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In this work we investigate the dynamics of a square mesoscopic superconducting vortex in the presence of a magnetic field parallel to its axis. The rectangular cross section of the sample is L2 and the defex value α is engineered from the d2 region at the center of the superconductor material. L = 12ξ (0) for all simulations, α is engineered with values of 0 and 0.5, while d varies with sizes 2ξ and 4ξ. We study the vortex configuration and its effect on the free energy state. Significant differences from the free energy graph were obtained at t = 0 to t = 70, and again differed at t > 120. From the energy graph comparison, this difference in free energy values was most influenced by the free condensate energy terms.