RRab stars are large amplitude pulsating stars in which the pulsation is associated with strong shock wake propagating in the atmosphere. The objective of this study is to provide a general overview of the dynamical structure of the atmosphere occurring over a typical pulsation cycle. We report new high-resolution observations with high time resolution of H$alpha$ and sodium lines in the brightest RR Lyrae star of the sky: RR Lyr (HD 182989). A detailed analysis of line profile variations over the whole pulsation cycle is performed to understand the dynamical structure of the atmosphere. The main shock wave appears when it exits from the photosphere at $varphisimeq0.89$, i.e., when the main H$alpha$ emission is observed. Whereas the acceleration phase of the shock is not observed, a significant deceleration of the shock front velocity is clearly present. The radiative stage of the shock wave is short: $4%$ of the pulsation period ($0.892<varphi<0.929$). A Mach number $M>10$ is required to get such a radiative shock. The sodium layer reaches its maximum expansion well before that of H$alpha$ ($Deltavarphi=0.135$). Thus, a rarefaction wave is induced between the H$alpha$ and sodium layers. A strong atmospheric compression occurring around $varphi=0.36$, which produces the third H$alpha$ emission, takes place in the highest part of the atmosphere. The region located lower in the atmosphere where the sodium line is formed is not involved. The amplification of gas turbulence seems mainly due to strong shock waves propagating in the atmosphere rather than to the global compression of the atmosphere caused by the pulsation. It has not yet been clearly established whether the microturbulence velocity increases or decreases with height in the atmosphere. Furthermore, it seems very probable that an interstellar component is visible within the sodium profile.
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