[gpaw-users] Problem simulating STM images

[Jens Jørgen Mortensen]

Den 25-09-2013 13:16, Jens Jørgen Mortensen skrev:
> 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.

Done.  There is an example for a FCC(111) surface here:

   https://wiki.fysik.dtu.dk/gpaw/tutorials/stm/stm.html

Jens Jørgen

>
> 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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>
>
>
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