f1);
# Line 1210 | Line 1241 | namespace OpenMD {
1241  
1242   #else
1243      pairwisePot += *(idat.pot);
1244 +    excludedPot += *(idat.excludedPot);
1245  
1246      snap_->atomData.force[atom1] += *(idat.f1);
1247      snap_->atomData.force[atom2] -= *(idat.f1);

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