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Primary cosmic rays (CR) include in their composition different types of particles (electrons, various nuclei and protons, the percentage of which varies within 85-90 percent). Invading the atmosphere of the Earth, these particles transmit its energy to the substance through a series of successive processes, and if ionization prevails at a conditional height from 80 km to 10-15 km, then the nuclear-active component undergoes inelastic collisions in denser layers. As a result, cascades of secondary CRs are formed. Investigation of the characteristics of these particles (energy spectra, ionization profiles, angular distributions, altitude profiles) is one of the most important tasks of astrophysics of the CR. At the present day, mostly experimental methods are used for this, but with the development of information technologies, numerical models based on the Monte Carlo method are increasingly being used. This approach makes it possible to significantly expand the field of studying CR in the Earth's atmosphere. In this paper, the results of calculating the passage of CR particles of different types through the atmosphere of the Earth, obtained with the program complex RUSCOSMICS, are presented. This software is a development of the PGI team, based on GEANT4 tools and adapted for narrowly focused tasks.