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Abstract We demonstrate programmable control over the spatial distribution of ultra-cold atoms confined in an optical lattice. The control is facilitated through a combination of spatial manipulation of the magneto-optical trap and atomic population shelving to a metastable state. We first employ the technique to load an extended (5 mm) atomic sample with uniform density in an optical lattice clock (OLC), reducing atomic interactions and realizing remarkable frequency homogeneity across the atomic cloud. We also prepare multiple spatially separated atomic ensembles, and realize multi-ensemble clock operation within the standard one-dimensional (1D) OLC architecture. Leveraging this technique, we prepare two oppositely spin-polarized ensembles that are independently addressable, offering a platform for implementing spectroscopic protocols for enhanced tracking of local oscillator phase. Finally, we demonstrate a relative fractional frequency instability at one second of $2.4\left(1\right)\times {10}^{-17}$between two ensembles, useful for characterization of intra-lattice differential systematics. 

Grating magneto-optical traps are an enabling quantum technology for portable metrological devices with ultracold atoms. However, beam diffraction efficiency and angle are affected by wavelength, creating a single-optic design challenge for laser cooling in two stages at two distinct wavelengths – as commonly used for loading, e.g., Sr or Yb atoms into optical lattice or tweezer clocks. Here, we optically characterize a wide variety of binary gratings at different wavelengths to find a simple empirical fit to experimental grating diffraction efficiency data in terms of dimensionless etch depth and period for various duty cycles. The model avoids complex 3D light-grating surface calculations, yet still yields results accurate to a few percent across a broad range of parameters. Gratings optimized for two (or more) wavelengths can now be designed in an informed manner suitable for a wide class of atomic species enabling advanced quantum technologies.