[ase-users] adding tags to bulk crystals (Lars Grabow)

[John Kitchin]

I think the tags must be integers. here is a way to do something close to
what you suggest using integers:

http://gilgamesh.cheme.cmu.edu/doc/software/jacapo/3-surfaces/3.1-making-slabs/3.1.0-making-slabs.html?highlight=tagging#advanced-tagging

I think you want to set the tags after you make the bulk structure.
maybe you can do:

O = 2
T1 = 4
T2 = 8
...
mfi.set_tags([O*26,+[T1, T2,...])



John

-----------------------------------
John Kitchin
Associate Professor
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu


Message: 2
> Date: Mon, 19 Sep 2011 17:23:46 -0500
> From: Lars Grabow <grabow at uh.edu>
> Subject: [ase-users] adding tags to bulk crystals
> To: ase-users at listserv.fysik.dtu.dk
> Message-ID: <E494E887-E8D4-4B5E-B58D-C6E5F345FDE9 at uh.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> for personal convenience when working with ZSM-5 structures, I would like
> to tag all the T-sites (positions of Si/Al sites), with T1, T2, etc. There's
> a total of 12 crystallographically different T-sites and I'm building ZSM 5
> with the following script which gives me a total of 96 T sites (multiplicity
> of 8). What's the best way to tag these sites? Ideally, I'd like to include
> another keyword in the 'crystal' module to which I'd supply a list of tags.
> Like crystal(['O']*26+['Si']*12, tags = ['0']*26+['T1','T2','T3',...],
> basis=[...]
>
> Otherwise, can I assume that the list of atoms is repeated in the same
> order and do the tagging afterwards? Is there a better way?
>
> Thanks a lot!
> Lars
>
> from ase import *
> from ase.lattice.spacegroup import crystal
>
> x = [20.09, 19.738, 13.142]
> a = x[0]
> b = x[1]
> c = x[2]
>
> mfi=crystal(['O']*26+['Si']*12, basis=[
>             (0.5012, 0.0699, 0.7018),
>             (0.3875, 0.0743, 0.8008),
>             (0.3995, 0.1366, 0.6251),
>             (0.3972, 0.0034, 0.6326),
>             (0.329, 0.0385, 0.9722),
>             (0.3297, 0.9555, 0.8155),
>             (0.2571, 0.0663, 0.8106),
>             (0.291, 0.1296, 0.106),
>             (0.2034, 0.0455, 0.0275),
>             (0.2936, 0.001, 0.1564),
>             (0.1075, 0.1265, 0.0883),
>             (0.0846, 0.037, 0.9443),
>             (0.1301, 0.0781, 0.767),
>             (0.0728, 0.9589, 0.7832),
>             (0.2201, 0.1313, 0.6456),
>             (0.4911, 0.8548, 0.7169),
>             (0.3681, 0.8311, 0.7743),
>             (0.4263, 0.75, 0.6431),
>             (0.3217, 0.8611, 0.9561),
>             (0.241, 0.8582, 0.799),
>             (0.2943, 0.75, 0.0579),
>             (0.1976, 0.8313, 0.0003),
>             (0.0948, 0.75, 0.0205),
>             (0.0809, 0.867, 0.9275),
>             (0.1177, 0.837, 0.7406),
>             (0.2116, 0.75, 0.6913),
>             (0.4214, 0.0711, 0.6898),
>             (0.3259, 0.0336, 0.85),
>             (0.2792, 0.0536, 0.0655),
>             (0.1246, 0.0514, 0.0481),
>             (0.0721, 0.036, 0.8233),
>             (0.2034, 0.0687, 0.7197),
>             (0.4195, 0.8274, 0.6805),
>             (0.3152, 0.8765, 0.8361),
>             (0.2733, 0.8278, 0.0402),
>             (0.1185, 0.8279, 0.0183),
>             (0.0657, 0.8794, 0.8087),
>             (0.1947, 0.8288, 0.7092)],
>             spacegroup=62, cellpar=[a, b, c, 90, 90,
> 90],primitive_cell=False)
>
> view(mfi)
>
>
>
>
>
> -------------------------------------------------------------------------------------------------------------
> Lars C. Grabow
> Assistant Professor of Chemical and Biomolecular Engineering
> University of Houston
> S341 Engineering Building 1
> Houston, TX 77204-4004
> email: grabow at uh.edu                    web:
> http://www.chee.uh.edu/faculty/grabow
> phone: (+1) 713-743-9899         fax: (+1) 713-743-4323
>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/ase-users/attachments/20110920/a1ce81c4/attachment.html>