The required precision to perform quantum simulations beyond the capabilities of classical computers imposes major experimental and theoretical challenges. Here, we develop a characterization technique to benchmark the implementation precision of a specific quantum simulation task. We infer all parameters of the bosonic Hamiltonian that governs the dynamics of excitations in a two-dimensional grid of nearest-neighbour coupled superconducting qubits. We devise a robust algorithm for identification of Hamiltonian parameters from measured times series of the expectation values of single-mode canonical coordinates. Using super-resolution and denoising methods, we first extract eigenfrequencies of the governing Hamiltonian from the complex time domain measurement; next, we recover the eigenvectors of the Hamiltonian via constrained manifold optimization over the orthogonal group. For five and six coupled qubits, we identify Hamiltonian parameters with sub-MHz precision and construct a spatial implementation error map for a grid of 27 qubits. Our approach enables us to distinguish and quantify the effects of state preparation and measurement errors and show that they are the dominant sources of errors in the implementation. Our results quantify the implementation accuracy of analog dynamics and introduce a diagnostic toolkit for understanding, calibrating, and improving analog quantum processors.
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