[gpaw-users] NEGF-STM

[Lars Smykalla]

Hi all,

I really can't get the stm module to work, not even the tutorial with H on  
a Al slab. I hope someone can help me because I have no idea what to try  
further.

When I do stm.scan() and stm.plot(), I get this UnicodeDecodeError:

Exception in Tkinter callback
Traceback (most recent call last):
   File "/usr/lib/python2.7/lib-tk/Tkinter.py", line 1413, in __call__
     return self.func(*args)
   File  
"/usr/lib/pymodules/python2.7/matplotlib/backends/backend_tkagg.py", line  
245, in resize
     self.show()
   File  
"/usr/lib/pymodules/python2.7/matplotlib/backends/backend_tkagg.py", line  
248, in draw
     FigureCanvasAgg.draw(self)
   File "/usr/lib/pymodules/python2.7/matplotlib/backends/backend_agg.py",  
line 394, in draw
     self.figure.draw(self.renderer)
   File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in  
draw_wrapper
     draw(artist, renderer, *args, **kwargs)
   File "/usr/lib/pymodules/python2.7/matplotlib/figure.py", line 798, in  
draw
     func(*args)
   File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in  
draw_wrapper
     draw(artist, renderer, *args, **kwargs)
   File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 1946, in  
draw
     a.draw(renderer)
   File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in  
draw_wrapper
     draw(artist, renderer, *args, **kwargs)
   File "/usr/lib/pymodules/python2.7/matplotlib/axis.py", line 1032, in  
draw
     self.label.draw(renderer)
   File "/usr/lib/pymodules/python2.7/matplotlib/artist.py", line 55, in  
draw_wrapper
     draw(artist, renderer, *args, **kwargs)
   File "/usr/lib/pymodules/python2.7/matplotlib/text.py", line 526, in draw
     bbox, info = self._get_layout(renderer)
   File "/usr/lib/pymodules/python2.7/matplotlib/text.py", line 305, in  
_get_layout
     clean_line, ismath = self.is_math_text(line)
   File "/usr/lib/pymodules/python2.7/matplotlib/text.py", line 989, in  
is_math_text
     if cbook.is_math_text(s):
   File "/usr/lib/pymodules/python2.7/matplotlib/cbook.py", line 1793, in  
is_math_text
     s = unicode(s)
   File "/usr/lib/python2.7/encodings/utf_8.py", line 16, in decode
     return codecs.utf_8_decode(input, errors, True)
UnicodeDecodeError: 'utf8' codec can't decode byte 0xc5 in position 0:  
unexpected end of data
GPAW CLEANUP for serial binary: <type 'exceptions.UnicodeDecodeError'>  
occured. Calling sys.exit()




I also tried to calculate a STM image of Si(111)-(7x7), but because of the  
hexagonal cell, I get:

File "/usr/local/lib/python2.7/dist-packages/gpaw/transport/jstm.py", line  
1667, in smallestbox
     new_ct = np.dot(R(theta), ct.T).T
NameError: global name 'R' is not defined
GPAW CLEANUP for serial binary: <type 'exceptions.NameError'> occured.  
Calling sys.exit()


So I suppose, in the code of jstm.py it should call rotate:

new_ct = np.dot(rotate(theta), ct.T).T



But after I changed this, I get a new error:

File "/usr/local/lib/python2.7/dist-packages/gpaw/transport/jstm.py", line  
1667, in smallestbox
     new_ct = np.dot(rotate(theta), ct.T).T
ValueError: matrices are not aligned



Greetings,

Lars



Am 02.12.2011, 18:58 Uhr, schrieb Lars Smykalla  
<lars.smykalla at physik.tu-chemnitz.de>:

> Hi,
>
> I read a localized basis is necessary for STM simulation, so from the
> tutorial and documentation I it seems only possible for lcao mode.
> But now I read it also works when I create Wannier functions from a plane
> wave or grid based calculation.
>
> What python code do I have to use exactly to do this and to dump in this
> case the overlap matrix and the Hamiltonian matrix?
>
>
>
> Further, I don't understand in the NEGF-STM tutorial:
>
> # Here the keyword 'cvl' refers  to the number of basis functions in the
> # in the convergence layer, i.e. for the present system four atomic  
> layers
> are used.
> dump_hs(calc, 'srf', region='surface', cvl=4*4*9)
>
>
> There a 16 Ag atoms in 4 layers, but where does this 9 come from?
>
>
> Greetings,
> Lars
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