[gpaw-users] Problem simulating STM images

[Jens Jørgen Mortensen]

Den 25-09-2013 09:01, Jens Jørgen Mortensen skrev:
> 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?

OK, I figured it out.  Matplotlib's contour() function can do it - it 
just needs arrays of x and y coordinates.  Let me fix ASE's STM.scan() 
method so that it delivers that.

Jens Jørgen

>
> 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
>>>
>
>
>
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