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