Issue with slab builder

General Discussion
1

Hi,

I am currently using Avogadro 1.1.0 on a Mac and am having problems with building a surface slab. I’ve read the directions,

Import >> Crystal >> ZnO.cif

Crystallography >> Build >> Slab

For my particular problem I would like to build a 2 x 2 surface in the xy plane with a thickness of about 12 Angstroms. The Miller indices for this particular surface is 1-210. I enter these and click on Build. It is at this point that the cartesian coordinates disappear from the text box and the atoms disappear from the display. Have I missed some part of the procedure for constructing this model? I would really like this feature of Avogadro to work since it seems to be so useful.

Any help is much appreciated.

Troy Wymore
UT/ORNL Center for Molecular Biophysics

2

Hi,

I am currently using Avogadro 1.1.0 on a Mac and am having problems with building a surface slab. I’ve read the directions,

Import >> Crystal >> ZnO.cif

Crystallography >> Build >> Slab

For my particular problem I would like to build a 2 x 2 surface in the xy plane with a thickness of about 12 Angstroms. The Miller indices for this particular surface is 1-210. I enter these and click on Build. It is at this point that the cartesian coordinates disappear from the text box and the atoms disappear from the display. Have I missed some part of the procedure for constructing this model? I would really like this feature of Avogadro to work since it seems to so useful.

Any help is much appreciated.

Troy Wymore
UT/ORNL Center for Molecular Biophysics

3

Huh. I can definitely reproduce this, but I don’t have any idea what’s going on.

If I do the same surface for 1-1-1, it works.

I’ll look into it, but it could take a few days.

Thanks,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

On Nov 6, 2015, at 5:02 PM, Wymore, Troy W. wymoretw@ornl.gov wrote:

Hi,

I am currently using Avogadro 1.1.0 on a Mac and am having problems with building a surface slab. I’ve read the directions,

Import >> Crystal >> ZnO.cif

Crystallography >> Build >> Slab

For my particular problem I would like to build a 2 x 2 surface in the xy plane with a thickness of about 12 Angstroms. The Miller indices for this particular surface is 1-210. I enter these and click on Build. It is at this point that the cartesian coordinates disappear from the text box and the atoms disappear from the display. Have I missed some part of the procedure for constructing this model? I would really like this feature of Avogadro to work since it seems to so useful.

Any help is much appreciated.

Troy Wymore
UT/ORNL Center for Molecular Biophysics

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4

Hey, I am having a very similar issue. Has this been resolved?

5

My strong suggestion for creating slabs is to use pymatgen - the link points to a tutorial walking through the process.

I’m not going to port the Avogadro 1.x slab code because it’s to inefficient - pymatgen is definitely better.