Recent experiments on ultracold Bose gases in two dimensions have provided evidence for the existence of the Berezinskii-Kosterlitz- Thouless (BKT) phase via analysis of the interference between two independent systems. In this work we study the two-dimensional quantum degenerate Bose gas at finite temperature using the projected Gross-Pitaevskii equation classical field method. Although this describes the highly occupied modes of the gas below a momentum cutoff, we have developed a method to incorporate the higher momentum states in our model. We concentrate on finite-sized homogeneous systems in order to simplify the analysis of the vortex pairing. We determine the dependence of the condensate fraction on temperature and compare this to the calculated superfluid fraction. By measuring the first order correlation function we determine the boundary of the Bose-Einstein condensate and BKT phases, and find it is consistent with the superfluid fraction decreasing to zero. We reveal the characteristic unbinding of vortex pairs above the BKT transition via a coarse-graining procedure. Finally, we model the procedure used in experiments to infer system correlations [Hadzibabic et al., Nature 441, 1118 (2006)], and quantify its level of agreement with directly calculated in situ correlation functions.
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