The zero-energy level in Siesta is defined as the mean value over the unit cell of the delta V_H, defined in Section 4 of the technical paper of Siesta (J. Soler et al., J. Phys.: Condens. Matter 14, 2745 (2002)).
Both the Fermi level and the one particle eigenvalues are referred to this value. To learn more about the zero-energy level in Siesta you can read the Appendix of the paper by J. Junquera et al., Phys. Rev. B 67, 155327 (2003)
