We present an inelastic neutron scattering study of phonon lineshapes in the vortex state of the type-II superconductor YNi$_2$B$_2$C. In a previous study [Phys. Rev. Lett. textbf{101}, 237002 (2008)] it was shown that certain phonons exhibit a clear signature of the superconducting gap $2Delta$ on entering the superconducting state. Our interest was to find out whether or not the lineshape of such phonons reflects the inhomogeneous nature of the vortex state induced by a magnetic field smaller than the upper critical field $B_{c2}$ .We found that this is indeed the case because the observed phonon lineshapes can be well described by a model considering the phonon as a local probe of the spatial variation of the superconducting gap. We found that even at $B=3,rm{T}$, where the inter-vortex distance is less than $300,$AA, the phonon lineshape still shows evidence for a variation of the gap.
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