[QE-users] Creating a 2 × 2 × 3 Surface of Crystal Structure with 10 Å Vacuum in Burai or XCrysDen

[Giovanni Cantele]

Dear Moses,

there is not actually a universal recipe and the means used depends on your
feeling. I'm not an expert about Burai. As far as XCrysDen is concerned, I
use it a lot to visualize the structure, not to build it.

Personally, I've always found it instructive try, to the best of what I can
do, to build structures "by hand", because this is in my opinion the best
way to "enter a crystal" and know how it is done!

Few general hints, whatever tool you use:
1) first identify the direction of the surface, e.g. 100, 110, 111, ...
2) identify the "in-plane" lattice vectors. This can coincide with those of
the bulk lattice or not. For example, should you want to build the 001
surface of a simple cubic crystal, the 1x1 surface will have a1 = (a,0,0)
and a2 = (0,a,0) as surface in-plane vectors
3) as a corollary of point two there are cases where complex
reconstructions (e.g. 2x2, sqrt(3) x sqrt(3), ....) might occur. In these
cases, there are the "simplest" systems where you should just take the
in-plane vectors of the 1x1 surface unit cell and double, triple, ....
them. The trickiest cases are instead when the in-plane vectors of the
reconstructed surface ar not only scaled but also rotated with respect to
the starting ones.
4) build, according to the chosen a1 and a2, slab models consisting of n
planes, obtained as a periodic repetition of the first plane along the 3d
direction.
5) take the resulting thickness in the correct units, and add the vacuum in
the same units, this will be the length of the 3d vector.

Be careful: sometimes one has coordinates in Ang, other times in 2 pi / a
units, other times in crystal units. It is important that one makes the new
coordinates consistent with the units used for the surface.

Imagine, for example, that you have a simple cubic system with one atom in
the unit cell at (0,0,0) and lattice constant a. A 4-slab model will have a
unit cell with atoms at
(0,0,0)
(0,0,a)
(0,0,2a)
(0,0,3a)
The in-plane lattice vectors will be (a,0,0) and (0,a,0). The lattice
vector orthogonal to the surface will be (0,0,c) where c = 3a + vacuum
space.

Always visualize your new structure before running any calculation!

More specific help could be provided for specific structures.
Giovanni

-- 

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cantele at spin.cnr.it <giovanni.cantele at spin.cnr.it>
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: https://sites.google.com/view/giovanni-cantele/home


Il giorno lun 8 apr 2024 alle ore 17:26 MOSES NTSIFUL <
moses.ntsiful001 at stu.ucc.edu.gh> ha scritto:

> Dear All,
>
> I hope this email finds you well. I am writing to request your assistance
> with a specific task related to crystal structure visualization and
> manipulation. I am currently working on a project that requires the
> creation of a 2 × 2 × 3 surface of a crystal structure with a 10 Å vacuum
> using either Burai or XCrysDen. Despite my efforts, I have not been able to
> successfully complete this task.
>
> I was wondering if I could be provided with some guidance on how to
> proceed. Specifically, I would appreciate any insights you might have on:
>
>    1.
>
>    How to create a 2 × 2 × 3 surface of a crystal structure in Burai or
>    XCrysDen.
>    2.
>
>    How to ensure that the resulting surface has a 10 Å vacuum.
>
> Thank you in advance for the assistance. I look forward to hearing from
> you soon.
>
>
>
> Best regards,
>
> Moses Ntsiful
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