-alignx
This option aligns the first supercell vector with the cartesian X axis, and aligns the second supercell vector in the XY plane. In other words, it rotates the system so that the base vectors form a lower-triangular matrix H':
H'1 = ( H'(1,1) 0.00000 0.00000 )
H'2 = ( H'(2,1) H'(2,2) 0.00000 )
H'3 = ( H'(3,1) H'(3,2) H'(3,3) )
Of course the atom coordinates are also rotated accordingly.
This option will affect some properties of the system (e.g. the elastic tensor) if they were read with the option -properties before the present option.
Note that this option does not modify the system, it simply rotates it.
By default the supercell vectors are not aligned.
atomsk system.gin -alignx xsf
This will read the file system.gin, align its supercell axes, and output the result into system.xsf.