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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC vs.
Revision 1971 by gezelter, Fri Feb 28 13:25:13 2014 UTC

# Line 99 | Line 99 | namespace OpenMD {
99      nGroups_ = info_->getNLocalCutoffGroups();
100      // gather the information for atomtype IDs (atids):
101      idents = info_->getIdentArray();
102 +    regions = info_->getRegions();
103      AtomLocalToGlobal = info_->getGlobalAtomIndices();
104      cgLocalToGlobal = info_->getGlobalGroupIndices();
105      vector<int> globalGroupMembership = info_->getGlobalGroupMembership();
# Line 118 | Line 119 | namespace OpenMD {
119      
120   #ifdef IS_MPI
121  
122 <    MPI::Intracomm row = rowComm.getComm();
123 <    MPI::Intracomm col = colComm.getComm();
122 >    MPI_Comm row = rowComm.getComm();
123 >    MPI_Comm col = colComm.getComm();
124  
125      AtomPlanIntRow = new Plan<int>(row, nLocal_);
126      AtomPlanRealRow = new Plan<RealType>(row, nLocal_);
# Line 163 | Line 164 | namespace OpenMD {
164      
165      AtomPlanIntRow->gather(idents, identsRow);
166      AtomPlanIntColumn->gather(idents, identsCol);
167 +
168 +    regionsRow.resize(nAtomsInRow_);
169 +    regionsCol.resize(nAtomsInCol_);
170      
171 +    AtomPlanIntRow->gather(regions, regionsRow);
172 +    AtomPlanIntColumn->gather(regions, regionsCol);
173 +    
174      // allocate memory for the parallel objects
175      atypesRow.resize(nAtomsInRow_);
176      atypesCol.resize(nAtomsInCol_);
# Line 308 | Line 315 | namespace OpenMD {
315    
316    void ForceMatrixDecomposition::createGtypeCutoffMap() {
317      
318 +    GrCut.clear();
319 +    GrCutSq.clear();
320 +    GrlistSq.clear();
321 +
322      RealType tol = 1e-6;
323      largestRcut_ = 0.0;
324      int atid;
# Line 413 | Line 424 | namespace OpenMD {
424                                       gTypeCutoffs.end());
425  
426   #ifdef IS_MPI
427 <    MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE,
428 <                              MPI::MAX);
427 >    MPI_Allreduce(MPI_IN_PLACE, &groupMax, 1, MPI_REALTYPE,
428 >                  MPI_MAX, MPI_COMM_WORLD);
429   #endif
430      
431      RealType tradRcut = groupMax;
432  
433 +    GrCut.resize( gTypeCutoffs.size() );
434 +    GrCutSq.resize( gTypeCutoffs.size() );
435 +    GrlistSq.resize( gTypeCutoffs.size() );
436 +
437 +
438      for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
439 +      GrCut[i].resize( gTypeCutoffs.size() , 0.0);
440 +      GrCutSq[i].resize( gTypeCutoffs.size(), 0.0 );
441 +      GrlistSq[i].resize( gTypeCutoffs.size(), 0.0 );
442 +
443        for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {      
444          RealType thisRcut;
445          switch(cutoffPolicy_) {
# Line 442 | Line 462 | namespace OpenMD {
462            break;
463          }
464  
465 <        pair<int,int> key = make_pair(i,j);
446 <        gTypeCutoffMap[key].first = thisRcut;
465 >        GrCut[i][j] = thisRcut;
466          if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
467 <        gTypeCutoffMap[key].second = thisRcut*thisRcut;
468 <        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
467 >        GrCutSq[i][j] = thisRcut * thisRcut;
468 >        GrlistSq[i][j] = pow(thisRcut + skinThickness_, 2);
469 >
470 >        // pair<int,int> key = make_pair(i,j);
471 >        // gTypeCutoffMap[key].first = thisRcut;
472 >        // gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
473          // sanity check
474          
475          if (userChoseCutoff_) {
476 <          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
476 >          if (abs(GrCut[i][j] - userCutoff_) > 0.0001) {
477              sprintf(painCave.errMsg,
478                      "ForceMatrixDecomposition::createGtypeCutoffMap "
479                      "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
# Line 463 | Line 486 | namespace OpenMD {
486      }
487    }
488  
489 <  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
489 >  void ForceMatrixDecomposition::getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) {
490      int i, j;  
491   #ifdef IS_MPI
492      i = groupRowToGtype[cg1];
# Line 472 | Line 495 | namespace OpenMD {
495      i = groupToGtype[cg1];
496      j = groupToGtype[cg2];
497   #endif    
498 <    return gTypeCutoffMap[make_pair(i,j)];
498 >    rcut = GrCut[i][j];
499 >    rcutsq = GrCutSq[i][j];
500 >    rlistsq = GrlistSq[i][j];
501 >    return;
502 >    //return gTypeCutoffMap[make_pair(i,j)];
503    }
504  
505    int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
506      for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) {
507        if (toposForAtom[atom1][j] == atom2)
508          return topoDist[atom1][j];
509 <    }
509 >    }                                          
510      return 0;
511    }
512  
# Line 889 | Line 916 | namespace OpenMD {
916      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
917        RealType ploc1 = pairwisePot[ii];
918        RealType ploc2 = 0.0;
919 <      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
919 >      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
920        pairwisePot[ii] = ploc2;
921      }
922  
923      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
924        RealType ploc1 = excludedPot[ii];
925        RealType ploc2 = 0.0;
926 <      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
926 >      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
927        excludedPot[ii] = ploc2;
928      }
929  
930      // Here be dragons.
931 <    MPI::Intracomm col = colComm.getComm();
931 >    MPI_Comm col = colComm.getComm();
932  
933 <    col.Allreduce(MPI::IN_PLACE,
933 >    MPI_Allreduce(MPI_IN_PLACE,
934                    &snap_->frameData.conductiveHeatFlux[0], 3,
935 <                  MPI::REALTYPE, MPI::SUM);
935 >                  MPI_REALTYPE, MPI_SUM, col);
936  
937  
938   #endif
# Line 924 | Line 951 | namespace OpenMD {
951      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
952        RealType ploc1 = embeddingPot[ii];
953        RealType ploc2 = 0.0;
954 <      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
954 >      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
955        embeddingPot[ii] = ploc2;
956      }    
957      for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) {
958        RealType ploc1 = excludedSelfPot[ii];
959        RealType ploc2 = 0.0;
960 <      MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM);
960 >      MPI_Allreduce(&ploc1, &ploc2, 1, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
961        excludedSelfPot[ii] = ploc2;
962      }    
963   #endif
# Line 939 | Line 966 | namespace OpenMD {
966  
967  
968  
969 <  int ForceMatrixDecomposition::getNAtomsInRow() {  
969 >  int& ForceMatrixDecomposition::getNAtomsInRow() {  
970   #ifdef IS_MPI
971      return nAtomsInRow_;
972   #else
# Line 950 | Line 977 | namespace OpenMD {
977    /**
978     * returns the list of atoms belonging to this group.  
979     */
980 <  vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
980 >  vector<int>& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){
981   #ifdef IS_MPI
982      return groupListRow_[cg1];
983   #else
# Line 958 | Line 985 | namespace OpenMD {
985   #endif
986    }
987  
988 <  vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
988 >  vector<int>& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){
989   #ifdef IS_MPI
990      return groupListCol_[cg2];
991   #else
# Line 981 | Line 1008 | namespace OpenMD {
1008      return d;    
1009    }
1010  
1011 <  Vector3d ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
1011 >  Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){
1012   #ifdef IS_MPI
1013      return cgColData.velocity[cg2];
1014   #else
# Line 989 | Line 1016 | namespace OpenMD {
1016   #endif
1017    }
1018  
1019 <  Vector3d ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
1019 >  Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){
1020   #ifdef IS_MPI
1021      return atomColData.velocity[atom2];
1022   #else
# Line 1027 | Line 1054 | namespace OpenMD {
1054      return d;    
1055    }
1056  
1057 <  RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1057 >  RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) {
1058   #ifdef IS_MPI
1059      return massFactorsRow[atom1];
1060   #else
# Line 1035 | Line 1062 | namespace OpenMD {
1062   #endif
1063    }
1064  
1065 <  RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1065 >  RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) {
1066   #ifdef IS_MPI
1067      return massFactorsCol[atom2];
1068   #else
# Line 1058 | Line 1085 | namespace OpenMD {
1085      return d;    
1086    }
1087  
1088 <  vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1088 >  vector<int>& ForceMatrixDecomposition::getExcludesForAtom(int atom1) {
1089      return excludesForAtom[atom1];
1090    }
1091  
# Line 1148 | Line 1175 | namespace OpenMD {
1175      idat.excluded = excludeAtomPair(atom1, atom2);
1176    
1177   #ifdef IS_MPI
1178 <    idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1179 <    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1180 <    //                         ff_->getAtomType(identsCol[atom2]) );
1181 <    
1178 >    //idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1179 >    idat.atid1 = identsRow[atom1];
1180 >    idat.atid2 = identsCol[atom2];
1181 >
1182 >    if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) {
1183 >      idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]);
1184 >    } else {
1185 >      idat.sameRegion = false;
1186 >    }
1187 >
1188      if (storageLayout_ & DataStorage::dslAmat) {
1189        idat.A1 = &(atomRowData.aMat[atom1]);
1190        idat.A2 = &(atomColData.aMat[atom2]);
# Line 1204 | Line 1237 | namespace OpenMD {
1237  
1238   #else
1239      
1240 <    idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1240 >    //idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]);
1241 >    idat.atid1 = idents[atom1];
1242 >    idat.atid2 = idents[atom2];
1243  
1244 +    if (regions[atom1] >= 0 && regions[atom2] >= 0) {
1245 +      idat.sameRegion = (regions[atom1] == regions[atom2]);
1246 +    } else {
1247 +      idat.sameRegion = false;
1248 +    }
1249 +
1250      if (storageLayout_ & DataStorage::dslAmat) {
1251        idat.A1 = &(snap_->atomData.aMat[atom1]);
1252        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 1316 | Line 1357 | namespace OpenMD {
1357     * first element of pair is row-indexed CutoffGroup
1358     * second element of pair is column-indexed CutoffGroup
1359     */
1360 <  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1361 <      
1362 <    vector<pair<int, int> > neighborList;
1360 >  void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1361 >    
1362 >    neighborList.clear();
1363      groupCutoffs cuts;
1364      bool doAllPairs = false;
1365  
1366      RealType rList_ = (largestRcut_ + skinThickness_);
1367 +    RealType rcut, rcutsq, rlistsq;
1368      Snapshot* snap_ = sman_->getCurrentSnapshot();
1369      Mat3x3d box;
1370      Mat3x3d invBox;
# Line 1350 | Line 1392 | namespace OpenMD {
1392      Vector3d boxY = box.getColumn(1);
1393      Vector3d boxZ = box.getColumn(2);
1394      
1395 <    nCells_.x() = (int) ( boxX.length() )/ rList_;
1396 <    nCells_.y() = (int) ( boxY.length() )/ rList_;
1397 <    nCells_.z() = (int) ( boxZ.length() )/ rList_;
1395 >    nCells_.x() = int( boxX.length() / rList_ );
1396 >    nCells_.y() = int( boxY.length() / rList_ );
1397 >    nCells_.z() = int( boxZ.length() / rList_ );
1398      
1399      // handle small boxes where the cell offsets can end up repeating cells
1400      
# Line 1448 | Line 1490 | namespace OpenMD {
1490          }
1491          
1492          // find xyz-indices of cell that cutoffGroup is in.
1493 <        whichCell.x() = nCells_.x() * scaled.x();
1494 <        whichCell.y() = nCells_.y() * scaled.y();
1495 <        whichCell.z() = nCells_.z() * scaled.z();
1493 >        whichCell.x() = int(nCells_.x() * scaled.x());
1494 >        whichCell.y() = int(nCells_.y() * scaled.y());
1495 >        whichCell.z() = int(nCells_.z() * scaled.z());
1496          
1497          // find single index of this cell:
1498          cellIndex = Vlinear(whichCell, nCells_);
# Line 1506 | Line 1548 | namespace OpenMD {
1548                    if (usePeriodicBoundaryConditions_) {
1549                      snap_->wrapVector(dr);
1550                    }
1551 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1552 <                  if (dr.lengthSquare() < cuts.third) {
1551 >                  getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1552 >                  if (dr.lengthSquare() < rlistsq) {
1553                      neighborList.push_back(make_pair((*j1), (*j2)));
1554                    }                  
1555                  }
# Line 1533 | Line 1575 | namespace OpenMD {
1575                      if (usePeriodicBoundaryConditions_) {
1576                        snap_->wrapVector(dr);
1577                      }
1578 <                    cuts = getGroupCutoffs( (*j1), (*j2) );
1579 <                    if (dr.lengthSquare() < cuts.third) {
1578 >                    getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1579 >                    if (dr.lengthSquare() < rlistsq) {
1580                        neighborList.push_back(make_pair((*j1), (*j2)));
1581                      }
1582                    }
# Line 1554 | Line 1596 | namespace OpenMD {
1596            if (usePeriodicBoundaryConditions_) {
1597              snap_->wrapVector(dr);
1598            }
1599 <          cuts = getGroupCutoffs( j1, j2 );
1600 <          if (dr.lengthSquare() < cuts.third) {
1599 >          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1600 >          if (dr.lengthSquare() < rlistsq) {
1601              neighborList.push_back(make_pair(j1, j2));
1602            }
1603          }
# Line 1569 | Line 1611 | namespace OpenMD {
1611            if (usePeriodicBoundaryConditions_) {
1612              snap_->wrapVector(dr);
1613            }
1614 <          cuts = getGroupCutoffs( j1, j2 );
1615 <          if (dr.lengthSquare() < cuts.third) {
1614 >          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1615 >          if (dr.lengthSquare() < rlistsq) {
1616              neighborList.push_back(make_pair(j1, j2));
1617            }
1618          }    
# Line 1583 | Line 1625 | namespace OpenMD {
1625      saved_CG_positions_.clear();
1626      for (int i = 0; i < nGroups_; i++)
1627        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1586 –    
1587 –    return neighborList;
1628    }
1629   } //end namespace OpenMD

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