[ase-users] question on ase.spacegroup.crystal

[Jay Wai]

Hello users,

I am learning for myself how to create atoms objects using the crystal
function.
I succeeded in creating various objects but failed to create a correct
object for CuO.
My code begins with setting up the cell parameters taken from
http://aflowlib.org/CrystalDatabase/AB_mC8_15_c_e.html

from ase.spacegroup import crystal
from math import sin, cos, radians
a_cuo = 4.684
b_cuo=3.423
c_cuo=5.129
al_cuo = 90.000
be_cuo = 99.54 (this was set 120.xx in the website, which seems to be
incorrect)
ga_cuo = 90.000
y2 = 0.4184

The followings are my calls for the crystal function:
(1) Basis vectors in terms of primitive vectors
cuo = crystal(['Cu', 'O'], basis=[(0.0,0.5,0.0), (-y2,y2,0.25)],
spacegroup=15, cellpar=[a_cuo,
b_cuo, c_cuo, al_cuo, be_cuo, ga_cuo])

(2) Basis vectors in terms of cartesian unit vectors

coeff_y = 0.4184
coeff_x = 0.25*c_cuo/a_cuo*cos(radians(be_cuo))
coeff_z = 0.25*sin(radians(be_cuo))
cuo = crystal(['Cu', 'O'], basis=[(0.25,0.25,0.0), (coeff_x,y2,coeff_z)],
spacegroup=15, cellpar=[a_cuo, b_cuo, c_cuo, al_cuo, be_cuo, ga_cuo])

Neither (1) and (2) produces a correct crystal. For example, in (2), excess
oxygen atoms are produced.

I guess my setting of basis vectors in the crystal call might be incorrect.

Could anybody help me with this?


By the way, I looked through examples in the ase website and found that
some examples express basis vectors in terms of primitive vectors (e.g. Mg)
and other express basis vectors in terms of cartesian unit vectors (e.g
skutterudite).

How should I express basis vectors when calling the crystal function?

Thank you and regards,

Jay
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