[gpaw-users] Problem simulating STM images

[Jens Jørgen Mortensen]

Den 26-09-2013 09:07, Susi Toma skrev:
> On 26.9.2013, at 7.51, Jens Jørgen Mortensen <jensj at fysik.dtu.dk 
> <mailto:jensj at fysik.dtu.dk>>
>  wrote:
>
>> 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
>
> Great, I see you added a possibility to repeat as well, that's very 
> useful.
>
> Is the z0 parameter that was previously discussed now deprecated, or 
> am I missing something...?

No, it's still there.  Isn't it?

Jens Jørgen

>
> -Toma
>
>>
>>>
>>> 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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>>
>
>
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