Direct numerical simulation (DNS) is performed to investigate the modes of shedding of the wake of a wall-mounted finite-length square cylinder with an aspect ratio (AR) of 7 for six different boundary layer thicknesses (0.0–0.30) at a Reynolds number of 250. For all the cases of wall boundary layer considered in this study, two modes of shedding, namely, anti-symmetric and symmetric modes of shedding, were found to coexist in the cylinder wake with symmetric one occurring intermittently for smaller time duration. The phase-averaged flow field revealed that the symmetric modes of shedding occur only during instances when the near wake experiences the maximum strength of upwash/downwash flow. The boundary layer thickness seems to have a significant effect on the area of dominance of both downwash and upwash flow in instantaneous and time-averaged flow field. It is observed that the near-wake topology and the total drag force acting on the cylinder are significantly affected by the bottom-wall boundary layer thickness. The overall drag coefficient is found to decrease with thickening of the wall boundary layer thickness.

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