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Is there any way to fix the separations between two atoms constant during calculation but can move freely in space ?



<span class='smallblacktext'>[ Edited ]</span>

To my knowledge this is not possible.

Actually, it's possible, but only if you're willing to add some programming to the geometry updating algorithm. This feature -- geometry optimization with arbitrary linear constraints on the positional degrees of freedom -- was implemented in abinit a few years ago. For details see http://www.abinit.org/Infos_v4.5/varrlx.html#wtatcon