We study the fidelity of single qubit quantum gates performed with two-frequency laser fields that have a Gaussian or super Gaussian spatial mode. Numerical simulations are used to account for imperfections arising from atomic motion in an optical trap, spatially varying Stark shifts of the trapping and control beams, and transverse and axial misalignment of the control beams. Numerical results that account for the three dimensional distribution of control light show that a super Gaussian mode with intensity $I\sim e^{-2(r/w_0)^n}$ provides reduced sensitivity to atomic motion and beam misalignment. Choosing a super Gaussian with $n=6$ the decay time of finite temperature Rabi oscillations can be increased by a factor of 60 compared to an $n=2$ Gaussian beam, while reducing crosstalk to neighboring qubit sites.
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