We propose and analyze an extended Fourier pseudospectral (eFP) method for the spatial discretization of the Gross-Pitaevskii equation (GPE) with low regularity potential by treating the potential in an extended window for its discrete Fourier transform. The proposed eFP method maintains optimal convergence rates with respect to the regularity of the exact solution even if the potential is of low regularity and enjoys similar computational cost as the standard Fourier pseudospectral method, and thus it is both efficient and accurate. Furthermore, similar to the Fourier spectral/pseudospectral methods, the eFP method can be easily coupled with different popular temporal integrators including finite difference methods, time-splitting methods and exponential-type integrators. Numerical results are presented to validate our optimal error estimates and to demonstrate that they are sharp as well as to show its efficiency in practical computations.

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