Rapid development of X-ray free-electron laser (XFEL) science has taken place in recent years owing to the consecutive launch of large-scale XFEL instruments around the world. Research areas such as warm dense matter physics and coherent X-ray imaging take advantage of the unprecedentedly high intensities of XFELs. A single XFEL pulse can induce very complex dynamics within matter initiated by core-hole photoionization. Owing to this complexity, theoretical modeling revealing details of the excitation and relaxation of irradiated matter is important for the correct interpretation of the measurements and for proposing new experiments. XMDYN is a computer simulation tool developed for modeling dynamics of matter induced by high-intensity X-rays. It utilizes atomic data calculated by the ab initio XATOM toolkit. Here these tools are discussed in detail.