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A framework based on physical optics for simulating the effect of imperfect compound refractive lenses (CRLs) upon an X-ray beam is described, taking into account measured phase errors obtained from at-wavelength metrology. A CRL stack is modelled, with increasing complexity, as a single thin phase element, then as a more realistic compound element including absorption and thickness effects, and finally adding realistic optical imperfections to the CRL. Coherent and partially coherent simulations using Synchrotron Radiation Workshop (SRW)