Most often, atmosphere is crafted through word choice and sentence structure. For instance, descriptions can greatly affect the tone of the story, whether it is supposed to be melancholic, scary or suspenseful. In this way, atmosphere can greatly change the subtext of the writing. Depending on how a writer describes a scene, the reader can pick up a large amount of implied meaning, lending deeper development to the narrative. Writers will opt for certain kinds of grammar to craft mood or atmosphere, as well.
For example, if a sentence is written with progressive tense verbs, which can be spotted by having an "ing" as their ending and a longer sentence structure, the writer can create an atmosphere that has a faster pace, lending itself to suspense or action. By contrast, a writer can use short sentences with repeated end punctuation to slow down the pace of the writing, instead. This will also greatly affect the mood.
Atmosphere, also sometimes called ambiance, could also refer to the emotional meaning of a work taken as a whole. This would often apply to what subjects are discussed in the work and the settings where the story's action took place.