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The atomistic modeling method of the ion beam sputtering (IBS) process, oriented at supercomputers calculations is presented. Corresponding algorithm is organized as a sequence of identical molecular dynamic steps. On each step several groups of the deposited atoms are injected into the modeling box and interact with the substrate and film forming new chemical bonds. The method was implemented for the simulation of the SIO2 thin films growth. For the calculation of the interatomic potential energy the original force filed DESIL has been elaborated. It provides high computational efficiency and is capable of describing all major structural properties of bulk fused silica dioxide and silica dioxide thin films. Our model includes substrate modeling, modeling of the source of deposited atoms, a special way for taking into account chemical reactions in the deposition chamber, temperature variations, angular and energy distributions of deposited atoms, various types of boundary conditions and various statistical ensembles accounting for environment of modeling volume. The deposition process is organized as a sequence of molecular dynamic cycles when deposited atoms interact with the substrate and earlier deposited layers and form new Si-O chemical bonds. The atomic flow density is chosen so that subsequent interactions of deposited high-energy atoms with film surface could be considered as independent events. The elaborated method has been implemented in the frame of KUVALDA code; simulations were performed on the Lomonosov supercomputer of Moscow State University. For MD modeling KUVALDA exploits one of the most effective standard MD software packages GROMACS. Atomistic modeling of thin film deposition processes was performed for the film thickness up to 40 nm (number of the atoms one millions). The dependence of thin film density on film thickness has been investigated. It was shown that film density exceeds the density of fused silica substrate for 0.1-0.2 g/cm^3. Thickness of interface layer between thin film and substrate is about 1-2 nm. The dependence of film density on film thickness has been investigated and it has been shown that density variations of about 0.1-0.2 g/cm^3 are still possible in rather deep film layers that are located at distances of 10 nm beyond the film surface. Two approaches for calculating optical parameters of thin films have been investigated. The first one is based on quantum-mechanics considerations while the second one utilizes the macroscopic electrodynamic considerations that establish relations between optical parameters of thin film and thin film density. It has been found that the with the current state-of-art in quantum-mechanics calculations the second approach allows to obtain results that are in better agreement with the existing experimental data. Based on the obtained results for thin film density dynamics, the dynamics of thin film optical properties has been studied.