We derive the basic formalism of density functional theory for time-dependent electron-nuclear systems. The basic variables of this theory are the electron density in body-fixed frame coordinates and the diagonal of the nuclear N-body density matrix. The body-fixed frame transformation is carried out in order to achieve an electron density that reflects the internal symmetry of the system. We discuss the implications of this bodyfixed frame transformation and establish a Runge-Gross-type theorem and derive Kohn-Sham equations for the electrons and nuclei. We illustrate the formalism by performing calculations on a one-dimensional diatomic molecule for which the many-body Schrödinger equation can be solved numerically. These benchmark results are then compared to the solution of the time-dependent Kohn-Sham equations in the Hartree approximation. Furthermore, we analyze the excitation energies obtained from the linear response formalism in the single pole approximation. We find that there is a clear need for improved functionals that go beyond the simple Hartree approximation.

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