Re: [Kwant] Onsite and hopping values in QHE

2 Jul 2018

      Hello everyone,

While this is working in a system with leads, I am getting an error in  
the case of a closed system.

--------------------------------------------------------------------------------------------------------
sym = kwant.TranslationalSymmetry(
     lattice.vec((1, 0, 0)),
     lattice.vec((0, 1, 0)),
	lattice.vec((0, 0, 1))
)

[....]

#Hall bar
def onsite(site, B):
   (x, y, z) = site.pos
   return stored_model[site]

def hopping_Ax(site1, site2, B):
       x1, y1, z1 = site1.pos
       x2, y2, z2 = site2.pos
       return stored_model[site1,site2] * np.exp(-0.5j * B * (x1 + x2)  
* (y1 - y2))

kwant_model[lattice.shape(shape, (0, 0, 15))] = onsite
kwant_model[lattice.neighbors()] = hopping_Ax

kwant_sys = wraparound.wraparound(kwant_model).finalized()

  B = 0.02
# Obtain the Hamiltonian as a dense matrix
ham_mat = kwant_sys.hamiltonian_submatrix(args=[B], sparse=True)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
~\Anaconda3\lib\site-packages\kwant\builder.py in hamiltonian(self, i,  
j, params, *args)
    2000                     try:
-> 2001                         value = value(self.sites[i], *args)
    2002                     except Exception as exc:

~\Anaconda3\lib\site-packages\wraparound.py in <lambda>(*args)
      81         return lambda *args: sum((val(*args) if callable(val)  
else val)
---> 82                                  for val in vals)
      83

~\Anaconda3\lib\site-packages\wraparound.py in <genexpr>(.0)
      81         return lambda *args: sum((val(*args) if callable(val)  
else val)
---> 82                                  for val in vals)
      83

~\Anaconda3\lib\site-packages\wraparound.py in <lambda>(a, *args)
      59         assert callable(val)
---> 60         return lambda a, *args: val(a, *args[:mnp])
      61

TypeError: onsite() missing 1 required positional argument: 'B'

The above exception was the direct cause of the following exception:

UserCodeError                             Traceback (most recent call last)
<ipython-input-19-dd56ba85dfde> in <module>()
       1 B = 0.02
       2 # Obtain the Hamiltonian as a dense matrix
----> 3 ham_mat = kwant_sys.hamiltonian_submatrix(args=[B], sparse=True)
       4

kwant\_system.pyx in kwant._system.hamiltonian_submatrix()

~\Anaconda3\lib\site-packages\kwant\builder.py in hamiltonian(self, i,  
j, params, *args)
    2001                         value = value(self.sites[i], *args)
    2002                     except Exception as exc:
-> 2003                         _raise_user_error(exc, value)
    2004         else:
    2005             edge_id = self.graph.first_edge_id(i, j)

~\Anaconda3\lib\site-packages\kwant\builder.py in _raise_user_error(exc, func)
    1883     msg = ('Error occurred in user-supplied value function "{0}".\n'
    1884            'See the upper part of the above backtrace for  
more information.')
-> 1885     raise UserCodeError(msg.format(func.__name__)) from exc
    1886
    1887

UserCodeError: Error occurred in user-supplied value function "<lambda>".
See the upper part of the above backtrace for more information.

--------------------------------------------------------------------------------------------

Eleni

Quoting elchatz@auth.gr:
...
Hello Joseph,
Thank you. It is working when I copy the model and each lead after I  
have attached them.
Regards,
Eleni
Quoting Joseph Weston :
...
HI,
...
I am trying to reproduce the QHE bar device calculations
http://nbviewer.jupyter.org/github/topocm/topocm_content/blob/master/w3_pump...
However, I am having difficulty with the onsite and hopping values as
I am using TBModels
https://github.com/Z2PackDev/TBmodels
and therefore the values are not the same for all sites.
I am unsure of the output format of TBModels. Glancing at their
documentation I can't see any way of getting the raw matrix elements
from a "Model". Looking into the source code it seems that they are
stored in a format that will be annoying to query manually.
...
The problem is that after the scalar values have been passed on to the
Builder, these will then be overriden when using functions for the
position-dependent Hamiltonian.
I tried making a deep copy of the model, which would then serve as a
data structure where to draw the scalar values from when calling the
Onsite and Hopping functions. The problem with this is
a) I am getting a KeyError which I am still not sure why it happens
b) It does not feel very memory-efficient.
I am wondering if there is another way that this could be done on the
Kwant side that I have not been able to think of.
I can't think of a better way to accomplish this. Using TBModels'
internal datastructures directly is IMO too much hassle unless your
systems are really big.
Did you check that the symmetry of your Kwant system and the TBModels
Model are compatible?
Joe
-- 
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elchatz@auth.gr - tel:+30 2310 998109
-- 
Dr. Eleni Chatzikyriakou
Computational Physics lab
Aristotle University of Thessaloniki
elchatz@auth.gr - tel:+30 2310 998109

Re: [Kwant] Onsite and hopping values in QHE

elchatz＠auth.gr