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We study the best attainable measurement precision when a double-well trap with bosons inside acts as an interferometer to measure the energy difference of the atoms on the two sides of the trap. We introduce time independent perturbation theory as the main tool in both analytical arguments and numerical computations. Nonlinearity from atom-atom interactions will not indirectly allow the interferometer to beat the Heisenberg limit, but in many regimes of the operation the Heisenberg limit scaling of measurement precision is preserved in spite of added tunneling of the atoms and atom-atom interactions, often even with the optimal prefactor.

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