The paper discusses a numerical model to facilitate more accurate analysis of electro-hydro-dynamic processes at the level of atoms and NANO-EMS structures. In the relevant procedures, a hydrogen atom is used to test the properties of the given model based on a toroidal element Exploiting previous examinations of graphene structures [1] and utilizing traditional modeling techniques, the authors employ diverse analyses of relevant limiting parameters to propose a structural analysis that could allow the evaluation of the numerical models of the hydrogen atom examined. A simple example is used to demonstrate the properties of the given approach to the current multiscale modeling of structures of matter.