We analyze the anomalous wave structure appearing in flow dynamics under the influence of magnetic field in materials described by non-ideal equations of state. We consider the system of magnetohydrodynamics equations closed by a general equation of state (EOS) and propose a complete spectral decomposition of the fluxes that allows us to derive an expression of the nonlinearity factor as the mathematical tool to determine the nature of the wave phenomena. We prove that the possible formation of non-classical wave structure is determined by both the thermodynamic properties of the material and the magnetic field as well as its possible rotation. We demonstrate that phase transitions induced by material properties do not necessarily imply the loss of genuine nonlinearity of the wavefields as is the case in classical hydrodynamics. The analytical expression of the nonlinearity factor allows us to determine the specific amount of magnetic field necessary to prevent formation of complex structure induced by phase transition in the material. We illustrate our analytical approach by considering two non-convex EOS that exhibit phase transitions and anomalous behavior in the evolution. We present numerical experiments validating the analysis performed through a set of one-dimensional Riemann problems. In the examples we show how to determine the appropriate amount of magnetic field in the initial conditions of the Riemann problem to transform a thermodynamic composite wave into a simple nonlinear wave.

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