A Stellar Atmosphere is the gas/plasma around the star. The border between the Atmosphere and the rest of the star is taken to be the lowest region where the light emitted by the star is produced, which by definition is the lower edge of the Photosphere. The rest of the atmosphere above it are the Chromosphere, the Corona (region of Plasma surrounding a star that emits Electromagnetic Radiation (EMR)), and the Transition Region between the chromosphere and the corona.
Stellar Model Atmosphere
Zeeman-Doppler Imaging (ZDI)