Can two atoms be a crystal?

Coulomb crystals are the structures formed by ions in a trap when they are sufficiently cold: once they stop jiggling around, they come down to equilibrium positions which need to balance the need to get down to the center of the trap, where the trapping potential is at its minimum, with the mutual repulsion between the ions.

This usually results in an orderly stacking of the ions, often with very clear local symmetries in a bunch of places. Here's one example, formed in an elongated ion trap (with experiment on the left and a simulation on the right; the lines are blurry because the whole thing is rigidly rotating about its vertical axis):

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Within an ion-trapping context, the phrase "two-ion crystal" is a perfectly natural phrase to use for the case where you have coulomb-crystal dynamics, with a trapping potential and a Coulomb repulsion balancing out to give the equilibrium positions, and you have $N=2$ ions in the structure. If the phrase doesn't make sense to you, then that's just an indication that you're not within that text's intended audience.

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Now, is the word "crystal" being used correctly here? The real answer is that it doesn't matter, at all: this is unambiguous notation, and lack of ambiguity is the single requirement that we make of notation.