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Dependence of the crystallographic orientation on annealing process (post- and in-situ annealing) of in the 40-nm-thick single-layered FePt films fabricated by magnetron sputtering onto glass substrates have been investigated. The progress of L10 ordering for both series of samples is nearly the same, verified by X-ray diffraction. For the post-annealing films, there is a dramatic change of crystallographic orientation from (111) to (001) planes with an increase of temperature from 350 °C to 700 °C. On the contrary, the orientation evolves from a (111) texture to isotropic state for the in-situ annealing samples in the same temperature range. The different atomic mobility during annealing leads to a discrepancy in the residual stress behavior and microstructure, which further causes the disparity of crystallographic orientation.