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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 1736 by jmichalk, Tue Jun 5 17:51:31 2012 UTC vs.
Revision 1761 by gezelter, Fri Jun 22 20:01:37 2012 UTC

# Line 175 | Line 175 | namespace OpenMD {
175  
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_);
# Line 461 | Line 464 | namespace OpenMD {
464      }
465    }
466  
464 –
467    groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
468      int i, j;  
469   #ifdef IS_MPI
# Line 485 | Line 487 | namespace OpenMD {
487    void ForceMatrixDecomposition::zeroWorkArrays() {
488      pairwisePot = 0.0;
489      embeddingPot = 0.0;
490 +    excludedPot = 0.0;
491 +    excludedSelfPot = 0.0;
492  
493   #ifdef IS_MPI
494      if (storageLayout_ & DataStorage::dslForce) {
# Line 501 | Line 505 | namespace OpenMD {
505           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
506  
507      fill(pot_col.begin(), pot_col.end(),
508 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
509 +
510 +    fill(expot_row.begin(), expot_row.end(),
511 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
512 +
513 +    fill(expot_col.begin(), expot_col.end(),
514           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
515  
516      if (storageLayout_ & DataStorage::dslParticlePot) {    
# Line 781 | Line 791 | namespace OpenMD {
791  
792      vector<potVec> pot_temp(nLocal_,
793                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
794 +    vector<potVec> expot_temp(nLocal_,
795 +                              Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
796  
797      // scatter/gather pot_row into the members of my column
798            
799      AtomPlanPotRow->scatter(pot_row, pot_temp);
800 +    AtomPlanPotRow->scatter(expot_row, expot_temp);
801  
802 <    for (int ii = 0;  ii < pot_temp.size(); ii++ )
802 >    for (int ii = 0;  ii < pot_temp.size(); ii++ )
803        pairwisePot += pot_temp[ii];
804 +
805 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
806 +      excludedPot += expot_temp[ii];
807          
808      if (storageLayout_ & DataStorage::dslParticlePot) {
809        // This is the pairwise contribution to the particle pot.  The
# Line 805 | Line 821 | namespace OpenMD {
821  
822      fill(pot_temp.begin(), pot_temp.end(),
823           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
824 +    fill(expot_temp.begin(), expot_temp.end(),
825 +         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
826        
827      AtomPlanPotColumn->scatter(pot_col, pot_temp);    
828 +    AtomPlanPotColumn->scatter(expot_col, expot_temp);    
829      
830      for (int ii = 0;  ii < pot_temp.size(); ii++ )
831        pairwisePot += pot_temp[ii];    
832  
833 +    for (int ii = 0;  ii < expot_temp.size(); ii++ )
834 +      excludedPot += expot_temp[ii];    
835 +
836      if (storageLayout_ & DataStorage::dslParticlePot) {
837        // This is the pairwise contribution to the particle pot.  The
838        // embedding contribution is added in each of the low level
# Line 853 | Line 875 | namespace OpenMD {
875      }
876  
877      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
878 <      RealType ploc1 = embeddingPot[ii];
878 >      RealType ploc1 = excludedPot[ii];
879        RealType ploc2 = 0.0;
880        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
881 <      embeddingPot[ii] = ploc2;
881 >      excludedPot[ii] = ploc2;
882      }
883 <    
883 >
884      // Here be dragons.
885      MPI::Intracomm col = colComm.getComm();
886  
# Line 871 | Line 893 | namespace OpenMD {
893  
894    }
895  
896 +  /**
897 +   * Collects information obtained during the post-pair (and embedding
898 +   * functional) loops onto local data structures.
899 +   */
900 +  void ForceMatrixDecomposition::collectSelfData() {
901 +    snap_ = sman_->getCurrentSnapshot();
902 +    storageLayout_ = sman_->getStorageLayout();
903 +
904 + #ifdef IS_MPI
905 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
906 +      RealType ploc1 = embeddingPot[ii];
907 +      RealType ploc2 = 0.0;
908 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
909 +      embeddingPot[ii] = ploc2;
910 +    }    
911 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
912 +      RealType ploc1 = excludedSelfPot[ii];
913 +      RealType ploc2 = 0.0;
914 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
915 +      excludedSelfPot[ii] = ploc2;
916 +    }    
917 + #endif
918 +    
919 +  }
920 +
921 +
922 +
923    int ForceMatrixDecomposition::getNAtomsInRow() {  
924   #ifdef IS_MPI
925      return nAtomsInRow_;
# Line 993 | Line 1042 | namespace OpenMD {
1042     * We need to exclude some overcounted interactions that result from
1043     * the parallel decomposition.
1044     */
1045 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1046 <    int unique_id_1, unique_id_2;
1045 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1046 >    int unique_id_1, unique_id_2, group1, group2;
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];
1054   #else
1055      unique_id_1 = AtomLocalToGlobal[atom1];
1056      unique_id_2 = AtomLocalToGlobal[atom2];
1057 +    group1 = cgLocalToGlobal[cg1];
1058 +    group2 = cgLocalToGlobal[cg2];
1059   #endif  
1060  
1061      if (unique_id_1 == unique_id_2) return true;
# Line 1013 | Line 1066 | namespace OpenMD {
1066        if ((unique_id_1 + unique_id_2) % 2 == 0) return true;
1067      } else {
1068        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1069 +    }
1070 + #endif    
1071 +
1072 + #ifndef IS_MPI
1073 +    if (group1 == group2) {
1074 +      if (unique_id_1 < unique_id_2) return true;
1075      }
1076   #endif
1077      
# Line 1116 | Line 1175 | namespace OpenMD {
1175  
1176   #else
1177      
1119 –
1120 –    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1121 –    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1122 –    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1123 –
1178      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1125 –    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1126 –    //                         ff_->getAtomType(idents[atom2]) );
1179  
1180      if (storageLayout_ & DataStorage::dslAmat) {
1181        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 1178 | Line 1230 | namespace OpenMD {
1230   #ifdef IS_MPI
1231      pot_row[atom1] += RealType(0.5) *  *(idat.pot);
1232      pot_col[atom2] += RealType(0.5) *  *(idat.pot);
1233 +    expot_row[atom1] += RealType(0.5) *  *(idat.excludedPot);
1234 +    expot_col[atom2] += RealType(0.5) *  *(idat.excludedPot);
1235  
1236      atomRowData.force[atom1] += *(idat.f1);
1237      atomColData.force[atom2] -= *(idat.f1);
# Line 1194 | Line 1248 | namespace OpenMD {
1248  
1249   #else
1250      pairwisePot += *(idat.pot);
1251 +    excludedPot += *(idat.excludedPot);
1252  
1253      snap_->atomData.force[atom1] += *(idat.f1);
1254      snap_->atomData.force[atom2] -= *(idat.f1);

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