Boundary layer transition over a lifting body of 1.6 m length at $2^\circ$ angle of attack has been simulated at Mach 6 and a unit Reynolds number $1.0 \times 10^7$ m$^{-1}$. The model geometry is the same as the Hypersonic Transition Research Vehicle designed by the China Aerodynamics Research and Development Center. Four distinct transitional regions are identified, i.e. windward vortex region, shoulder vortex region, windward cross-flow region and shoulder cross-flow region. Multi-dimensional linear stability analyses by solving the two-dimensional eigenvalue problem (spatial BiGlobal approach) and the plane-marching parabolized stability equations (PSE3D approach) are further carried out to uncover the dominant instabilities in the last three regions as well as the shoulder attachment-line region. The shoulder vortex is conducive to both inner and outer modes of shear-layer instability, of which the latter most likely trigger the vortex breakdown. A novel method is presented to substantially reduce the computational cost of BiGlobal and PSE3D in resolving the cross-flow instabilities in cross-flow regions. The peak frequencies of cross-flow modes lie between 15 and 45 kHz. Whereas oblique second Mack modes are marginally unstable in the windward cross-flow region, they could be strong enough to compete with the cross-flow modes in the shoulder cross-flow region. In the shoulder attachment-line region, there exists only one unstable mode of Mack instability, differing from previous studies that show a hierarchy of modes in the context of symmetrical attachment-line flows. Results of the numerical simulation and multi-dimensional stability analyses are compared when possible, showing a fair agreement between the two approaches and highlighting the necessity of considering non-parallel effects.
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