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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 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
Revision 1760 by gezelter, Thu Jun 21 19:26:46 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  
492   #ifdef IS_MPI
493      if (storageLayout_ & DataStorage::dslForce) {
# Line 501 | 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 781 | 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 805 | 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 853 | Line 874 | namespace OpenMD {
874      }
875  
876      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
877 <      RealType ploc1 = embeddingPot[ii];
877 >      RealType ploc1 = excludedPot[ii];
878        RealType ploc2 = 0.0;
879        MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
880 <      embeddingPot[ii] = ploc2;
880 >      excludedPot[ii] = ploc2;
881      }
882 <    
882 >
883      // Here be dragons.
884      MPI::Intracomm col = colComm.getComm();
885  
# Line 868 | Line 889 | namespace OpenMD {
889  
890  
891   #endif
892 +
893 +  }
894 +
895 +  /**
896 +   * Collects information obtained during the post-pair (and embedding
897 +   * functional) loops onto local data structures.
898 +   */
899 +  void ForceMatrixDecomposition::collectSelfData() {
900 +    snap_ = sman_->getCurrentSnapshot();
901 +    storageLayout_ = sman_->getStorageLayout();
902  
903 + #ifdef IS_MPI
904 +    for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
905 +      RealType ploc1 = embeddingPot[ii];
906 +      RealType ploc2 = 0.0;
907 +      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
908 +      embeddingPot[ii] = ploc2;
909 +    }    
910 + #endif
911 +    
912    }
913  
914 +
915 +
916    int ForceMatrixDecomposition::getNAtomsInRow() {  
917   #ifdef IS_MPI
918      return nAtomsInRow_;
# Line 993 | Line 1035 | namespace OpenMD {
1035     * We need to exclude some overcounted interactions that result from
1036     * the parallel decomposition.
1037     */
1038 <  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) {
1039 <    int unique_id_1, unique_id_2;
1038 >  bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) {
1039 >    int unique_id_1, unique_id_2, group1, group2;
1040          
1041   #ifdef IS_MPI
1042      // in MPI, we have to look up the unique IDs for each atom
1043      unique_id_1 = AtomRowToGlobal[atom1];
1044      unique_id_2 = AtomColToGlobal[atom2];
1045 +    group1 = cgRowToGlobal[cg1];
1046 +    group2 = cgColToGlobal[cg2];
1047   #else
1048      unique_id_1 = AtomLocalToGlobal[atom1];
1049      unique_id_2 = AtomLocalToGlobal[atom2];
1050 +    group1 = cgLocalToGlobal[cg1];
1051 +    group2 = cgLocalToGlobal[cg2];
1052   #endif  
1053  
1054      if (unique_id_1 == unique_id_2) return true;
# Line 1014 | Line 1060 | namespace OpenMD {
1060      } else {
1061        if ((unique_id_1 + unique_id_2) % 2 == 1) return true;
1062      }
1063 + #endif    
1064 +
1065 + #ifndef IS_MPI
1066 +    if (group1 == group2) {
1067 +      if (unique_id_1 < unique_id_2) return true;
1068 +    }
1069   #endif
1070      
1071      return false;
# Line 1116 | Line 1168 | namespace OpenMD {
1168  
1169   #else
1170      
1119 –
1120 –    // cerr << "atoms = " << atom1 << " " << atom2 << "\n";
1121 –    // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n";
1122 –    // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n";
1123 –
1171      idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1125 –    //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
1126 –    //                         ff_->getAtomType(idents[atom2]) );
1172  
1173      if (storageLayout_ & DataStorage::dslAmat) {
1174        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 1178 | 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);
1231  
1232      if (storageLayout_ & DataStorage::dslFlucQForce) {              
1233 <      atomRowData.flucQFrc[atom1] += *(idat.dVdFQ1);
1234 <      atomColData.flucQFrc[atom2] += *(idat.dVdFQ2);
1233 >      atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1234 >      atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1235      }
1236  
1237      if (storageLayout_ & DataStorage::dslElectricField) {              
# Line 1194 | 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);
# Line 1208 | Line 1256 | namespace OpenMD {
1256      }
1257      
1258      if (storageLayout_ & DataStorage::dslFlucQForce) {              
1259 <      snap_->atomData.flucQFrc[atom1] += *(idat.dVdFQ1);
1259 >      snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1);
1260        snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2);
1261      }
1262  

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