Establish the atmosphere of your story by choosing an appropriate point of view, or the perspective from which you, as the author, are telling the story. Two in particular might be helpful: first-person point of view, in which you use the word “I” and are the narrator of the story, and omniscient point of view, which allows you to fully reveal the thoughts and emotions of all the characters in your story.
Be consistent with your tone, which is largely established through word choices. If your descriptions are enthusiastic, they will add energy to the atmosphere; if the descriptions are terse and angry, they will darken the atmosphere. Strive for symmetry between your tone -- the “voice” of the story -- and the atmosphere you seek to create.
Describe the setting of your story in rich detail. Too often, students equate “atmosphere” and “mood” with doom and gloom, and so write a story they do not feel passionately about. In fact, you can create a compelling atmosphere in the kitchen of a typical American home if you describe what's going on there -- externally and also behind the scenes.
Write compelling dialogue, but don't make the common mistake of buttressing attribution with adverbs, as in, “he said thunderously” or “he said rudely.” Nine times out of 10, the word “said” should suffice. It's the words you choose in the dialogue that will help seal the atmosphere of your story.
Allow the reader to experience the atmosphere by showing how it feels, rather than telling how it feels. Every piece of writing contains declarative sentences, but the success of fiction depends on the writer making the reader feel as if she were there in the story, experiencing it for herself.