The writing of Josephson weak links, in an electron microscope, onto films of YBa₂Cu₃O_7-x is an example of the high sensitivity of high-T_c superconductors to structural disorder and oxygen concentration. Radiation damage occurs from electron beams with energy much less than the threshold normally required in compounds for knock-on of oxygen ions. Finite-element methods are used to simulate thermal and charge effects in the superconducting film and substrate. The calculations show that interstitials, under electric and thermal field gradients, drift away from the beam during damage and that diffusion-induced equilibrium is inhibited by the relatively rapid temperature fall after translating the beam.