An implicit variable-step BDF2 scheme is established for solving the space fractional Cahn-Hilliard equation, involving the fractional Laplacian, derived from a gradient flow in the negative order Sobolev space $H^{-\alpha}$, $\alpha\in(0,1)$. The Fourier pseudo-spectral method is applied for the spatial approximation. The proposed scheme inherits the energy dissipation law in the form of the modified discrete energy under the sufficient restriction of the time-step ratios. The convergence of the fully discrete scheme is rigorously provided utilizing the newly proved discrete embedding type convolution inequality dealing with the fractional Laplacian. Besides, the mass conservation and the unique solvability are also theoretically guaranteed. Numerical experiments are carried out to show the accuracy and the energy dissipation both for various interface widths. In particular, the multiple-time-scale evolution of the solution is captured by an adaptive time-stepping strategy in the short-to-long time simulation.
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