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Here are my edits so far. I do not want to post a new question yet. According to this post it is a good solution if it is a descriptive comment and helpful for others.

I put my x1-8 variables in a map instead. It results in a cleaner less duplicated code and simplifies the printing as @Caridorc has suggested.

Map

var atomTemplates:Map[String,Atom] = Map(
 "x1" -> new Atom(Up) .fuse(-50 , new Atom(Up)) .fuse(99, new Atom(Up)),
 "x2" -> new Atom(Down) .fuse(-50 , new Atom(Up)) .fuse(99, new Atom(Up)),
 "x3" -> new Atom(Up) .fuse(-50 , new Atom(Down)) .fuse(99, new Atom(Up)),
 "x4" -> new Atom(Up) .fuse(-50 , new Atom(Up)) .fuse(99, new Atom(Down)),
 "x5" -> new Atom(Down) .fuse(-50 , new Atom(Down)) .fuse(99, new Atom(Up)),
 "x6" -> new Atom(Up) .fuse(-50 , new Atom(Down)) .fuse(99, new Atom(Down)),
 "x7" -> new Atom(Down) .fuse(-50 , new Atom(Up)) .fuse(99, new Atom(Down)),
 "x8" -> new Atom(Down) .fuse(-50 , new Atom(Down)) .fuse(99, new Atom(Down))
)

Printing

model.atomTemplates.toList.sortBy(_._1).foreach(entry => {
 println("E(" + entry._1 + ",w) = " + model.calcStableState(entry._2))
})