You don't need to know anything about atoms to be able to use and enjoy AtomBox. The user guide (included in the download) explains how everything works and it also teaches you the basics about atoms.
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Gave it a try and it seems pretty good.
I think it would make a really great teaching aid for people interested in learning about atoms. The UI is nice and simple which I appreciate.
I had a little look through the PDF it was quite helpful but a little overwhelming at first.
Overall I think it's a pretty neat project and I think you've done a great job man!