Mailman 3 January 2017 - Kwant-discuss

the path in the Brillouin zone
by Weiyuan Tong 18 Jan '17

18 Jan '17

Dear all, I used kwant to calculate the band structure of zigzag and armchair graphene nanoribbons. For zigzag graphene nanoribbons, we have sym= kwant.TranslationalSymmetry(lat.a.vec((-1, 0))). For armchair graphene nanoribbons, we have sym= kwant.TranslationalSymmetry(lat.a.vec((-1, 2))). My question is: which is the path in the Brillouin zone that we use and label the x-axis accordingly? My figure is attached. Thanks in advance! Weiyuan

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Re: [Kwant] Fwd: Regarding smatrix and spin
by Andrey Antipov 18 Jan '17

18 Jan '17

Не вопрос, напишу мануал. On Tuesday, January 17, 2017 at 02:51 Anton Akhmerov <anton.akhmerov+kd(a)gmail.com> wrote: Привет, можешь девушке помочь? (В смысле поделиться на нашем списке рассылки как ты квант на WSL установл.) ---------- Forwarded message ---------- From: Anton Akhmerov Date: Tue, Jan 17, 2017 at 10:48 AM Subject: Re: [Kwant] Regarding smatrix and spin To: Camilla Espedal Cc: "kwant-discuss(a)kwant-project.org" Dear Camilla, It seems that you are trying to install Kwant on windows. This is a very hard task, and I fear none of the Kwant developers has enough knowledge of it right now (our Windows packages are built by Christoph Gohlke, see [1] for the build environment description). However if you are using windows 10, I suggest to try to install Kwant using the windows subsystem for linux. That way the standard Ubuntu build procedure should work for you. Best, Anton [1]: http://www.lfd.uci.edu/~gohlke/pythonlibs/ On Mon, Jan 16, 2017 at 9:45 AM, Camilla Espedal wrote: > Thanks a lot. I tried to install the cons_laws_combined, but I get the following error message: > > "LINK: fatal error LNK1181: cannot open input file 'lapack.lib'" > > Is there some package or installation I am missing? > > Best regards, > Camilla > > -----Original Message----- > From: anton.akhmerov(a)gmail.com [mailto:anton.akhmerov@gmail.com] On Behalf Of Anton Akhmerov > Sent: 8. januar 2017 16:35 > To: Tómas Örn Rosdahl > Cc: Camilla Espedal ; kwant-discuss(a)kwant-project.org > Subject: Re: [Kwant] Regarding smatrix and spin > > Hi Camilla, everyone, > > I've slightly modified Tómas's example to a case where the spins do get coupled, check it out: > http://nbviewer.jupyter.org/url/antonakhmerov.org/misc/spin_conductance.ipy… > > I've also provided more detailed installation instructions in the notebook. > > Cheers, > Anton > > On Sun, Jan 8, 2017 at 2:45 PM, Tómas Örn Rosdahl wrote: >> Dear Camilla, >> >> For a Hamiltonian with degeneracies due to a conservation law, the >> scattering states will in general not have a definite value of the >> conservation law. In your case, Kwant returns scattering states that >> are arbitrary linear combinations of spin up and down, so it is not >> possible to label the amplitudes in the scattering matrix by spin. >> >> However, in Kwant 1.3 a feature will be added that allows for the >> construction of scattering states with definite values of a >> conservation law. See here for an explanation of the basic idea behind the algorithm. >> >> We're currently working on implementing this feature in Kwant itself. >> The good news is that we're practically done - here is a link to a git >> repo with a functioning implementation. After you clone the repo, >> check out the branch cons_laws_combined, which contains a version of >> Kwant with conservation laws implemented. This notebook contains a >> simple example to illustrate how to work with conservation laws and the scattering matrix. >> >> I invite you and anyone else who is interested to give it a try. We'd >> appreciate any feedback! >> >> In your case specifically, there would be two projectors in the new >> implementation - P0 which projects out the spin up block, and P1 that >> projects out the spin down block. If they are specified in this order, >> then the spin up and down blocks in the Hamiltonian have block indices >> 0 and 1, respectively. In the new implementation, it is possible to >> ask for subblocks of the scattering matrix relating not only any two >> leads, but also any two conservation law blocks in any leads. To get >> the reflection amplitude of an incident spin up electron from lead 0 >> into an outgoing spin down electron in lead 0, you could simply do >> smat.submatrix((0, 1), (0, 0)). Here, the arguments are tuples of indices (lead index, block index). >> >> Best regards, >> Tómas >> >> On Fri, Jan 6, 2017 at 3:46 PM, Camilla Espedal >> >> wrote: >>> >>> Hi again, >>> >>> >>> >>> This question is basically the same as this: >>> https://www.mail-archive.com/kwant-discuss@kwant-project.org/msg00076 >>> .html >>> >>> >>> >>> I want to calculate some things using the scattering matrix. I >>> started out with a very simple system, most basic two-terminal >>> system. For some energy there is one propagating mode. I now add >>> matrix structure to the mix (just multiply by s_0 everywhere) and >>> there are now 2 propagating modes (which makes sense). >>> >>> >>> >>> Now, if I look at the reflection coefficients for lead 0 by using >>> submatrix(0,0), it is now a 2x2 matrix after I introduced the >>> matrices. How are the elements ordered? Is it >>> >>> >>> >>> [[r_upup, r_updown],[r_downup, r_downdown]] >>> >>> >>> >>> I know that I could make two lattices, but since I do not plan to use >>> the other functions such as transmission. I just want the smatrix. >>> >>> >>> >>> Hope you can help me, and thanks in advance. >>> >>> >>> >>> Best regards, >>> >>> Camilla >> >>

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Re: [Kwant] putting disorder (kwant.digest.uniform) in graphene with shape function
by Sudin Ganguly 14 Jan '17

14 Jan '17

Dear Sir, That helps a lot. Thank you very much. With Regards, Sudin

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Re: [Kwant] putting disorder (kwant.digest.uniform) in graphene with shape function
by SUDIN GANGULY 13 Jan '17

13 Jan '17

Dear Sir, Thank you for the quick reply. I think my institute mail is not working properly, so I used this mail-id. By using the line: lambda site: sys_2['sys'][site] I got another error massage, which says that, "TypeError: 'int' object is not callable". With regards, Sudin -- সুদিন

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putting disorder (kwant.digest.uniform) in graphene with shape function
by Sudin Ganguly 13 Jan '17

13 Jan '17

Dear Sir, I'm trying to put disorder in graphene with shape function. I got some help from the link: http://nullege.com/codes/show/src@k@w@kwant-1.0.0@kwant@tests@test_comprehe… But when I want to see the onsite values using the comment below, kwant.plotter.plot(sys_2['sys'],site_color=lambda site: sys_2['sys'][site],colorbar = True, cmap='gist_heat') It says, "cannot convert argument to rgb sequence". Is there any way to see the onsite values through plot? Also it seems that all the onsite values have the same disorder. Can I make them different using kwant.digest.uniform()? Here is my code. #==================================== import kwant from matplotlib import pyplot def onsite(site, salt): return kwant.digest.uniform(repr(site), salt) - 0.5 def make_sys(l, w): def rect(pos): x, y = pos return 0 < x < l and 0 < y < w sys=kwant.Builder() lat = kwant.lattice.honeycomb() a,b= lat.sublattices sys[lat.shape(rect, (1, 1))] = onsite sys[lat.neighbors()] = -1 # left lead sym = kwant.TranslationalSymmetry((-1,0)) sym.add_site_family(lat.sublattices[0], other_vectors=[(-1, 2)]) sym.add_site_family(lat.sublattices[1], other_vectors=[(-1, 2)]) def lead_shape(pos): x, y = pos return 0 < y < w lead = kwant.Builder(sym) lead[lat.shape(lead_shape, (1, 1))] = 0 lead[lat.neighbors()] = -1 sys.attach_lead(lead) sys.attach_lead(lead.reversed()) return {'sys': sys } def main(): sys_2 = make_sys(l=10, w=23) kwant.plotter.plot(sys_2['sys'],site_color=lambda site: sys_2['sys'][site],colorbar = True, cmap='gist_heat') # Call the main function if the script gets executed (as opposed to imported). # See <http://docs.python.org/library/__main__.html>. if __name__ == '__main__': main() #============================================ With Regards, Sudin

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Current density
by Harshad Sahasrabudhe 11 Jan '17

11 Jan '17

Hi All, I am trying to calculate current density from the wavefunctions using the following code: for i in range(Np): for j in range(Nc): lat_idx_i = i-floor(Np/2) lat_idx_j = j-floor(Nc/2) site_i = lat(lat_idx_i, lat_idx_j) idx_i = sys.sites.index(site_i) if i < Np-1: site_j = lat(lat_idx_i+1, lat_idx_j) idx_j = sys.sites.index(site_j) H_ij = sys.hamiltonian(idx_i, idx_j, V, peierls_phase_factor) current_density_bond_x[i][j] = -2 * (wf_orb[idx_i].conjugate() \ * H_ij * wf_orb[idx_j]).imag if j < Nc-1: site_j = lat(lat_idx_i, lat_idx_j+1) idx_j = sys.sites.index(site_j) H_ij = sys.hamiltonian(idx_i, idx_j, V, peierls_phase_factor) current_density_bond_y[i][j] = -2 * (wf_orb[idx_i].conjugate() \ * H_ij * wf_orb[idx_j]).imag However, this code snippet takes about one and a half hours to run. The total number of sites in the system is about 201000. Is there any other way to write the code so that it runs faster? THanks, Harshad

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STM tip as lead
by Eric Mascot 08 Jan '17

08 Jan '17

Hello I was wondering, is it possible to have a lead that hovers above a 2D system? I'm guessing that I have to use a 3D system where the system is in the XY plane and the lead has a translational symmetry in the Z direction. Thanks, Eric

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problem with installing kwant on supercomputer
by Shizeng Lin 04 Jan '17

04 Jan '17

Hi, I try to install kwant on a supercomputer in my institute. I do not have root access, so I built the package from source. I am using python/3.5-anaconda-4.1.1. I installed tinyarray and kwant as a user module, with the following command pip install --user tinyarray/ pip install --user kwant/ The installation completed successfully. But when I try to run the test python -c 'import kwant; kwant.test()' I got the following error message: ========================Error message========================= Traceback (most recent call last): File "/turquoise/users/shizeng/kwant/kwant/__init__.py", line 14, in <module> from . import _system ImportError: cannot import name '_system' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "<string>", line 1, in <module> File "/turquoise/users/shizeng/kwant/kwant/__init__.py", line 22, in <module> raise ImportError(msg) ImportError: Error importing Kwant: You should not try to import Kwant from its source directory. Please exit the Kwant source distribution directory, and relaunch your Python intepreter from there. ==========================End================================= I followed the instruction to launch the test at different directory. but still got the same error message. I am appreciated if someone can help me to figure out the problem. Thanks. Shizeng

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On-site potential only at the edge of the sample in Kwant
by Dongwook Go 03 Jan '17

03 Jan '17

Dear developers, I’m interested in investigating the influence of the edge potential of the sample. For example, in an example by tutorial “quantum_wire.py”, I would like to put on-site potential only at the edge atoms. One could determine whether the site is edge or not by reading the number of neighbors of the site by using “degree”. For example, if the degree is 3 there is an on-site potentials , else 0. Is there any example code from which I can learn to use this function? Best, Dongwook.

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