Quantum engineering using photonic structures offer new capabilities for atom-photon interactions for quantum optics and atomic physics, which could eventually lead to integrated quantum devices. Despite the rapid progress in the variety of structures, coherent excitation of the motional states of atoms in a photonic waveguide using guided modes has yet to be demonstrated. Here, we use the waveguide mode of a hollow-core photonic crystal fibre to manipulate the mechanical Fock states of single atoms in a harmonic potential inside the fibre. We create a large array of Schrodinger cat states, a quintessential feature of quantum physics and a key element in quantum information processing and metrology, of approximately 15000 atoms along the fibre by entangling the electronic state with the coherent harmonic oscillator state of each individual atom. Our results provide a useful step for quantum information and simulation with a wide range of photonic waveguide systems.
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