By "opening passage," I believe that you are being limited to the first paragraph of Stave Two. It is not a large paragraph, and most of the information presented in it to readers is about how utterly dark of a night it is. The prompt lists atmosphere and effect on the reader as two different things, but atmosphere is another way of saying mood. Mood is focused on the reader because it deals with how the words and setting affect the reader. Tone deals with an author's attitude toward a subject.
Let's look at how this paragraph describes a setting in order to set a mood. Readers are not told that it is midnight until paragraph two, but paragraph one lets us know that it is a very dark night. It is so dark that the window to the outside world is as dark as the non-transparent walls. That's dark because we would at least expect starlight or moonlight of some kind to show through the window to the point that the window is discernible from the wall. This kind of inky blackness is scary. Anybody that has gone on a cave tour when the lights are turned off should understand. Not being able to see the hand in front of your face is eerie if not downright scary. This dark of night setting puts readers on edge. We are nervous because we've been nervous in that kind of darkness before and bad, evil, disturbing, etc. things tend to happen at night.
A key word to "zoom" in on is "ferret." Scrooge is said to have ferret eyes. That does offer a physical description, but it also helps deepen the ominous mood created by the setting. Ferrets are nocturnal. Their eyes are designed to work well at night, yet Scrooge's ferret eyes are not able to "pierce the darkness." That's just one more piece of evidence to let readers know it is really dark.