[ase-users] wrap without breaking molecules

[Jens Jørgen Mortensen]

On 11/28/2018 10:21 AM, Jonatan Öström via ase-users wrote:
>
> Hi, can I wrap water molecules into the box without breaking them?
>

If your molecules are ordered OHHOHHOHH...:

p1 = water.get_positions()
water.wrap()
p2 = water.positions
p2[1::3] = p2[0::3] + p1[1::3] - p1[0::3]
p2[2::3] = p2[0::3] + p1[2::3] - p1[0::3]

Jens Jørgen


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