We present a novel approach to generate higher-order initial conditions (ICs) for cosmological simulations that take into account the distinct evolution of baryons and dark matter. We focus on the numerical implementation and the validation of its performance, based on both collisionless N-body simulations and full hydrodynamic Eulerian and Lagrangian simulations. We improve in various ways over previous approaches that were limited to first-order Lagrangian perturbation theory (LPT). Specifically, we (1) generalize nth-order LPT to multi-fluid systems, allowing 2LPT or 3LPT ICs for two-fluid simulations, (2) employ a novel propagator perturbation theory to set up ICs for Eulerian codes that are fully consistent with 1LPT or 2LPT, (3) demonstrate that our ICs resolve previous problems of two-fluid simulations by using variations in particle masses that eliminate spurious deviations from expected perturbative results, (4) show that the improvements achieved by going to higher-order PT are comparable to those seen for single-fluid ICs, and (5) demonstrate the excellent (i.e., few per cent level) agreement between Eulerian and Lagrangian simulations, once high-quality initial conditions are used. The rigorous development of the underlying perturbation theory is presented in a companion paper. All presented algorithms are implemented in the Monofonic Music-2 package that we make publicly available.
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