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

[Hermes, Eric]

Jay,

I was able to generate what seems to be a valid crystal structure for Cu(II)O (Tenorite) using data from the American Mineralogist Crystal Structure Database (http://rruff.geo.arizona.edu/AMS/amcsd.php ):

cuo = crystal([‘Cu’, ‘O’], basis=[[0.25, 0.25, 0], [0, 0.4184, 0.25]], spacegroup=15, cellpar=[4.6837, 3.4226, 5.1288, 90, 99.54, 90])

I’m not sure what’s going on with aflowlib’s crystal definition, but I think your issue might have something to do with the strange value they are using for beta.

Eric

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From: <ase-users-bounces at listserv.fysik.dtu.dk> on behalf of Jay Wai via ase-users <ase-users at listserv.fysik.dtu.dk>
Reply-To: Jay Wai <jaywai412 at gmail.com>
Date: Tuesday, May 28, 2019 at 03:42
To: "ase-users at listserv.fysik.dtu.dk" <ase-users at listserv.fysik.dtu.dk>
Subject: [EXTERNAL] [ase-users] question on ase.spacegroup.crystal

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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