Program: 37796
Project: 37796
Buggy source:
public static Cell getSupercell(Cell c,List<List<Integer>> coefficients){
  Cell cell=c.getCellWithAllAtomsInCell();
  if (coefficients.size() != Constants.numDimensions)   throw new IllegalArgumentException("String_Node_Str" + coefficients.size());
  List<Vect> newVectors=new LinkedList<Vect>();
  for (int i=0; i < Constants.numDimensions; i++) {
    List<Integer> coefs=coefficients.get(i);
    if (coefs.size() != Constants.numDimensions)     throw new IllegalArgumentException("String_Node_Str" + coefs.size());
    Double x=coefs.get(0) * (cell.latticeVectors.get(0)).getCartesianComponents().get(0) + coefs.get(1) * (cell.latticeVectors.get(1)).getCartesianComponents().get(0) + coefs.get(2) * (cell.latticeVectors.get(2)).getCartesianComponents().get(0);
    Double y=coefs.get(0) * (cell.latticeVectors.get(0)).getCartesianComponents().get(1) + coefs.get(1) * (cell.latticeVectors.get(1)).getCartesianComponents().get(1) + coefs.get(2) * (cell.latticeVectors.get(2)).getCartesianComponents().get(1);
    Double z=coefs.get(0) * (cell.latticeVectors.get(0)).getCartesianComponents().get(2) + coefs.get(1) * (cell.latticeVectors.get(1)).getCartesianComponents().get(2) + coefs.get(2) * (cell.latticeVectors.get(2)).getCartesianComponents().get(2);
    newVectors.add(new Vect(x,y,z));
  }
  List<Site> newBasis=new LinkedList<Site>();
  int minx=0, maxx=0, miny=0, maxy=0, minz=0, maxz=0;
  for (int i=0; i <= 1; i++)   for (int j=0; j <= 1; j++)   for (int k=0; k <= 1; k++) {
    int combox=i * coefficients.get(0).get(0) + j * coefficients.get(1).get(0) + k * coefficients.get(2).get(0);
    minx=Math.min(minx,combox);
    maxx=Math.max(maxx,combox);
    int comboy=i * coefficients.get(0).get(1) + j * coefficients.get(1).get(1) + k * coefficients.get(2).get(1);
    miny=Math.min(miny,comboy);
    maxy=Math.max(maxy,comboy);
    int comboz=i * coefficients.get(0).get(2) + j * coefficients.get(1).get(2) + k * coefficients.get(2).get(2);
    minz=Math.min(minz,comboz);
    maxz=Math.max(maxz,comboz);
  }
  for (  Site s : cell.basis) {
    for (int i=minx; i <= maxx; i++) {
      for (int j=miny; j <= maxy; j++) {
        for (int k=minz; k <= maxz; k++) {
          Vect candidateSiteLoc=s.getCoords().plus(new Vect(new Double(i),new Double(j),new Double(k),cell.latticeVectors));
          List<Double> newFracCoords=candidateSiteLoc.getComponentsWRTBasis(newVectors);
          if (newFracCoords.get(0) > -Constants.epsilon && newFracCoords.get(0) <= 1 - Constants.epsilon && newFracCoords.get(1) > -Constants.epsilon && newFracCoords.get(1) <= 1 - Constants.epsilon && newFracCoords.get(2) > -Constants.epsilon && newFracCoords.get(2) <= 1 - Constants.epsilon)           newBasis.add(new Site(s.getElement(),candidateSiteLoc));
        }
      }
    }
  }
  return new Cell(newVectors,newBasis,cell.getLabel());
}

Fixed version (ground truth):
public static Cell getSupercell(Cell c,List<List<Integer>> coefficients){
  Cell cell=c.getCellWithAllAtomsInCell();
  if (coefficients.size() != Constants.numDimensions)   throw new IllegalArgumentException("String_Node_Str" + coefficients.size());
  List<Vect> newVectors=new LinkedList<Vect>();
  for (int i=0; i < Constants.numDimensions; i++) {
    List<Integer> coefs=coefficients.get(i);
    if (coefs.size() != Constants.numDimensions)     throw new IllegalArgumentException("String_Node_Str" + coefs.size());
    Double x=coefs.get(0) * (cell.latticeVectors.get(0)).getCartesianComponents().get(0) + coefs.get(1) * (cell.latticeVectors.get(1)).getCartesianComponents().get(0) + coefs.get(2) * (cell.latticeVectors.get(2)).getCartesianComponents().get(0);
    Double y=coefs.get(0) * (cell.latticeVectors.get(0)).getCartesianComponents().get(1) + coefs.get(1) * (cell.latticeVectors.get(1)).getCartesianComponents().get(1) + coefs.get(2) * (cell.latticeVectors.get(2)).getCartesianComponents().get(1);
    Double z=coefs.get(0) * (cell.latticeVectors.get(0)).getCartesianComponents().get(2) + coefs.get(1) * (cell.latticeVectors.get(1)).getCartesianComponents().get(2) + coefs.get(2) * (cell.latticeVectors.get(2)).getCartesianComponents().get(2);
    newVectors.add(new Vect(x,y,z));
  }
  int minx=0, maxx=0, miny=0, maxy=0, minz=0, maxz=0;
  for (int i=0; i <= 1; i++)   for (int j=0; j <= 1; j++)   for (int k=0; k <= 1; k++) {
    int combox=i * coefficients.get(0).get(0) + j * coefficients.get(1).get(0) + k * coefficients.get(2).get(0);
    minx=Math.min(minx,combox);
    maxx=Math.max(maxx,combox);
    int comboy=i * coefficients.get(0).get(1) + j * coefficients.get(1).get(1) + k * coefficients.get(2).get(1);
    miny=Math.min(miny,comboy);
    maxy=Math.max(maxy,comboy);
    int comboz=i * coefficients.get(0).get(2) + j * coefficients.get(1).get(2) + k * coefficients.get(2).get(2);
    minz=Math.min(minz,comboz);
    maxz=Math.max(maxz,comboz);
  }
  List<Site> newBasisCandidates=new LinkedList<Site>();
  for (  Site s : cell.basis) {
    for (int i=minx; i <= maxx; i++) {
      for (int j=miny; j <= maxy; j++) {
        for (int k=minz; k <= maxz; k++) {
          Vect candidateSiteLoc=s.getCoords().plus(new Vect(new Double(i),new Double(j),new Double(k),cell.latticeVectors));
          List<Double> newFracCoords=candidateSiteLoc.getComponentsWRTBasis(newVectors);
          newBasisCandidates.add((new Site(s.getElement(),candidateSiteLoc.getVectShiftedIntoBasis(newVectors))));
        }
      }
    }
  }
  for (int i=0; i < newBasisCandidates.size(); i++) {
    Cell cWithRedundantSites=new Cell(newVectors,newBasisCandidates,cell.getLabel());
    Site s=cWithRedundantSites.getSite(i);
    for (    Site r : cWithRedundantSites.getAtomsInSphereSorted(s.getCoords(),Constants.epsilon)) {
      if (r != s) {
        newBasisCandidates.remove(r);
      }
    }
  }
  return new Cell(newVectors,newBasisCandidates,cell.getLabel());
}