For the ground state of the Gross-Pitaevskii (GP) eigenvalue problem, we consider a fully discretized Sobolev gradient flow, which can be regarded as the Riemannian gradient descent on the sphere under a metric induced by a modified $H^1$-norm. We prove its global convergence to a critical point of the discrete GP energy and its local exponential convergence to the ground state of the discrete GP energy. The local exponential convergence rate depends on the eigengap of the discrete GP energy. When the discretization is the classical second-order finite difference in two dimensions, such an eigengap can be further proven to be mesh independent, i.e., it has a uniform positive lower bound, thus the local exponential convergence rate is mesh independent. Numerical experiments with discretization by high order $Q^k$ spectral element methods in two and three dimensions are provided to validate the efficiency of the proposed method.
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