We present a comprehensive derivation of linear perturbation equations for different matter species, including photons, baryons, cold dark matter, scalar fields, massless and massive neutrinos, in the presence of a generic conformal coupling. Starting from the Lagrangians, we show how the conformal transformation affects the dynamics. In particular, we discuss how to incorporate consistently the scalar coupling in the equations of the Boltzmann hierarchy for massive neutrinos and the subsequent fluid approximations. We use the recently proposed K-mouflage model as an example to demonstrate the numerical implementation of our linear perturbation equations. K-mouflage is a new mechanism to suppress the fifth force between matter particles induced by the scalar coupling, but in the linear regime the fifth force is unsuppressed and can change the clustering of different matter species in different ways. We show how the CMB, lensing potential and matter power spectra are affected by the fifth force, and find ranges of K-mouflage parameters whose effects could be seen observationally. We also find that the scalar coupling can have the nontrivial effect of shifting the amplitude of the power spectra of the lensing potential and density fluctuations in opposite directions, although both probe the overall clustering of matter. This paper can serve as a reference for those who work on generic coupled scalar field cosmology, or those who are interested in the cosmological behaviour of the K-mouflage model.
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