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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1895 by gezelter, Mon Jul 1 21:09:37 2013 UTC vs.
Revision 1939 by gezelter, Thu Oct 31 18:18:57 2013 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 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 419 | Line 430 | namespace OpenMD {
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) {
# 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]);
1178 >    //idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]);
1179      idat.atid1 = identsRow[atom1];
1180      idat.atid2 = identsCol[atom2];
1181 <    //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1182 <    //                         ff_->getAtomType(identsCol[atom2]) );
1183 <    
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 1206 | 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 1327 | Line 1364 | namespace OpenMD {
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 1354 | 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 1452 | 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 1510 | 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 1537 | 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 1558 | 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 1573 | 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          }    

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