[ase-users] Generating slabs for compounds
Glen Jenness
glenjenness at gmail.com
Thu Mar 12 19:25:37 CET 2015
Asif,
1) Be patient! Sending out the same message everyday will not get you a
response faster --- sometimes some of us get busy and it'll take some time
before we can respond. After all, we all have our own research to tend too
:)
2) I assume you want to define a bulk ZnO, then cleave the surface. Your
script does not do that. What you have done is define a ZnO "molecule",
within a small box.
I see that you imported the crystal function, if you wanted to define a
generic crystal, this is the function you want to us (see
https://wiki.fysik.dtu.dk/ase/tutorials/spacegroup/spacegroup.html).
However, note that ASE also has some VERY nice tools for creating specific
crystals as well (see https://wiki.fysik.dtu.dk/ase/ase/lattice.html). So
take a look, and see which one is more appropriate for your problem. For
me, I'm more comfortable with the crystal function, so I'll use that below.
Since you mentioned hexagonal ZnO (i.e. wurzite), this is what it would
look like (provided of course I grabbed the right space group!):
from ase.lattice.spacegroup import crystal
a = 3.35
c = 5.22
ZnO = crystal('ZnO', basis=[(1./3., 2./3., 0.3750), (1./3., 2./3., 0.0)],
cellpar=(a, a, c, 90., 90., 120.), spacegroup=186)
3) For making a surface, I'm not 100% sure how to make an oxide (0001)
surface. Generally, for making surfaces, one does something like:
slab = surface(ZnO, indices=(1, 0, 0), layers=4, vacuum=8.)
And this will make a (100) surface (which I *think* is close to your (0001)
--- but don't take my word! I don't work much with hexagonal unit cells,
so maybe someone else on this list that's more knowledgeable about this can
correct me ;) ).
Now, for oxides in order to get your termination right, you may need to
shift your atoms in the Z direction before passing to your surface
function. Something along the lines of:
cell = ZnO.get_cell()
for atom in ZnO:
atom.position += (0.3 * cell[2])
Where the 0.3 is just the fraction of your unit cell you're moving stuff
by. If you are uncertain as to which termination is correct, calculate the
surface energy for a couple different terminations, and take the lowest.
And yes, this is tedious --- but it works!
Glen
On Thu, Mar 12, 2015 at 6:46 AM, Asif Iqbal <bhatti.asif.iqbal at gmail.com>
wrote:
> Dear Sir/Madam,
>
> I have used ase scripts for generating slabs of different orientations.
> Now,
> I have to create more complex like ZnO(0001) and YBCO (superconductor
> compounds) surface but I cannot do that when I follow the example mentioned
> on the page it does not generate the hexagonal surface or other and there
> is
> no option for size like 2*2*6, the size of the supercell.
>
> The steps I know, first to generate to define the atoms position in the
> unit
> cell then invoke the surface compounds to generate the corresponding slab
> of
> particular plane.
>
> Can you give some example where it has been done before if there is option
> in ase for generating advance surface.
>
> Regards,
> Asif Iqbal BHATTI
>
> -----Original Message-----
> From: ase-users-bounces at listserv.fysik.dtu.dk
> [mailto:ase-users-bounces at listserv.fysik.dtu.dk] On Behalf Of
> ase-users-request at listserv.fysik.dtu.dk
> Sent: Tuesday, June 3, 2014 12:00 PM
> To: ase-users at listserv.fysik.dtu.dk
> Subject: ase-users Digest, Vol 72, Issue 3
>
> Send ase-users mailing list submissions to
> ase-users at listserv.fysik.dtu.dk
>
> To subscribe or unsubscribe via the World Wide Web, visit
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> or, via email, send a message with subject or body 'help' to
> ase-users-request at listserv.fysik.dtu.dk
>
> You can reach the person managing the list at
> ase-users-owner at listserv.fysik.dtu.dk
>
> When replying, please edit your Subject line so it is more specific than
> "Re: Contents of ase-users digest..."
>
>
> Today's Topics:
>
> 1. Re: query for generating surfaces on ASE (Glen Jenness)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 2 Jun 2014 11:13:25 -0400
> From: Glen Jenness <glenjenness at gmail.com>
> To: Asif Iqbal <bhatti.asif.iqbal at gmail.com>
> Cc: ase <ase-users at listserv.fysik.dtu.dk>
> Subject: Re: [ase-users] query for generating surfaces on ASE
> Message-ID:
> <CAHrrQpoHi0uC0xQ8rRECVnpzdxRz6hYs=
> b9xAkAGaBp-4MoWnA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Asif,
> I am not 100% sure, but this sounds like an issue with how some visualizers
> handle and display the PBC's --- some programs like to show atoms from a
> neighboring unit cell (VESTA I know does this). Have you tried visualizing
> in either the ASE-gui or VMD, which doesn't do this?
>
> Can you send a sample script so we have a clearer idea of your problem?
>
> Thanks!
>
> Glen
>
>
> On Mon, Jun 2, 2014 at 4:27 AM, Asif Iqbal <bhatti.asif.iqbal at gmail.com>
> wrote:
>
> > Hello,
> >
> >
> >
> > I would like to know about the surfaces. When I try to generate
> > surface like Pt(111) some of the atoms are outside the unit cell. Why is
> that?
> >
> >
> >
> > Then I have to verify through VESTA or if I am running calculation on
> > VASP then I use p4vasp but p4vasp clearly shows atoms outside the
> > supercell whereas, VESTA doesn?t shows is this a problem if I have to
> > run some calculation on VASP. I?ll be obliged for your response.
> >
> >
> >
> >
> >
> > Is there any option in ASE for rotating the surface layer on top of
> > another surface graphically because I have use only the GUI interface
> > so far.
> >
> >
> >
> > Regards,
> >
> > Asif Iqbal BHATTI
> >
> >
> >
> > _______________________________________________
> > ase-users mailing list
> > ase-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> >
>
>
>
> --
> Dr. Glen Jenness
> Catalysis Center for Energy Innovation (CCEI) University of Delaware
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> <
> http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20140602/e5ac7
> d53/attachment-0001.html>
>
> ------------------------------
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
> End of ase-users Digest, Vol 72, Issue 3
> ****************************************
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
--
Dr. Glen Jenness
Catalysis Center for Energy Innovation (CCEI)
University of Delaware
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20150312/a2263eb9/attachment-0001.html>
More information about the ase-users
mailing list