Quantum hydrodynamics is a formulation of quantum mechanics based on the probability density and flux (current) density of a quantum system. It can be used to define trajectories which allow for a particle-based interpretation of quantum mechanics, commonly known as Bohmian mechanics. However, quantum hydrodynamics rests on the usual time-dependent formulation of quantum mechanics where time appears as a parameter. This parameter describes the correlation of the state of the quantum system with an external system -- a clock -- which behaves according to classical mechanics. With the Exact Factorization of a quantum system into a marginal and a conditional system, quantum mechanics and hence quantum hydrodynamics can be generalized for quantum clocks. In this article, the theory is developed and it is shown that trajectories for the quantum system can still be defined, and that these trajectories depend conditionally on the trajectory of the clock. Such trajectories are not only interesting from a fundamental point of view, but they can also find practical applications whenever a dynamics relative to an external time parameter is composed of fast and slow degrees of freedom and the interest is in the fast ones, while quantum effects of the slow ones (like a branching of the wavepacket) cannot be neglected. As an illustration, time- and clock-dependent trajectories are calculated for a model system of a non-adiabatic dynamics, where an electron is the quantum system, a nucleus is the quantum clock, and an external time parameter is provided, e.g. via an interaction with a laser field that is not treated explicitly.
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