We describe the Stagger code for simulations of magnetohydrodynamic (MHD) systems. This is a modular code with a variety of physics modules that will let the user run simulations of deep stellar atmospheres, sunspot formation, stellar chromospheres and coronae, proto-stellar disks, star formation from giant molecular clouds, and even galaxy formation. The Stagger code is efficiently and highly parallelizable, enabling such simulations with large ranges of both spatial and temporal scales. We describe the methodology of the code and present the most important of the physics modules, as well as its input and output variables. We show results of a number of standard MHD tests to enable comparison with other, similar codes. In addition, we provide an overview of tests that have been carried out against solar observations, ranging from spectral line shapes, spectral flux distribution, limb darkening, intensity and velocity distributions of granulation, to seismic power spectra and the excitation of p-modes. The Stagger code has proven to be a high-fidelity code with a large range of uses.
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