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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 1896 by gezelter, Tue Jul 2 20:02:31 2013 UTC

# Line 308 | Line 308 | namespace OpenMD {
308    
309    void ForceMatrixDecomposition::createGtypeCutoffMap() {
310      
311 +    GrCut.clear();
312 +    GrCutSq.clear();
313 +    GrlistSq.clear();
314 +
315      RealType tol = 1e-6;
316      largestRcut_ = 0.0;
317      int atid;
# Line 418 | Line 422 | namespace OpenMD {
422   #endif
423      
424      RealType tradRcut = groupMax;
425 +
426 +    GrCut.resize( gTypeCutoffs.size() );
427 +    GrCutSq.resize( gTypeCutoffs.size() );
428 +    GrlistSq.resize( gTypeCutoffs.size() );
429  
430 +
431      for (unsigned int i = 0; i < gTypeCutoffs.size();  i++) {
432 +      GrCut[i].resize( gTypeCutoffs.size() , 0.0);
433 +      GrCutSq[i].resize( gTypeCutoffs.size(), 0.0 );
434 +      GrlistSq[i].resize( gTypeCutoffs.size(), 0.0 );
435 +
436        for (unsigned int j = 0; j < gTypeCutoffs.size();  j++) {      
437          RealType thisRcut;
438          switch(cutoffPolicy_) {
# Line 442 | Line 455 | namespace OpenMD {
455            break;
456          }
457  
458 <        pair<int,int> key = make_pair(i,j);
446 <        gTypeCutoffMap[key].first = thisRcut;
458 >        GrCut[i][j] = thisRcut;
459          if (thisRcut > largestRcut_) largestRcut_ = thisRcut;
460 <        gTypeCutoffMap[key].second = thisRcut*thisRcut;
461 <        gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
460 >        GrCutSq[i][j] = thisRcut * thisRcut;
461 >        GrlistSq[i][j] = pow(thisRcut + skinThickness_, 2);
462 >
463 >        // pair<int,int> key = make_pair(i,j);
464 >        // gTypeCutoffMap[key].first = thisRcut;
465 >        // gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2);
466          // sanity check
467          
468          if (userChoseCutoff_) {
469 <          if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) {
469 >          if (abs(GrCut[i][j] - userCutoff_) > 0.0001) {
470              sprintf(painCave.errMsg,
471                      "ForceMatrixDecomposition::createGtypeCutoffMap "
472                      "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_);
# Line 463 | Line 479 | namespace OpenMD {
479      }
480    }
481  
482 <  groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) {
482 >  void ForceMatrixDecomposition::getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) {
483      int i, j;  
484   #ifdef IS_MPI
485      i = groupRowToGtype[cg1];
# Line 472 | Line 488 | namespace OpenMD {
488      i = groupToGtype[cg1];
489      j = groupToGtype[cg2];
490   #endif    
491 <    return gTypeCutoffMap[make_pair(i,j)];
491 >    rcut = GrCut[i][j];
492 >    rcutsq = GrCutSq[i][j];
493 >    rlistsq = GrlistSq[i][j];
494 >    return;
495 >    //return gTypeCutoffMap[make_pair(i,j)];
496    }
497  
498    int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) {
# Line 1327 | Line 1347 | namespace OpenMD {
1347      bool doAllPairs = false;
1348  
1349      RealType rList_ = (largestRcut_ + skinThickness_);
1350 +    RealType rcut, rcutsq, rlistsq;
1351      Snapshot* snap_ = sman_->getCurrentSnapshot();
1352      Mat3x3d box;
1353      Mat3x3d invBox;
# Line 1510 | Line 1531 | namespace OpenMD {
1531                    if (usePeriodicBoundaryConditions_) {
1532                      snap_->wrapVector(dr);
1533                    }
1534 <                  cuts = getGroupCutoffs( (*j1), (*j2) );
1535 <                  if (dr.lengthSquare() < cuts.third) {
1534 >                  getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1535 >                  if (dr.lengthSquare() < rlistsq) {
1536                      neighborList.push_back(make_pair((*j1), (*j2)));
1537                    }                  
1538                  }
# Line 1537 | Line 1558 | namespace OpenMD {
1558                      if (usePeriodicBoundaryConditions_) {
1559                        snap_->wrapVector(dr);
1560                      }
1561 <                    cuts = getGroupCutoffs( (*j1), (*j2) );
1562 <                    if (dr.lengthSquare() < cuts.third) {
1561 >                    getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq );
1562 >                    if (dr.lengthSquare() < rlistsq) {
1563                        neighborList.push_back(make_pair((*j1), (*j2)));
1564                      }
1565                    }
# Line 1558 | Line 1579 | namespace OpenMD {
1579            if (usePeriodicBoundaryConditions_) {
1580              snap_->wrapVector(dr);
1581            }
1582 <          cuts = getGroupCutoffs( j1, j2 );
1583 <          if (dr.lengthSquare() < cuts.third) {
1582 >          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq);
1583 >          if (dr.lengthSquare() < rlistsq) {
1584              neighborList.push_back(make_pair(j1, j2));
1585            }
1586          }
# Line 1573 | Line 1594 | namespace OpenMD {
1594            if (usePeriodicBoundaryConditions_) {
1595              snap_->wrapVector(dr);
1596            }
1597 <          cuts = getGroupCutoffs( j1, j2 );
1598 <          if (dr.lengthSquare() < cuts.third) {
1597 >          getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq );
1598 >          if (dr.lengthSquare() < rlistsq) {
1599              neighborList.push_back(make_pair(j1, j2));
1600            }
1601          }    

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