The capability to model the nonlinear magnetohydrodynamic (MHD) evolution of stellarator plasmas is developed by extending the M3D-$C^1$ code to allow non-axisymmetric domain geometry. We introduce a set of logical coordinates, in which the computational domain is axisymmetric, to utilize the existing finite-element framework of M3D-$C^1$. A $C^1$ coordinate mapping connects the logical domain to the non-axisymmetric physical domain, where we use the M3D-$C^1$ extended MHD models essentially without modifications. We present several numerical verifications on the implementation of this approach, including simulations of the heating, destabilization, and equilibration of stellarator plasmas with strongly anisotropic thermal conductivity, and of the relaxation of stellarator equilibria to integrable and non-integrable magnetic field configurations in realistic geometries.
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