It has to do with the crystalline structure of the thing thats magnetic. As some eluded to, individual atoms have electrons that orbit the nucleus in a certain direction or spin. If, when all joined together in their crystalline structure. The perimeter of the molecular configuration has all electrons traveling in the same direction, then the thing is magnetic. It just happens that it occurs in some alloys and metals but it can happen in other things too, specifically things that are doped to force magnetic configuration.
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