[gpaw-users] Problem simulating STM images

[Jens Jørgen Mortensen]

Den 24-09-2013 12:31, Susi Toma skrev:
> Hello again,
>
> I have a few further questions.
>
> First of all, my graphene unit cell is not a square, but orthorhombic, 
> and furthermore, it is 8 unit cells in one direction and 6 in the 
> other (made with the attached script). The stm image simulation, 
> however, yields square images, resulting in a significant and 
> non-trivial distortion compared to the actual real-space structure. 
> This makes interpretation of the images rather hard.
>
> Can the stm functionality somehow create non-square images? Or if not, 
> is there a way to automatically overlay the structure on the images?

You could repeat your calculation in a rectangular cell which should be 
possible for your 8*6 cell (since 6 is even).

See also:

http://matplotlib.org/api/axes_api.html#matplotlib.axes.Axes.set_aspect

Alternatively, you will have to teach yourself some matplotlib magic - 
I'm sure there is an elegant way to do it, but I don't know it. Any 
matplotlib masters here?

You could also do the interpolation to a rectangular grid yourself just 
using some ndarray tricks - we should have such an example on the ASE 
web-page.

Jens Jørgen

>
> Many thanks,
> Toma
>
>
> On 5.9.2013, at 15.28, Toma Susi <toma.susi at aalto.fi 
> <mailto:toma.susi at aalto.fi>> wrote:
>
>> Hi,
>>
>> After Jussi kindly updated the gpaw-env module on the CSC Taito 
>> cluster, the simulations now run correctly following Jens' 
>> instructions. I'm now getting reasonable looking STM image 
>> simulations for my system, with no problems with either of the 
>> previous errors regardless of the values I use for z, bias or z0.
>>
>> With any luck we'll have a chance to compare the simulations to 
>> experimental measurements that we are hoping to do soon.
>>
>> Thanks a lot for all your help!
>>
>> Best,
>> Toma
>>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://listserv.fysik.dtu.dk/pipermail/gpaw-users/attachments/20130925/5f88f2fd/attachment.html>