Mailman 3 February 2016 - Kwant-discuss

How the spin is positioned in the Smatrix?
by Qingtian Zhang March 6, 2022

March 6, 2022

Dear all, I am trying square lattice with spin-orbit coupling and Zeeman splititng just like the example of Tutorial 2.3.1. Now I want to get the spin-dependent conductance：Guu,Gud,Gdu,and Gdd, where "u" indicates up spin, d indicates down spin. We can have the scattering matrix through Smatrix=kwant.smatrix(sys, energy), but how the spin is positioned in the scattering matrix? I have checked some simple cases, it seems the Smatrix is organized like this: | r t | S= | t' r' | but how the spin is included? Thanks in advance. Qingtiian Zhang The code is: import kwant from matplotlib import pyplot from numpy import matrix import tinyarray sigma_0 = tinyarray.array([[1, 0], [0, 1]]) sigma_x = tinyarray.array([[0, 1], [1, 0]]) sigma_y = tinyarray.array([[0, -1j], [1j, 0]]) sigma_z = tinyarray.array([[1, 0], [0, -1]]) sys=kwant.Builder() lat=kwant.lattice.square() a=1 t=1.0 alpha=0.5 e_z=0.08 W=2 L=2 sys[(lat(x, y) for x in range(L) for y in range(W))] = \ 4 * t * sigma_0 + e_z * sigma_z # hoppings in x-direction sys[kwant.builder.HoppingKind((1, 0), lat, lat)] = \ -t * sigma_0 - 1j * alpha * sigma_y # hoppings in y-directions sys[kwant.builder.HoppingKind((0, 1), lat, lat)] = \ -t * sigma_0 + 1j * alpha * sigma_x #### Define the left lead. #### lead = kwant.Builder(kwant.TranslationalSymmetry((-a, 0))) lead[(lat(0, j) for j in xrange(W))] = 4 * t * sigma_0 + e_z * sigma_z # hoppings in x-direction lead[kwant.builder.HoppingKind((1, 0), lat, lat)] = \ -t * sigma_0 - 1j * alpha * sigma_y # hoppings in y-directions lead[kwant.builder.HoppingKind((0, 1), lat, lat)] = \ -t * sigma_0 + 1j * alpha * sigma_x #### Attach the leads and return the finalized system. #### sys.attach_lead(lead) sys.attach_lead(lead.reversed()) kwant.plot(sys) sys=sys.finalized() print "Hamiltonian=" print sys.hamiltonian_submatrix() Smatrix=kwant.smatrix(sys, energy=3.) print "The scattering matrix=" print matrix.round((Smatrix.data),2) print "T=",(Smatrix.transmission(1, 0))

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How to caculate hall resistance
by ZHANG Bing Sept. 12, 2021

Sept. 12, 2021

Dear Sir, I am a PhD student of Hong Kong University of Science and Technology. I want to use KWANT to caculate Hall resistance of a Hall bar structure.We can get the conductance between 6 electrodes, but how to get hall resistance? Can you give me some help? Thank you very much. Best Regards, Zhang Bing

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Kwant for bulk system
by Weiyuan Tong June 8, 2016

June 8, 2016

Dear all, I want to calculate the conductance and the band structure of a bulk graphene system.(infinite in y direction) I have checked the source code for the calculation of band structure. https://github.com/kwantproject/kwant/blob/7c55b0cb2d0dec163e5483dea8ffdbc8… It seems that we can get the sys.cell_hamiltonian and hopping between the sys.cell_hamiltonian in kwant. In y direction, we can also have sys.cell_hamiltonian and hopping, then it can be extended to infinite in y direction: V^\dagger e^{iky} + H + Ve^{-iky}. I am not familiar with kwant coding. Can anyone help me to write some code lines to do these calculations? Or you can also change the Tutorial 2.2.3 as an example. Thanks in advance! Best wishes Weiyuan Tong

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Re: [Kwant] Problems with band in tutoral 2.5 graphene ( 고운 )
by Sumit Ghosh Feb. 28, 2016

Feb. 28, 2016

Hi Lee, As Anton pointed out, it is due to the dangling bond. For graphene each unit cell contains two atoms. When you make the lead you actually specify the boundary in space which may take half of an unit cell - this will give you a flat line at zero energy in your band structure and also a small gap. This is not incorrect. The results of nanoribbon from analytical model deals with complete unit cell (it is 2x2 hamiltonian with boundary condition), that is why you can't see it there. I guess you have to fix it manually - either use proper r value or change the width of lead (it is actually 0.4*r) such that each slice of your lead have even number of atoms. Hope it will help. Best, Sumit On 28 February 2016 at 15:02, <kwant-discuss-request(a)kwant-project.org> wrote: > Send Kwant-discuss mailing list submissions to > kwant-discuss(a)kwant-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman-mail5.webfaction.com/listinfo/kwant-discuss > or, via email, send a message with subject or body 'help' to > kwant-discuss-request(a)kwant-project.org > > You can reach the person managing the list at > kwant-discuss-owner(a)kwant-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Kwant-discuss digest..." > > > Today's Topics: > > 1. Re: Problems with band in tutoral 2.5 graphene (Anton Akhmerov) > 2. Re: Problems with band in tutoral 2.5 graphene ( 고운 ) > 3. Re: Problems with band in tutoral 2.5 graphene (Anton Akhmerov) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 27 Feb 2016 16:20:50 +0100 > From: Anton Akhmerov <anton.akhmerov+kd(a)gmail.com> > To: 고운 <rhdnsi(a)hanmail.net> > Cc: "kwant-discuss(a)kwant-project.org" > <kwant-discuss(a)kwant-project.org> > Subject: Re: [Kwant] Problems with band in tutoral 2.5 graphene > Message-ID: > < > CADr1H-853of8DduXzNGYyCXK0qdhXmXKM7Kdiq_ZL92ajPWsZQ(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Lee, > > What exactly do you want to fix? From your description I didn't notice > anything going wrong. > > Cheers, > Anton > > On Sat, Feb 27, 2016 at 6:25 AM, 고운 <rhdnsi(a)hanmail.net> wrote: > > > > Hello, I am just starting with KWANT. I have a question about the energy > band in lead. In the tutorial "2.5 Beyond square lattices: graphene", the > energy band in lead is semimetallic and is consistent with that of > zigzag-edge graphene nanoribbon when "r=10" ( default value given in the > tutorial). However, when I set r=9 (or a value larger than 10), the energy > band in lead becomes insulating and the conductance of scattering region > also changes greatly. How can I fix it? > > > > > > > > thanks, > > > > Lee > > > > > > > > > ------------------------------ > > Message: 2 > Date: Sun, 28 Feb 2016 12:32:41 +0900 (KST) > From: " 고운 " <rhdnsi(a)hanmail.net> > To: <kwant-discuss(a)kwant-project.org> > Subject: Re: [Kwant] Problems with band in tutoral 2.5 graphene > Message-ID: > <20160228123241.HM.000000000000rzW(a)rhdnsi.wwl1454.hanmail.net> > Content-Type: text/plain; charset="utf-8" > > An HTML attachment was scrubbed... > URL: < > http://mailman-mail5.webfaction.com/pipermail/kwant-discuss/attachments/201… > > > > ------------------------------ > > Message: 3 > Date: Sun, 28 Feb 2016 09:52:50 +0100 > From: Anton Akhmerov <anton.akhmerov(a)gmail.com> > To: 고운 <rhdnsi(a)hanmail.net> > Cc: "kwant-discuss(a)kwant-project.org" > <kwant-discuss(a)kwant-project.org> > Subject: Re: [Kwant] Problems with band in tutoral 2.5 graphene > Message-ID: > < > CADr1H-9srdLxt5wjuYDAvZpRNVAN8v7koTZ4zCL68ZrzdAtJBg(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > > I think that the energy band in lead should be the semimetallic band of > zigzag-edge graphene nanoribbon regardless of the parameter r. > > Did you plot the system and the dispersion of the lead? I suspect one > of the edges has dangling bonds (corresponding to the "bearded" > boundary condition). This would open a gap in the lead band structure. > > Anton > > > > > If the band in lead is incorrect and changes from metall to insulator > depending on the parameter r, how can i trust the resulting conductance of > scattering region ? So, I thought someting is wrong. > > > > > > > > Thanks, again > > > > Lee > > > > > > > > > > > > --------- 원본 메일 --------- > > > > 보낸사람: Anton Akhmerov <anton.akhmerov+kd(a)gmail.com> > > 받는사람 : 고운 <rhdnsi(a)hanmail.net> > > 참조 : "kwant-discuss(a)kwant-project.org" <kwant-discuss(a)kwant-project.org> > > 날짜: 2016년 2월 28일 일요일, 00시 20분 50초 +0900 > > 제목: Re: [Kwant] Problems with band in tutoral 2.5 graphene > > > > Hi Lee, > > > > What exactly do you want to fix? From your description I didn't notice > > anything going wrong. > > > > Cheers, > > Anton > > > > On Sat, Feb 27, 2016 at 6:25 AM, 고운 <rhdnsi(a)hanmail.net> wrote: > > > > > > Hello, I am just starting with KWANT. I have a question about the > energy band in lead. In the tutorial "2.5 Beyond square lattices: > graphene", the energy band in lead is semimetallic and is consistent with > that of zigzag-edge graphene nanoribbon when "r=10" ( default value given > in the tutorial). However, when I set r=9 (or a value larger than 10), the > energy band in lead becomes insulating and the conductance of scattering > region also changes greatly. How can I fix it? > > > > > > > > > > > > thanks, > > > > > > Lee > > > > > > > > > > > > > > > > > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Kwant-discuss mailing list > Kwant-discuss(a)kwant-project.org > https://mailman-mail5.webfaction.com/listinfo/kwant-discuss > > > ------------------------------ > > End of Kwant-discuss Digest, Vol 30, Issue 15 > ********************************************* > -- Sumit Ghosh Spintronics Theory Group PSE Division KAUST -- ------------------------------ This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Re: [Kwant] Problems with band in tutoral 2.5 graphene
by 고운 Feb. 28, 2016

Feb. 28, 2016

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Problems with band in tutoral 2.5 graphene
by 고운 Feb. 27, 2016

Feb. 27, 2016

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Linking MUMPS and other libraries
by Abdulkareem Afandi Feb. 20, 2016

Feb. 20, 2016

Hi everyone, So I’ve compiled MUMPS, scotch, metis from source, and now trying to like MUMPS in the build.conf file, but with no luck. I am doing this on a Linux cluster, so I don’t have root access, and to improve performance I built everything from source. From documentation, I understand the build.conf file should look like this: [mumps] libraries = zmumps mumps_common pord metis esmumps scotch scotcherr mpiseq gfortran However I’m trying to link everything to static libraries. I tries using the full source to .a library files for each option, but I keep getting compile errors for every library, such as: warning: no library file corresponding to ‘/user/MUMPS_5.0.1/lib/libzmumps.a’ found (skipping) and compilation ends without mumps being linked to kwant. Any help is appreciated. Best regards, Abdul

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Conda packages for Kwant
by Bas Nijholt Feb. 19, 2016

Feb. 19, 2016

Hi all, I've compiled conda packages for kwant (and it's dependencies) for Python 2.7, 3.4, and 3.5 for both Linux and OS X. They can be found on anaconda.org/basnijholt/kwant. The advantage of having these packages is that they are already compiled. Conda is a packaging tool and installer that aims to do more than what pip does; handle library dependencies outside of the Python packages as well as the Python packages themselves. In this way you won't have to install any other dependencies, so when you have a fresh Ubuntu install, all you need to do is install miniconda <http://conda.pydata.org/miniconda.html> or Anaconda <https://www.continuum.io/downloads> and run: conda install -c https://conda.anaconda.org/basnijholt kwant That's it! Let me know if you run into any trouble. Best, Bas Nijholt

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site_pos in kwant
by Weiyuan Tong Feb. 15, 2016

Feb. 15, 2016

Dear developers， When I print site_pos in kwant 1.2.2, I find that the index of the atoms for the system are changing every time. site_pos: [[ 0.5 3.17542648] ### site 0 [ 1. 1.73205081] ### site 1 [ 0. 2.30940108] [ 0. 3.46410162] [-0.5 3.17542648] [ 0.5 2.59807621] [ 0. 1.73205081] [-0.5 4.33012702] [ 1. 4.04145188] [ 0.5 4.33012702] [ 0. 4.04145188] [ 1. 3.46410162] [-0.5 2.59807621] [ 0.5 1.44337567] [ 1. 2.30940108] [-0.5 1.44337567]] I run the code again and get: site_pos: [[ 0.5 3.17542648] ### site 0 [ 0.5 4.33012702] ### site 1 [ 0. 3.46410162] [ 1. 2.30940108] [ 0.5 1.44337567] [ 0. 2.30940108] [-0.5 2.59807621] [ 1. 3.46410162] [-0.5 1.44337567] [ 0.5 2.59807621] [ 0. 4.04145188] [-0.5 4.33012702] [ 1. 1.73205081] [-0.5 3.17542648] [ 0. 1.73205081] [ 1. 4.04145188]] I have tried this in kwant 1.0, it gives the same results every time. It seems that it is inconvenient for us to know or overwrite the hopping between two atoms such as sys.hamiltonian(1,0). Is there an easy way to do this in kwant 1.2.2? Best wishes, Weiyuan Tong

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Re: [Kwant] Kwant for bulk system
by weiyuanphysics Feb. 12, 2016

Feb. 12, 2016

Dear Christoph, Sorry for the late reply. Gmail and Google is blocked by the Chinese government, so it is really inconvenient for the communication. I use another mailbox to discuss with you about my proposed topic. Now, I can run your code for bulk system on my computer according to your guide. I had tried to install kwant 1.1 after its release, but it showed some error message like "lack of lapack". Do I need to install lapack before I install all the kwant codes? It seems i do not need to do this for kwant 1.0. Best wishes, Weiyuan Tong

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