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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 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC vs.
Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC

# Line 61 | Line 61 | namespace OpenMD {
61      nGroups_ = info_->getNLocalCutoffGroups();
62      cerr << "in dId, nGroups = " << nGroups_ << "\n";
63      // gather the information for atomtype IDs (atids):
64 <    identsLocal = info_->getIdentArray();
64 >    idents = info_->getIdentArray();
65      AtomLocalToGlobal = info_->getGlobalAtomIndices();
66      cgLocalToGlobal = info_->getGlobalGroupIndices();
67      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
68 <    vector<RealType> massFactorsLocal = info_->getMassFactors();
68 >    massFactors = info_->getMassFactors();
69 >
70      PairList excludes = info_->getExcludedInteractions();
71      PairList oneTwo = info_->getOneTwoInteractions();
72      PairList oneThree = info_->getOneThreeInteractions();
# Line 108 | Line 109 | namespace OpenMD {
109      identsRow.resize(nAtomsInRow_);
110      identsCol.resize(nAtomsInCol_);
111      
112 <    AtomCommIntRow->gather(identsLocal, identsRow);
113 <    AtomCommIntColumn->gather(identsLocal, identsCol);
112 >    AtomCommIntRow->gather(idents, identsRow);
113 >    AtomCommIntColumn->gather(idents, identsCol);
114      
115      AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
116      AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
# Line 117 | Line 118 | namespace OpenMD {
118      cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
119      cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
120  
121 <    AtomCommRealRow->gather(massFactorsLocal, massFactorsRow);
122 <    AtomCommRealColumn->gather(massFactorsLocal, massFactorsCol);
121 >    AtomCommRealRow->gather(massFactors, massFactorsRow);
122 >    AtomCommRealColumn->gather(massFactors, massFactorsCol);
123  
124      groupListRow_.clear();
125      groupListRow_.resize(nGroupsInRow_);
# Line 232 | Line 233 | namespace OpenMD {
233      set<AtomType*> atypes = info_->getSimulatedAtomTypes();
234      vector<RealType> atypeCutoff;
235      atypeCutoff.resize( atypes.size() );
236 <
236 >      
237      for (set<AtomType*>::iterator at = atypes.begin();
238           at != atypes.end(); ++at){
238 –      rc = interactionMan_->getSuggestedCutoffRadius(*at);
239        atid = (*at)->getIdent();
240 <      atypeCutoff[atid] = rc;
240 >
241 >      if (userChoseCutoff_)
242 >        atypeCutoff[atid] = userCutoff_;
243 >      else
244 >        atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at);
245      }
246  
247      vector<RealType> gTypeCutoffs;
# Line 309 | Line 313 | namespace OpenMD {
313        for (vector<int>::iterator ia = atomList.begin();
314             ia != atomList.end(); ++ia) {            
315          int atom1 = (*ia);
316 <        atid = identsLocal[atom1];
316 >        atid = idents[atom1];
317          if (atypeCutoff[atid] > groupCutoff[cg1]) {
318            groupCutoff[cg1] = atypeCutoff[atid];
319          }
# Line 378 | Line 382 | namespace OpenMD {
382            if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
383              sprintf(painCave.errMsg,
384                      "ForceMatrixDecomposition::createGtypeCutoffMap "
385 <                    "user-specified rCut does not match computed group Cutoff\n");
385 >                    "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
386              painCave.severity = OPENMD_ERROR;
387              painCave.isFatal = 1;
388              simError();            
# Line 410 | Line 414 | namespace OpenMD {
414    }
415  
416    void ForceMatrixDecomposition::zeroWorkArrays() {
417 <
418 <    for (int j = 0; j < N_INTERACTION_FAMILIES; j++) {
415 <      longRangePot_[j] = 0.0;
416 <    }
417 >    pairwisePot = 0.0;
418 >    embeddingPot = 0.0;
419  
420   #ifdef IS_MPI
421      if (storageLayout_ & DataStorage::dslForce) {
# Line 430 | Line 432 | namespace OpenMD {
432           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
433  
434      fill(pot_col.begin(), pot_col.end(),
435 <         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
434 <    
435 <    pot_local = Vector<RealType, N_INTERACTION_FAMILIES>(0.0);
435 >         Vector<RealType, N_INTERACTION_FAMILIES> (0.0));  
436  
437      if (storageLayout_ & DataStorage::dslParticlePot) {    
438        fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), 0.0);
# Line 606 | Line 606 | namespace OpenMD {
606      AtomCommPotRow->scatter(pot_row, pot_temp);
607  
608      for (int ii = 0;  ii < pot_temp.size(); ii++ )
609 <      pot_local += pot_temp[ii];
609 >      pairwisePot += pot_temp[ii];
610      
611      fill(pot_temp.begin(), pot_temp.end(),
612           Vector<RealType, N_INTERACTION_FAMILIES> (0.0));
# Line 614 | Line 614 | namespace OpenMD {
614      AtomCommPotColumn->scatter(pot_col, pot_temp);    
615      
616      for (int ii = 0;  ii < pot_temp.size(); ii++ )
617 <      pot_local += pot_temp[ii];
618 <    
617 >      pairwisePot += pot_temp[ii];    
618   #endif
619 +
620    }
621  
622    int ForceMatrixDecomposition::getNAtomsInRow() {  
# Line 691 | Line 691 | namespace OpenMD {
691   #ifdef IS_MPI
692      return massFactorsRow[atom1];
693   #else
694 <    return massFactorsLocal[atom1];
694 >    cerr << "mfs = " << massFactors.size() << " atom1 = " << atom1 << "\n";
695 >    return massFactors[atom1];
696   #endif
697    }
698  
# Line 699 | Line 700 | namespace OpenMD {
700   #ifdef IS_MPI
701      return massFactorsCol[atom2];
702   #else
703 <    return massFactorsLocal[atom2];
703 >    return massFactors[atom2];
704   #endif
705  
706    }
# Line 754 | Line 755 | namespace OpenMD {
755      for (vector<int>::iterator i = skipsForAtom[atom1].begin();
756           i != skipsForAtom[atom1].end(); ++i) {
757        if ( (*i) == unique_id_2 ) return true;
758 <    }    
758 >    }
759  
760 +    return false;
761    }
762  
763  
# Line 776 | Line 778 | namespace OpenMD {
778    }
779  
780      // filling interaction blocks with pointers
781 <  InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) {    
782 <    InteractionData idat;
781 <
781 >  void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat,
782 >                                                     int atom1, int atom2) {    
783   #ifdef IS_MPI
784      
785      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
786                               ff_->getAtomType(identsCol[atom2]) );
786 –
787      
788      if (storageLayout_ & DataStorage::dslAmat) {
789        idat.A1 = &(atomRowData.aMat[atom1]);
# Line 822 | Line 822 | namespace OpenMD {
822  
823   #else
824  
825 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
826 <                             ff_->getAtomType(identsLocal[atom2]) );
825 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
826 >                             ff_->getAtomType(idents[atom2]) );
827  
828      if (storageLayout_ & DataStorage::dslAmat) {
829        idat.A1 = &(snap_->atomData.aMat[atom1]);
# Line 840 | Line 840 | namespace OpenMD {
840        idat.t2 = &(snap_->atomData.torque[atom2]);
841      }
842  
843 <    if (storageLayout_ & DataStorage::dslDensity) {
843 >    if (storageLayout_ & DataStorage::dslDensity) {    
844        idat.rho1 = &(snap_->atomData.density[atom1]);
845        idat.rho2 = &(snap_->atomData.density[atom2]);
846      }
# Line 861 | Line 861 | namespace OpenMD {
861      }
862  
863   #endif
864 –    return idat;
864    }
865  
866    
867 <  void ForceMatrixDecomposition::unpackInteractionData(InteractionData idat, int atom1, int atom2) {    
867 >  void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) {    
868   #ifdef IS_MPI
869      pot_row[atom1] += 0.5 *  *(idat.pot);
870      pot_col[atom2] += 0.5 *  *(idat.pot);
# Line 873 | Line 872 | namespace OpenMD {
872      atomRowData.force[atom1] += *(idat.f1);
873      atomColData.force[atom2] -= *(idat.f1);
874   #else
875 <    longRangePot_ += *(idat.pot);
876 <    
875 >    pairwisePot += *(idat.pot);
876 >
877      snap_->atomData.force[atom1] += *(idat.f1);
878      snap_->atomData.force[atom2] -= *(idat.f1);
879   #endif
# Line 882 | Line 881 | namespace OpenMD {
881    }
882  
883  
884 <  InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){
885 <
887 <    InteractionData idat;
884 >  void ForceMatrixDecomposition::fillSkipData(InteractionData &idat,
885 >                                              int atom1, int atom2) {
886   #ifdef IS_MPI
887      idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
888                               ff_->getAtomType(identsCol[atom2]) );
# Line 893 | Line 891 | namespace OpenMD {
891        idat.eFrame1 = &(atomRowData.electroFrame[atom1]);
892        idat.eFrame2 = &(atomColData.electroFrame[atom2]);
893      }
894 +
895      if (storageLayout_ & DataStorage::dslTorque) {
896        idat.t1 = &(atomRowData.torque[atom1]);
897        idat.t2 = &(atomColData.torque[atom2]);
898      }
899 +
900 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
901 +      idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]);
902 +      idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]);
903 +    }
904   #else
905 <    idat.atypes = make_pair( ff_->getAtomType(identsLocal[atom1]),
906 <                             ff_->getAtomType(identsLocal[atom2]) );
905 >    idat.atypes = make_pair( ff_->getAtomType(idents[atom1]),
906 >                             ff_->getAtomType(idents[atom2]) );
907  
908      if (storageLayout_ & DataStorage::dslElectroFrame) {
909        idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]);
910        idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]);
911      }
912 +
913      if (storageLayout_ & DataStorage::dslTorque) {
914        idat.t1 = &(snap_->atomData.torque[atom1]);
915        idat.t2 = &(snap_->atomData.torque[atom2]);
916      }
917 +
918 +    if (storageLayout_ & DataStorage::dslSkippedCharge) {
919 +      idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]);
920 +      idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]);
921 +    }
922   #endif    
923    }
924  
925 +
926 +  void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) {    
927 + #ifdef IS_MPI
928 +    pot_row[atom1] += 0.5 *  *(idat.pot);
929 +    pot_col[atom2] += 0.5 *  *(idat.pot);
930 + #else
931 +    pairwisePot += *(idat.pot);  
932 + #endif
933 +
934 +  }
935 +
936 +
937    /*
938     * buildNeighborList
939     *
# Line 957 | Line 979 | namespace OpenMD {
979   #ifdef IS_MPI
980      for (int i = 0; i < nGroupsInRow_; i++) {
981        rs = cgRowData.position[i];
982 +
983        // scaled positions relative to the box vectors
984        scaled = invHmat * rs;
985 +
986        // wrap the vector back into the unit box by subtracting integer box
987        // numbers
988 <      for (int j = 0; j < 3; j++)
988 >      for (int j = 0; j < 3; j++) {
989          scaled[j] -= roundMe(scaled[j]);
990 +        scaled[j] += 0.5;
991 +      }
992      
993        // find xyz-indices of cell that cutoffGroup is in.
994        whichCell.x() = nCells_.x() * scaled.x();
# Line 971 | Line 997 | namespace OpenMD {
997  
998        // find single index of this cell:
999        cellIndex = Vlinear(whichCell, nCells_);
1000 +
1001        // add this cutoff group to the list of groups in this cell;
1002        cellListRow_[cellIndex].push_back(i);
1003      }
1004  
1005      for (int i = 0; i < nGroupsInCol_; i++) {
1006        rs = cgColData.position[i];
1007 +
1008        // scaled positions relative to the box vectors
1009        scaled = invHmat * rs;
1010 +
1011        // wrap the vector back into the unit box by subtracting integer box
1012        // numbers
1013 <      for (int j = 0; j < 3; j++)
1013 >      for (int j = 0; j < 3; j++) {
1014          scaled[j] -= roundMe(scaled[j]);
1015 +        scaled[j] += 0.5;
1016 +      }
1017  
1018        // find xyz-indices of cell that cutoffGroup is in.
1019        whichCell.x() = nCells_.x() * scaled.x();
# Line 991 | Line 1022 | namespace OpenMD {
1022  
1023        // find single index of this cell:
1024        cellIndex = Vlinear(whichCell, nCells_);
1025 +
1026        // add this cutoff group to the list of groups in this cell;
1027        cellListCol_[cellIndex].push_back(i);
1028      }
1029   #else
1030      for (int i = 0; i < nGroups_; i++) {
1031        rs = snap_->cgData.position[i];
1032 +
1033        // scaled positions relative to the box vectors
1034        scaled = invHmat * rs;
1035 +
1036        // wrap the vector back into the unit box by subtracting integer box
1037        // numbers
1038 <      for (int j = 0; j < 3; j++)
1038 >      for (int j = 0; j < 3; j++) {
1039          scaled[j] -= roundMe(scaled[j]);
1040 +        scaled[j] += 0.5;
1041 +      }
1042  
1043        // find xyz-indices of cell that cutoffGroup is in.
1044        whichCell.x() = nCells_.x() * scaled.x();
# Line 1010 | Line 1046 | namespace OpenMD {
1046        whichCell.z() = nCells_.z() * scaled.z();
1047  
1048        // find single index of this cell:
1049 <      cellIndex = Vlinear(whichCell, nCells_);
1049 >      cellIndex = Vlinear(whichCell, nCells_);      
1050 >
1051        // add this cutoff group to the list of groups in this cell;
1052        cellList_[cellIndex].push_back(i);
1053      }
# Line 1068 | Line 1105 | namespace OpenMD {
1105                }
1106              }
1107   #else
1108 +
1109              for (vector<int>::iterator j1 = cellList_[m1].begin();
1110                   j1 != cellList_[m1].end(); ++j1) {
1111                for (vector<int>::iterator j2 = cellList_[m2].begin();
1112                     j2 != cellList_[m2].end(); ++j2) {
1113 <                              
1113 >
1114                  // Always do this if we're in different cells or if
1115                  // we're in the same cell and the global index of the
1116                  // j2 cutoff group is less than the j1 cutoff group
# Line 1092 | Line 1130 | namespace OpenMD {
1130          }
1131        }
1132      }
1133 <
1133 >    
1134      // save the local cutoff group positions for the check that is
1135      // done on each loop:
1136      saved_CG_positions_.clear();
1137      for (int i = 0; i < nGroups_; i++)
1138        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1139 <
1139 >  
1140      return neighborList;
1141    }
1142   } //end namespace OpenMD

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