For ultra-light scalar particles like axions, dark matter can form a state of the Bose-Einstein condensate (BEC) with a coherent classical wave whose wavelength is of order galactic scales. In the context of an oscillating scalar field with mass $m$, this BEC description amounts to integrating out the field oscillations over the Hubble time scale $H^{-1}$ in the regime $m gg H$. We provide a gauge-invariant general relativistic framework for studying cosmological perturbations in the presence of a self-interacting BEC associated with a complex scalar field. In particular, we explicitly show the difference of BECs from perfect fluids by taking into account cold dark matter, baryons, and radiation as a Schutz-Sorkin description of perfect fluids. We also scrutinize the accuracy of commonly used Newtonian treatment based on a quasi-static approximation for perturbations deep inside the Hubble radius. For a scalar field which starts to oscillate after matter-radiation equality, we show that, after the BEC formation, a negative self-coupling hardly leads to a Laplacian instability of the BEC density contrast. This is attributed to the fact that the Laplacian instability does not overwhelm the gravitational instability for self-interactions within the validity of the nonrelativistic BEC description. Our analysis does not accommodate the regime of parametric resonance which can potentially occur for a large field alignment during the transient epoch prior to the BEC formation.
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