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This paper presents a new approach for applying non-periodic boundary conditions in the context of FFT-based methods to solve micromechanical problems in heterogeneous solids. The domain of the original problem is extended to satisfy the periodicity requirements at the boundary of the extended domain. The velocity constraint on the boundary of the original domain is replaced by a corresponding constraint on the velocity gradient in the extended volume, and a two-level augmented Lagrangian method is used to enforce the constraint. The proposed method is implemented as an extension of the large-strain elasto-viscoplastic FFT-based (LS-EVPFFT) model of Zecevic et al. (2022). The proposed method is verified in the cases of fully imposed velocity boundary conditions and mixed velocity/traction-free boundary conditions. The accuracy and convergence of the method are studied next, followed by applications to bending and indentation of polycrystals that illustrate the extended capabilities of the proposed formulation.