[ase-users] rotate atoms to minimize the surrounding cuboid volume

[GENG SUN]

Dear Ask and David,

Thanks so much for your reply.

I used the idea from David's answer, just to find two base vectors (a, b)
to ensure that the diagonal aligns with the maximum distance vector between
atoms.
This can reduce the total volume a little bit, but unfortunately, the
computational cost does not decrease a lot.
So maybe I should find other ways to speed up my calculations.

Best Regards,

Geng


On Sat, Jan 25, 2020 at 4:15 PM David Ollodart <davidollodart at gmail.com>
wrote:

> Dear Geng,
>
> If you know the principal axis, and you want to rotate it to the diagonal,
> it is just a matter of defining the unit vector perpendicular to the two,
> and rotating the principle axis to align with the diagonal. I think the
> optimization problem, to find the orientation of a molecule in a box such
> that the box volume is minimum provided each atom must be at least a
> distance x away from each atom in other images, is not easy, even if you
> consider only a cube. If you guess that the principal axis with greatest
> moment of inertia should be perpendicular with the diagonal it just
> requires calculating the principal axes if you don't know them.
>
> Best,
>
> David
>
> <snippet>
> import numpy as np
> p = np.array((1,0,0))
> d = np.ones(3)/np.sqrt(3)
> v = np.cross(p,d)
> v *= np.arcsin(np.linalg.norm(v))/np.linalg.norm(v) #magnitude = angle in
> radians
> from scipy.spatial.transform import Rotation
> R = Rotation.from_rotvec(v)
>
> from ase import Atoms
> atoms = Atoms('H2', positions=((0,0,0),(0.54,0,0)))
> cell = [(10,0,0),(0,10,0),(0,0,10)]
> atoms.cell = cell
> atoms.center()
> COP = atoms.positions.mean(axis=0)
> atoms.positions = R.apply(atoms.positions - COP) + COP
>
> from ase.visualize import view
> view(atoms)
> </snippet>
>
>
> On Sat, Jan 25, 2020 at 9:00 AM Ask Hjorth Larsen via ase-users <
> ase-users at listserv.fysik.dtu.dk> wrote:
>
>> Dear Geng,
>>
>> Am Sa., 25. Jan. 2020 um 16:41 Uhr schrieb GENG SUN via ase-users
>> <ase-users at listserv.fysik.dtu.dk>:
>> >
>> > Dear ASE users,
>> >
>> > Is there a method in ase to rotate the atoms object to minimize the
>> surrounding vacuum space?
>> > Since the molecule is elongated in one principal axis, I hope I can
>> orient this axis with the diagonal of the box to minimize the total volume.
>> >
>> > Thank you very much in advance.
>>
>> No, but it would be nice to have this if someone is willing to open a
>> merge request.
>>
>> Best regards
>> Ask
>>
>> >
>> > Best,
>> >
>> > Geng
>> > _______________________________________________
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>> > ase-users at listserv.fysik.dtu.dk
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>
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