Program: 37767
Project: 37767
Buggy source:
/** 
 * Rotates the cell into the principle directions and then removes vertical padding  from the cell without changing the relative positions of the atoms. The magnitude  of the vertical cell vector of the unpadded cell is equal to the vertical distance  between highest and lowest atoms in the cell plus the minimum interatomic distance  (mid). The atoms are arranged in the unpadded cell such that highest atom is mid/2  from the top of cell, and the lowest atom is mid/2 from the bottom of the cell.   
 */
private void unpadOrg(){
  Cell oldCell=org.getCell();
  if (oldCell == null)   return;
  oldCell=oldCell.getCellRotatedIntoPrincDirs();
  double mid;
  if (GAParameters.getParams().getMinInteratomicDistance() == -1) {
    mid=maxMID();
  }
 else {
    mid=GAParameters.getParams().getMinInteratomicDistance();
  }
  double minz=Double.MAX_VALUE;
  double maxz=Double.MIN_VALUE;
  for (  Site s : oldCell.getSites()) {
    List<Double> cartComps=s.getCoords().getCartesianComponents();
    minz=Math.min(minz,cartComps.get(2));
    maxz=Math.max(maxz,cartComps.get(2));
  }
  double zlen=maxz - minz;
  List<Site> newSites=new ArrayList<Site>();
  Vect minv=new Vect(0.0,0.0,minz - mid / 2);
  for (  Site s : oldCell.getSites())   newSites.add(new Site(s.getElement(),s.getCoords().subtract(minv)));
  List<Vect> newBasis=new ArrayList<Vect>();
  newBasis.add(oldCell.getLatticeVectors().get(0));
  newBasis.add(oldCell.getLatticeVectors().get(1));
  newBasis.add(new Vect(0.0,0.0,zlen + mid));
  Cell newCell=new Cell(newBasis,newSites,oldCell.getLabel());
  org.setCell(newCell,false);
}

Fixed version (ground truth):
/** 
 * Rotates the cell into the principle directions and then removes vertical padding  from the cell without changing the relative positions of the atoms. The magnitude  of the vertical cell vector of the unpadded cell is equal to the vertical distance  between highest and lowest atoms in the cell plus the minimum interatomic distance  (mid). The atoms are arranged in the unpadded cell such that the highest atom is  mid/2 from the top of cell, and the lowest atom is mid/2 from the bottom of the cell.   
 */
private void unpadOrg(){
  Cell oldCell=org.getCell();
  if (oldCell == null)   return;
  oldCell=oldCell.getCellRotatedIntoPrincDirs();
  double mid;
  if (GAParameters.getParams().getMinInteratomicDistance() == -1) {
    mid=maxMID();
  }
 else {
    mid=GAParameters.getParams().getMinInteratomicDistance();
  }
  double minz=Double.MAX_VALUE;
  double maxz=Double.MIN_VALUE;
  for (  Site s : oldCell.getSites()) {
    List<Double> cartComps=s.getCoords().getCartesianComponents();
    minz=Math.min(minz,cartComps.get(2));
    maxz=Math.max(maxz,cartComps.get(2));
  }
  double zlen=maxz - minz;
  List<Site> newSites=new ArrayList<Site>();
  Vect minv=new Vect(0.0,0.0,minz - mid / 2);
  for (  Site s : oldCell.getSites())   newSites.add(new Site(s.getElement(),s.getCoords().subtract(minv)));
  List<Vect> newBasis=new ArrayList<Vect>();
  newBasis.add(oldCell.getLatticeVectors().get(0));
  newBasis.add(oldCell.getLatticeVectors().get(1));
  newBasis.add(new Vect(0.0,0.0,zlen + mid));
  Cell newCell=new Cell(newBasis,newSites,oldCell.getLabel());
  org.setCell(newCell,false);
}