Hi Ali,

A quick reply from my side. This

hamiltonian = semicon.models.foreman(

specify what will be spatial dependence of the parameters in the symbolic Hamiltonian that is used.
As far as I remember, two_deg_params provides you a single coordinate dependent parameters.
I suggest you either create parameter functions returned by two_deg_params by hand or
try to set coords of semicon.models.foreman to the single coordinate along which you want to
vary your parameters.

I will be able to look more in details into that next week.


Rafał Skolasiński 
Software Engineer

On Tue, 4 Dec 2018 at 16:14, Ali Asgharpour <asgharpour@sabanciuniv.edu> wrote:
Thanks for the feedback! If you find the bug, would you please let me know? Thanks in advance. By the way, I am also trying to code it myself from the beginning. Thanks again.

Best regards,


On Tue, Dec 4, 2018 at 6:57 PM Joseph Weston <joseph.weston08@gmail.com> wrote:

Thanks for the information!

Thank you for your quick response. I am using kwant 1.3.3 version and semicon 0.1.0 version. I think the error is related to calling parameters function which are stored as a tuple. By the way, this is the error I encountered:

TypeError                                 Traceback (most recent call last)
/home/ali/anaconda3/lib/python3.6/site-packages/kwant/builder.py in hamiltonian(self, i, j, params, *args)
   1995                     try:
-> 1996                         value = value(self.sites[i], **params)
   1997                     except Exception as exc:

<string> in onsite(site, Delta_0, E_0, E_v, P, gamma_0, gamma_1, gamma_2, hbar, k_y, m_0)

TypeError: __call__() takes 2 positional arguments but 3 were given

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

UserCodeError                             Traceback (most recent call last)
<ipython-input-5-9c34d828bfe1> in <module>()
     59     # compute the scattering matrix at a given energy
     60     p = {'k_y': 0, **two_deg_params}
---> 61     smatrix = kwant.smatrix(syst, energy, params=p)
     63     # compute the transmission probability from lead 0 to

/home/ali/anaconda3/lib/python3.6/site-packages/kwant/solvers/common.py in smatrix(self, sys, energy, args, out_leads, in_leads, check_hermiticity, params)
    370         linsys, lead_info = self._make_linear_sys(syst, in_leads, energy, args,
    371                                                   check_hermiticity, False,
--> 372                                                   params=params)
    374         kept_vars = np.concatenate([coords for i, coords in

/home/ali/anaconda3/lib/python3.6/site-packages/kwant/solvers/common.py in _make_linear_sys(self, sys, in_leads, energy, args, check_hermiticity, realspace, params)
    162         lhs, norb = syst.hamiltonian_submatrix(args, sparse=True,
    163                                                return_norb=True,
--> 164                                                params=params)[:2]
    165         lhs = getattr(lhs, 'to' + self.lhsformat)()
    166         lhs = lhs - energy * sp.identity(lhs.shape[0], format=self.lhsformat)

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

/home/ali/anaconda3/lib/python3.6/site-packages/kwant/builder.py in hamiltonian(self, i, j, params, *args)
   1996                         value = value(self.sites[i], **params)
   1997                     except Exception as exc:
-> 1998                         _raise_user_error(exc, value)
   1999                 else:
   2000                     try:

/home/ali/anaconda3/lib/python3.6/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

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

this certainly looks like a bug in semicon. I've managed to reproduce the bug, but I don't understand why it occurs. I inspected what was happening using the Python debugger and it seems to me that everything should work (but clearly it doesn't!).

Unfortunately the author of semicon is no longer working in academia, and the semicon project is currently without a maintainer (and it's not even v1.0!), so I am not sure what the best course of action is going forward.

Happy Kwanting,