Mailman 3 April 2023 - Kwant-discuss

FIll error
by Alejandro Alvarez Chico 28 Apr '23

28 Apr '23

Hello: Im simulating a nanotube with this hamiltonian: ns = {'hdiag':[[1,0,0,0],[0,-1,0,0],[0,0,1,0],[0,0,0,-1]], 'hA1':[[0,1,0,0],[1,0,0,0],[0,0,0,-1],[0,0,-1,0]], 'hA2r':[[0,0,0,1],[0,0,1,0],[0,0,0,0],[0,0,0,0]], 'hA2s':[[0,0,0,0],[0,0,0,0],[0,1,0,0],[1,0,0,0]] } ham=""" (C_0+C_1*k_z**2+C_2*(k_x**2+k_y**2))*identity(4)+(M_0+M_1*k_z**2+M_2*(k_x**2+k_y**2))*hdiag + (B_0*k_z)*hA1 + (1/sqrt(2)*(1+1j)*A_0*(k_x-1j*k_y))*hA2r + (1/sqrt(2)*(1-1j)*A_0*(k_x+1j*k_y))*hA2s """ ham= kwant.continuum.sympify(ham,ns) and this shape: def cuboid_shape(pos): x, y, z = pos return 0 <= x < Lx/2 and abs(y) <= R and abs(z) <= np.sqrt(R**2-y**2) When using : lat = kwant.lattice.general([(1, 0, 0),(0, 1, 0),(0, 0, 1)], norbs=4) syst = kwant.Builder() template = kwant.continuum.discretize(ham, coords =['x','y','z'], grid=a) syst.fill(template, cuboid_shape,(0,0,0)) I get this weird error that all the sites have been deleted because an exception with fill(); and i can't seem to find a similar error anywhere on the internet. Any ideas? Kind Regards Alejandro Álvarez Chico

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The tutorial quantum_wire.py giving different result
by Faruk Abdulla 27 Apr '23

27 Apr '23

Hi, I am a beginner to Kwant. I want to use it for computing conductance through an interface. To learn the basics, I started with the tutorials in the documentation. The tutorial quantum_wire.py is giving me very different result for the conductance than what I expect from the documentation (see the attachments). However, I have used it to compute band structure and Fermi arcs states in Weyl semimetals and that seem to work perfectly fine. I have installed Kwant through conda in my MacBook Air M1(Ventura 13.3.1). I don’t understand why the tutorial quantum_wire.py is not working properly in my machine. Do you think it is a compiler issue? Any help would be much appreciated. Thank you, Faruk Graduate Student Harish-Chandra Research Institute Prayagraj, 211019, India

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Methods for calculating Josephson Current ?
by guilhermewells＠gmail.com 21 Apr '23

21 Apr '23

Hi, I'm new to Kwant and I've been looking for calculating Josephson Current with it. The past three weeks I've been reading a lot the tutorials, the mailing list and some online courses. The problem is that I can't get a straight answer on where it is possible to calculate Josephson current reallistically. The most complete answer was given by J. Weston here [1], the problem is that the methods suggested are also not so clear, since I coundn't find tutorials using properly Self-Energy and Green's function with Kwant. Most of the topics are questions, so they usually are of people with code not working, so it doesn't point out the proper way to use. So, I'd like to know if I'm missing some tutorials with these subjects, or some online courses to understand this. The documentation itself is not enough for the applications (at least for me). I'm learning kwant alone, there is no one around in my department that even have heard of it. Right now I'm got a discontinuous current (only at the junction interface) through my junction using directly "kwant.operator.Current" and "plotter", which I think is to be expected due to the issue of the Andreev bound states. Thanks, I'm looking foward to use kwant at higher level [1] https://mail.python.org/archives/list/kwant-discuss@python.org/thread/6IP2Q… -- Guilherme Vieira Phd Student at Centro Brasileiro de Pesquisas Físicas Brazil, RJ

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Re: Josephson Junction bug
by Guilherme Vieira 20 Apr '23

20 Apr '23

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Josephson Junction bug
by guilhermewells＠gmail.com 18 Apr '23

18 Apr '23

Hi, I'm experiencing an issue on my cubic construction. It doesn't matter what I try it persists. I think it is a bug, but I'm not sure. I have the following code, and I'm getting that the top site of z at a "x,y" corner is always a different lattice, the botton lattice. If I eliminate "lat_ti" which is green, then this site becomes blue, "lat_tu", but never becomes "lat_sc" as stated. Even if I put this site above the sample, that is, unnconected, this issue mantains. This also was happening before stating colors for the lattices. Link for the plot: https://drive.google.com/file/d/13Z5XnGa-eyJGYJgyM_NGm0onp5MoQs_O/view?usp=… def make_system(a=1, W=21, L=15, H=4, Hs=6, barrier=1.5, mu=0.4, Delta=0.1, t=1.0): lat_sc = kwant.lattice.cubic(a,name='Supercondutor', norbs=2) lat_tu = kwant.lattice.cubic(a,name='Tunelamento', norbs=2) lat_ti = kwant.lattice.cubic(a,name='TopIns') syst = kwant.Builder() #### Scattering region. #### syst[(lat_ti(x, y, z) for x in range(W) for y in range(L) for z in range(H-1))] = 0 syst[(lat_ti(x, y, z) for x in range(int(W/3),int(2*W/3)) for y in range(L) for z in range(H-1,H))] = 0 syst[(lat_sc(x, y, z) for x in range(int(W/3)) for y in range(L) for z in range(H+1,H+Hs))] = onsite_sc syst[(lat_sc(x, y, z) for x in range(int(2*W/3),W) for y in range(L) for z in range(H+1,H+Hs))] = onsite_sc syst[(lat_sc(W-1, 0, H+Hs+2))] = 0 #bug ? # The tunnel barrier syst[(lat_tu(x, y, z) for x in range(int(W/3)) for y in range(L) for z in range(H-1, H+1))] = onsite_tu syst[(lat_tu(x, y, z) for x in range(int(2*W/3),W) for y in range(L) for z in range(H-1,H+1))] = onsite_tu def family_color(site): if site.family == lat_sc: return 'red' if site.family == lat_ti: return 'green' if site.family == lat_tu: return 'blue' return syst, family_color

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Does Kwant take Device Hamiltonian from file?
by MD NILOY KHAN 17 Apr '23

17 Apr '23

Hi everyone, I am a new kwant user. I have made hamiltonian taking interaction from wannier90. How can I give input this device hamiltonian to kwant?

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A two sites impurity on an infinite one-dimensional chain (double quantum dot)
by Gabriel Garcia 01 Apr '23

01 Apr '23

Dear Author, I am trying to reproduce the 2.7 section of Tkwant tutorial: Green Function. When i try to calculate the lesser and retard greens's function occurred this error: green_lesser = [] green_retard = [] for time in times: green.evolve(time, 0) green.refine_intervals() green_lesser.append(green.lesser(site_0, site_0)) green_retard.append(green.retarded(site_0, site_0)) /home/gabriel/.local/lib/python3.9/site-packages/kwantspectrum/kwant_spectrum.py:361: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray. pvec = np.array([b * b / 3, 0, a * a]) --------------------------------------------------------------------------- ImportError Traceback (most recent call last) /tmp/ipykernel_158862/3957660185.py in <module> 7 green.refine_intervals() 8 ----> 9 green_lesser.append(green.lesser(site_0, site_0)) 10 green_retard.append(green.retarded(site_0, site_0)) ~/.local/lib/python3.9/site-packages/tkwant/greenfunctions.py in lesser(self, i, j, root) 375 def lesser(self, i, j, root=0): 376 if self._green_lesser is None: --> 377 self._init_lesser() 378 self._do_jobs(self._jobs_lesser) 379 return self._green_lesser.evaluate(i, j, root) ~/.local/lib/python3.9/site-packages/tkwant/greenfunctions.py in _init_lesser(self) 430 def _init_lesser(self): 431 logger.debug('init G^<') --> 432 self._green_lesser = _GreenGeneric(*self._args, **self._kwargs) 433 434 def _init_retarded(self): ~/.local/lib/python3.9/site-packages/tkwant/greenfunctions.py in __init__(self, refine, *args, **kwargs) 36 37 # no refine on individual wave function based on density ---> 38 self._state0 = manybody.State(*args, **kwargs, refine=False) 39 self._state1 = manybody.State(*args, **kwargs, refine=False) 40 ~/.local/lib/python3.9/site-packages/tkwant/manybody.py in __init__(self, syst, tmax, occupations, params, spectra, boundaries, intervals, refine, combine, error_op, scattering_state_type, manybody_wavefunction_type, mpi_distribute, comm) 1511 tasks.update(tasks_) 1512 -> 1513 self.comm = mpi.get_communicator(comm) 1514 1515 psi_init = self._calc_initial_state(tasks, self.comm) ~/.local/lib/python3.9/site-packages/tkwant/mpi.py in get_communicator(comm) 66 if comm is None: 67 if _COMM is None: ---> 68 communicator_init() 69 comm = _COMM 70 return comm ~/.local/lib/python3.9/site-packages/tkwant/mpi.py in communicator_init(comm) 48 if _COMM is None: 49 if comm is None: ---> 50 from mpi4py import MPI 51 _COMM = MPI.COMM_WORLD.Dup() 52 else: ImportError: libmpi.so.12: cannot open shared object file: No such file or directory Someone knows what should i do? I am beginner in python and kwant.

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tkwant-green function
by 1833356804＠qq.com 01 Apr '23

01 Apr '23

Dear author, I am writing to seek your help regarding an issue I encountered while studying tkwant. Specifically, when trying to calculate the Green functions, I got an error message "AttributeError: module 'tkwant.manybody' has no attribute 'GreenFunction'". I was wondering if you could kindly explain to me what may be the cause of this error. Thank you very much for your time and attention. I greatly appreciate any guidance you could provide.

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Kwant-discuss April 2023