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root/OpenMD/trunk/src/parallel/ForceMatrixDecomposition.cpp
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Comparing trunk/src/parallel/ForceMatrixDecomposition.cpp (file contents):
Revision 1893 by gezelter, Wed Jun 19 17:19:07 2013 UTC vs.
Revision 1929 by gezelter, Mon Aug 19 13:12:00 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_);
# 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 1149 | Line 1176 | namespace OpenMD {
1176    
1177   #ifdef IS_MPI
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 +      
1185      //idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]),
1186      //                         ff_->getAtomType(identsCol[atom2]) );
1187      
# Line 1205 | Line 1238 | namespace OpenMD {
1238   #else
1239      
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 +
1247      if (storageLayout_ & DataStorage::dslAmat) {
1248        idat.A1 = &(snap_->atomData.aMat[atom1]);
1249        idat.A2 = &(snap_->atomData.aMat[atom2]);
# Line 1316 | Line 1354 | namespace OpenMD {
1354     * first element of pair is row-indexed CutoffGroup
1355     * second element of pair is column-indexed CutoffGroup
1356     */
1357 <  vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() {
1358 <      
1359 <    vector<pair<int, int> > neighborList;
1357 >  void ForceMatrixDecomposition::buildNeighborList(vector<pair<int,int> >& neighborList) {
1358 >    
1359 >    neighborList.clear();
1360      groupCutoffs cuts;
1361      bool doAllPairs = false;
1362  
1363      RealType rList_ = (largestRcut_ + skinThickness_);
1364 +    RealType rcut, rcutsq, rlistsq;
1365      Snapshot* snap_ = sman_->getCurrentSnapshot();
1366      Mat3x3d box;
1367      Mat3x3d invBox;
# Line 1506 | Line 1545 | namespace OpenMD {
1545                    if (usePeriodicBoundaryConditions_) {
1546                      snap_->wrapVector(dr);
1547                    }
1548 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1549 <                  if (dr.lengthSquare() < cuts.third) {
1548 >                  getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1549 >                  if (dr.lengthSquare() < rlistsq) {
1550                      neighborList.push_back(make_pair((*j1), (*j2)));
1551                    }                  
1552                  }
# Line 1533 | Line 1572 | namespace OpenMD {
1572                      if (usePeriodicBoundaryConditions_) {
1573                        snap_->wrapVector(dr);
1574                      }
1575 <                    cuts = getGroupCutoffs( (*j1), (*j2) );
1576 <                    if (dr.lengthSquare() < cuts.third) {
1575 >                    getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1576 >                    if (dr.lengthSquare() < rlistsq) {
1577                        neighborList.push_back(make_pair((*j1), (*j2)));
1578                      }
1579                    }
# Line 1554 | Line 1593 | namespace OpenMD {
1593            if (usePeriodicBoundaryConditions_) {
1594              snap_->wrapVector(dr);
1595            }
1596 <          cuts = getGroupCutoffs( j1, j2 );
1597 <          if (dr.lengthSquare() < cuts.third) {
1596 >          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1597 >          if (dr.lengthSquare() < rlistsq) {
1598              neighborList.push_back(make_pair(j1, j2));
1599            }
1600          }
# Line 1569 | Line 1608 | namespace OpenMD {
1608            if (usePeriodicBoundaryConditions_) {
1609              snap_->wrapVector(dr);
1610            }
1611 <          cuts = getGroupCutoffs( j1, j2 );
1612 <          if (dr.lengthSquare() < cuts.third) {
1611 >          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1612 >          if (dr.lengthSquare() < rlistsq) {
1613              neighborList.push_back(make_pair(j1, j2));
1614            }
1615          }    
# Line 1583 | Line 1622 | namespace OpenMD {
1622      saved_CG_positions_.clear();
1623      for (int i = 0; i < nGroups_; i++)
1624        saved_CG_positions_.push_back(snap_->cgData.position[i]);
1586 –    
1587 –    return neighborList;
1625    }
1626   } //end namespace OpenMD

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