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Using a self-consistent atmosphere code, we construct a new model of theatmosphere of the transiting extrasolar giant planet HD 209458b to investigatethe disparity between the observed strength of the sodium absorption feature at589 nm and the predictions of previous models. For the atmospherictemperature-pressure profile we derive, silicate and iron clouds reside at apressure of several mbar in the planet's atmosphere. These clouds havesignificant vertical extent and optical depth due to our slant viewing geometryand lead to increased absorption in bands directly adjacent to the sodium linecore. Using a non-LTE sodium ionization model that includes photoionization bystellar UV flux, collisional processes with H_2, and radiative recombination,we show that the ionization depth in the planet's atmosphere reaches ~1/2 mbarat the day/night terminator. Ionization leads to a slight weakening of thesodium feature. We present our baseline model, including ionization and clouds,which falls near the observational error bars. The sensitivity of ourconclusions to the derived atmospheric temperature-pressure profile isdiscussed.Comment: 15 pages, 9 figures -- Accepted to The Astrophysical Journal -- The  paper is significantly revised and expande

On the Indirect Detection of Sodium in the Atmosphere of the Planetary Companion to HD 209458