Mailman 3 July 2017 - Kwant-discuss

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by Prof. CHAN Kwok Sum July 18, 2017

July 18, 2017

Dear Kwant developer, I am trying to install kwant 1.3 on window 10. The installation went smoothly without warning. I encounter problems when I try to run the ab ring example with the following error messages. There was no warning about the installation of matplotlib during the installation. I ran pip list and can see matplotlib. KS Chan Warning (from warnings module): File "C:\Users\KSCHAN\AppData\Local\Programs\Python\Python36\lib\site-packages\kwant\plotter.py", line 49 "functions will work.", RuntimeWarning) RuntimeWarning: matplotlib is not available, only iterator-providing functions will work. Traceback (most recent call last): File "C:\Users\KSCHAN\Desktop\ab_ring.py", line 21, in <module> from matplotlib import pyplot File "C:\Users\KSCHAN\AppData\Local\Programs\Python\Python36\lib\site-packages\matplotlib\__init__.py", line 124, in <module> from matplotlib.rcsetup import (defaultParams, File "C:\Users\KSCHAN\AppData\Local\Programs\Python\Python36\lib\site-packages\matplotlib\rcsetup.py", line 32, in <module> from matplotlib.fontconfig_pattern import parse_fontconfig_pattern File "C:\Users\KSCHAN\AppData\Local\Programs\Python\Python36\lib\site-packages\matplotlib\fontconfig_pattern.py", line 25, in <module> from pyparsing import Literal, ZeroOrMore, \ ModuleNotFoundError: No module named 'pyparsing' Disclaimer: This email (including any attachments) is for the use of the intended recipient only and may contain confidential information and/or copyright material. If you are not the intended recipient, please notify the sender immediately and delete this email and all copies from your system. Any unauthorized use, disclosure, reproduction, copying, distribution, or other form of unauthorized dissemination of the contents is expressly prohibited.

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"typo" in the documentation?
by Tibor Sekera July 14, 2017

July 14, 2017

Dear all, on ordering of propagating modes. In the documentation https://kwant-project.org/doc/1/reference/generated/kwant.physics.Propagati… it says: "modes with negative velocity are ordered from larger to lower momenta" Shouldn't it be: "modes with negative velocity are ordered from lower to larger momenta"? As is mentioned in FAQ (in section "How does Kwant order the propagating modes of a lead?") https://test.kwant-project.org/doc/doc-faq/tutorial/FAQ namely: "Negative velocity modes are ordered by increasing momentum" Best, Tibor

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Making heterostructures of different lattice constants
by Jonathan Eaves July 13, 2017

July 13, 2017

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problem for installing kwant in ubuntu
by Prof. CHAN Kwok Sum July 11, 2017

July 11, 2017

Dear Kwant Developer, I tried to install the recent version of Kwant in Ubuntu 16.04 using anaconda 3 by following the instruction post in the discussion board on Feb 19 2016 by Bas Nijholt. The steps are: Install anaconda3 following the link <https://www.continuum.io/downloads> and run: conda install -c https://conda.anaconda.org/basnijholt kwant I received the following error message. Would you please help to solve the problem? KS Fetching package metadata ........... Solving package specifications: PackageNotFoundError: Dependencies missing in current linux-64 channels: - kwant -> blas 1.1 openblas - kwant -> mumps -> openblas 0.2.18.* - kwant -> @blas_openblas Close matches found; did you mean one of these? @blas_openblas: openblas (and similarly for the other packages) Disclaimer: This email (including any attachments) is for the use of the intended recipient only and may contain confidential information and/or copyright material. If you are not the intended recipient, please notify the sender immediately and delete this email and all copies from your system. Any unauthorized use, disclosure, reproduction, copying, distribution, or other form of unauthorized dissemination of the contents is expressly prohibited.

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Importing coordinates of the scattering region
by Patrik Arvoy July 11, 2017

July 11, 2017

Dear users and developers, I was wondering if I can import the coordinates of a scattering region without any particular symmetry and compute the conductance via kwant. If yes, how does one do that? Let's say the scattering region does not have any symmetry after optimizing the structure via MD or ... and I have a list of coordinates of all the sites. I appreciate any help. Regards Patrik

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SSH band diagram
by Steffen Wittek July 10, 2017

July 10, 2017

I know that the band diagram for the SSH can be easily obtained analytically, but I was wondering how one would go about it using kwant. If I understand correctly we require a translational symmetry such as to have an infinite lattice, so I defined a lead and tried to get the band structure from there. Unfortunately my code does not work and stops with a TypeError: Expecting an instance of SiteFamily. I thought that I implemented the hopping similar to the one from the graphene tutorial. Furthermore, I am wondering whether the definition of the lattice correct actually? To me it seems that the lattice vector [1,0] leaves us on the site of the b-sublattice. If I change it to [2,0] however I get a commensurate error The code that I have so far is below. Thank you, Steffen import numpy as np import kwant t = 1 SSH = kwant.lattice.general([[1, 0]], # lattice vectors [[0,0], [1,0]]) # Coordinates of the sites) a,b = SSH.sublattices SSH_lead = kwant.Builder(kwant.TranslationalSymmetry([-1, 0])) SSH_lead[a.shape((lambda pos: abs(pos[0]) == 0), (0, 0))] = 1 SSH_lead[b.shape((lambda pos: abs(pos[0]) == 1), (0, 0))] = 1 LongBond = (((1, 0), a, b)) ShortBond = (((-1, 0), a, b)) SSH_lead[[kwant.builder.HoppingKind(*hopping) for hopping in LongBond]] = 2 SSH_lead[[kwant.builder.HoppingKind(*hopping) for hopping in ShortBond]] = 1 kwant.plot(SSH_lead) kwant.plotter.bands(SSH_lead.finalized())

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Discretizing continuous Hamiltonians
by Khani Hosein July 7, 2017

July 7, 2017

Dear developers, We have a collection of tools for working with continuum models in Kwant 1.3. If we give it a Dirac equation, can we get the honeycomb lattice? It seems that we can only get a tight-binding model of square lattice, so it will not work for Dirac equation Hamiltonian? Regards, Hosein Khani

2 1

Number of orbitals
by Khani Hosein July 7, 2017

July 7, 2017

Dear all, How to define the number of orbitals when constructing the site families? In tutorial2.7, it is defined using: lat = kwant.lattice.square(norbs=2). For a new defined lattice with spin degree included, how to define the number of orbitals. For example, graphene = kwant.lattice.general([(1, 0), (sin_30, cos_30)], [(0, 0), (0, 1 / sqrt(3))]) a, b = graphene.sublattices How to declare the number of orbitals in the program? My second question is: I used the += operator in my program: lead0+=lead_U lead0+=lead_D it works well when i used kwant 1.2, but I got error messages in kwant 1.3. It shows: The += operator of builders is deprecated. Use 'Builder.update()' instead. How to fix this? Thanks in advance! Hosein Khani

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Local densities and currents
by Khani Hosein July 5, 2017

July 5, 2017

Dear all, I want to use kwant to calculate the local densities and currents, but I do not understand some of the code lines. For the local density of states, we can obtain it from: wf = kwant.wave_function(sys, energy) LDOS=((abs(wf(0))**2).sum(axis=0)+(abs(wf(1))**2).sum(axis=0))/(pi*2.) here wf(0) and wf(1) is the wavefunction for the left and right leads of a two terminal system. In Tutorial 2.7, we use wf = kwant.wave_function(syst, energy=-1, params=params) psi = wf(0)[0] Here wf(0)[0] includes all the leads and modes? In Tutorial 2.7, we use the following lines to calculate the local density: up, down = psi[::2], psi[1::2] density = np.abs(up)**2 + np.abs(down)**2 rho = kwant.operator.Density(syst) density = rho(psi) Will the two density give the same results as LDOS? Thanks in advance! Hosein Khani

2 3

passing site potential by its number in the finalized system
by Sergey Slizovskiy July 2, 2017

July 2, 2017

Dear all, Imagine that I have an external potential in a form of a list of values, corresponding to the site numbers in finalized system (this has appeared from mean-field account of Hubbard interactions). Now I want to feed this back to Kwant to compute the modes. The standard function to specify the potential has Site as an argument, with no access to its number in the finalized system. Is there a fast way to get the site number? I found an old reply of Anton: >/site_numbers = {tuple(site.pos(i)): i for i in xrange(sys.graph.num_nodes)} />/site_numbers[(1, 1)] # Find the number of the site with coordinates (1, 1). / but it does not look efficient. Any suggestions? Thanks, Sergey

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