the ab initio methods as the siesta package are based on the theory of the functional density (dft); this theory summarily tells us that we can solve the electron density of a material through a potential, because these are based on approximations will have a potential (u) plus a term (xc) called interchange and correlation.
this means that to be able to work it is necessary to know the atomic structure and to have or write those potentials; the results obtained are approximated to the data reported (provided the correct potential was reached) in such a way that these computational methods work in a great way and can be calculated from the network constant to obtain the optical, mechanical, transport properties etc. with a good approximation