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Radiolysis ionization under electron beam illumination induces dissociation and damage of organic and biological molecules; thus, it is impossible to image the related materials by transmission electron microscopy (TEM). To understand the atomistic mechanism of radiolysis damage, we developed a systematical procedure based on real-time time-dependent density functional theory (rt-TDDFT) for simulating the radiolysis damage processes of molecules; this procedure can describe the ionization cross sections of the electronic states and the