In this example, Einojuhani Rautavaara sometimes uses flat and sometimes uses sharp in some chords.
Once it's atonal music, what're the rules for sharps and flats?
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Fair question. Think about these things:
1.) Context (lots of sharps / flats already? Which would simplify the music?)
2.) The direction (sharps = up / flats = down)
3.) The instrument (strings more comfortable reading sharps / winds more comfortable with flats)
4.) Writing intervals the way they sound (does that really need to be "C-D#" or would "C-Eb" make more sense?)
5.) Voice-leading (this is part of "context" from above - what makes the most sense voice-leading wise? Atonality and functional harmony can coexist; just because your chords have functional voice-leading does not mean that they can't exist within an atonal framework.)
Make the decisions that make the most sense. The more you can simplify the music, the better.