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Glancing angle deposition (GLAD) is one of the technique for the fabrication of the anisotropic thin films with high porosity and low refractive index. In this technique the incoming flux of the deposited atoms is directed almost parallel to the substrate surface. Due to density fluctuation in the deposited atoms flow and shadow effect, it results in formation of the different separate nanostructures - tree-like column, slanted column, chevron-like structures and so on – on the substrate. GLAD films are widely used in the optical coating due to low reflectance and anisotropy properties. The structural and optical properties of GLAD-films essentially depend on their fabrication conditions. Experimental investigation of these dependencies is still challenge for the existing experimental techniques. On the other hand due to the progress in high performance computing, now it is possible to study thin films deposition process using the atomistic simulation. In the present work the anisotropy of the GLAD SiO2 films is investigated using the classical atomistic simulation and anisotropic Bruggeman effective medium theory. The depolarizing factors defining the difference of the refractive index components are calculated based on the geometry parameters of the pores between the slanted columns forming the large-scale GLAD structure. Averaged shape parameters of these ellipsoids are defined using the density gradient tensor. It is revealed that the values of difference of main components of refractive index tensor are equal 0,03 and 0,05 for deposition angles 60 and 80, if the free volume fraction is calculated using the dependence of film density on the deposition angle. The obtained values coincide with experimental results for silicon dioxide films. Simulation is carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University. The work is supported by the Russian Science Foundation (grant number 19-11-00053).