We develop a methodology for modeling of heat transfer dynamics of building atriums based on observational data on temperature and air-conditioning system. Following the companion paper [Y. Kono, Y. Susuki, M. Hayashida, and T. Hikihara, Trans. SICE 53-2], we focus on the phenomenon of heat transfer mainly due to the air movement inside a practically-used atrium, where the air slowly moves over the distance between individual rooms. The heat transfer is modeled as a two-dimensional advection equation with a coarse-grained velocity. The velocity is identified based on a spatio-temporal oscillatory pattern extracted from measurement data via Koopman mode decomposition. The identified velocity is verified with the characteristic numbers of fluid flow in the atrium and its architectural geometry.