-unskew
This option "unskews" the box. Consider the following supercell vectors:
| H(1,1) H(1,2) H(1,3) |
| H(2,1) H(2,2) H(2,3) |
| H(3,1) H(3,2) H(3,3) |
If a non-diagonal element is larger than its main component (i.e. |H(i,j)|>0.5*H(j,j) for i≠j) then the box is considered "skewed". This option reduces the skew (i.e. add or subtract H(j,j) to it) until it is not the case.
Note that the (Cartesian) coordinates of atoms are not affected by this option, so some atoms may be outside of the box after this option is applied, which can be fixed with the option -wrap.
By default the supercell vectors are not unskewed.
atomsk system.xsf -unskew lmp
This will read the file system.xsf, reduce the skew, and write the final result to the LAMMPS data file system.lmp.