Mailman 3 January 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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the phase of wave functions
by Fahriye Nur Gursoy Feb. 7, 2016

Feb. 7, 2016

Hello all, My question is about modifying the phase of wave functions. I want to calculate derivative of scattering matrix with respect to energy and they come out to be discontinuous because of the phases. To remedy this I need to modify these phases. Following the suggestion of Anton Akhmerov in this mail group I understood how to modify the phase of modes in the leads. But I also need to change the phase of wave functions in the scattering region to obtain continuous scattering matrices at different energies. I wonder if there is an another way to call wave functions in the scattering region (apart from kwant.solvers.default.wave_function) or a method to modify these phases. Thank you in advance. Nur

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superconducting leads
by anil Feb. 3, 2016

Feb. 3, 2016

Hello, I am trying to how understand how to compute the wavefunctions of a system with superconducting leads as a function of the phase difference, just as in the case of normal leads, using fsys.wave_function() where I would do it as a function of the energy. However, the result is always an empty array. Is there a way to make it work ? Thanks in advance, Anil

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Attaching different atom in vacant sublattice
by james edward hernandez Jan. 26, 2016

Jan. 26, 2016

Hello, I used the tutorial 2.5 for the circular graphene sheet, and in the example, an atom is deleted at sublattice a at (0,0) via del sys [a(0,0)] How can I replace this 'vacancy' with a different atom (with a different hopping parameter, say, 2)? Also, from adding this new atom, do I adjust the hopping in sys using sys[a(-2,1),b(2,2)] = -2 ? Regards James

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GPU speedup via PyCUDA
by Abdulkareem Afandi Jan. 25, 2016

Jan. 25, 2016

Hello, My name is Abdul, a research student, and I’ve been using kwant to simulate transmission in quantum devices. I’ve been thinking about speeding up the process by using GPU matrix operations under PyCUDA or something similar, and was wondering if this would speed things at all? Many systems that I’m studying take hours to calculate transmission, and It would be great if this can be reduced. I appreciate any help, especially with where sparse matrix operations take place in the source code. Kwant is a very useful piece of software, and making it faster would make my life much easier :) Best regards, Abdul Afandi

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(help request) Windows 7 Install:
by Brendan McDougall Jan. 17, 2016

Jan. 17, 2016

Hi Kwant Team, I tried running kwant again, but fail. <SIGH> (I posted this note as a reply to my original post about 48 weeks ago, but wasn't sure that that reply would feed properly. My apologizes if you see this post twice.) My system is Python 2.7.10 | 64-bit | (default, Oct 21 2015, 17:08:47) [MSC v.1500 64 bit (AMD64)] running inside Jupyter Notebook server 4.0.6. on Windows 7 Professional 64 bit OS. Here are versions of relevant libraries that are running: kwant==1.1.1 nose==1.3.4 numpy==1.9.2 scipy==0.16.1 six==1.10.0 tinyarray==1.1.0 matplotlib==1.5.1 Except for nose and kwant, I validated functionality of all packages within the Jupyter notebook. I validated that nose is operable from a shell. The surprising thing to me is that tinyarray worked. After executing jupyter notebook --matplotlib=inline from my kwant directory, I execute "import kwant". I receive the following output: --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-2e77c8a8f09d> in <module>() ----> 1 import kwant C:\Users\Brendan\AppData\Local\Enthought\Canopy\User\lib\site- packages\kwant\__init__.py in <module>() 30 31 for module in ['system', 'builder', 'lattice', 'solvers', 'digest', 'rmt']: ---> 32 exec 'from . import {0}'.format(module) 33 __all__.append(module) 34 <string> in <module>() C:\Users\Brendan\AppData\Local\Enthought\Canopy\User\lib\site- packages\kwant\lattice.py in <module>() 17 import tinyarray as ta 18 from . import builder ---> 19 from .linalg import lll 20 from ._common import ensure_isinstance 21 C:\Users\Brendan\AppData\Local\Enthought\Canopy\User\lib\site- packages\kwant\linalg\__init__.py in <module>() 8 9 __all__ = ['lapack'] ---> 10 from . import lapack 11 12 # Merge the public interface of the other submodules. ImportError: DLL load failed: The specified module could not be found. I did check the site-package and compare it to the github version. I couldn't find an issue. Thanks for your help and best regards. Brendan McDougall PS: in the event that a complete package list is useful, I append here. -registry-path==1.0 appinst==2.1.5 apptools==4.3.0 atom==0.3.9 backports-abc==0.4 backports.ssl-match-hostname==3.2a3 Canopy==1.6.1 canopy-dashboard==0.4.2 canopy-packman-plugin==0.1.3 canopy-platform==0.8.0b1 CanopyDebugger==0.1.2.dev0 casuarius==1.1 certifi==2015.11.20.1 chaco==4.5.0 click==4.0 cloud==2.4.6 configobj==5.0.6 cycler==0.9.0 decorator==4.0.4 distribute-remove==1.0.0 Django==1.9.1 docutils==0.12 enable==4.5.1 enaml==0.9.8 enapp==1.0.0 enclosure==0.2 encore==0.6.0 enstaller==4.8.10 envisage==4.4.0 esky==0.9.8 etsproxy==0.1.2 Examples==7.3 faulthandler==2.4 feedparser==5.2.0 futures==2.2.0 grits-client==0.1 hatcher==0.8.7 idle==2.7.3 ipykernel==4.2.0 ipyparallel==4.1.0 ipython==4.0.0 ipython-genutils==0.1.0 ipython4==4.0.1 ipywidgets==4.1.1 jigna==0.9.5 Jinja2==2.8 jsonpickle==0.4.0 jsonschema==2.4.0 jupyter==1.0.0 jupyter-client==4.1.1 jupyter-console==4.0.3 jupyter-core==4.0.6 kernmagic==0.2.0 keyring==4.0 kiwisolver==0.1.3 kwant==1.1.1 libsodium==1.0.3 MarkupSafe==0.23 matplotlib==1.5.1 mistune==0.7.1 MKL==10.3 mysqlclient==1.3.7 nbconvert==4.1.0 nbformat==4.0.1 nose==1.3.4 notebook==4.0.6 numpy==1.9.2 okonomiyaki==0.9.0 pandas==0.17.1 path.py==8.1.1 pickleshare==0.5 PIL-remove==1.0.0 pillow==3.0.0 ply==3.8 psutil==2.2.1 pyaudio==0.2.4 pycrypto==2.6.1 pyface==5.0.0 pyflakes==0.4.5 pyglet==1.1.4 Pygments==2.0.2 pyparsing==2.0.3 pyreadline==2.1 PySide==1.2.2 python-dateutil==2.4.2 PythonDoc==2.7.3 pytz==2015.7 pywin32==219.0.0 PyYAML==3.11 pyzmq==15.1.0 qtconsole==4.1.1 requests==2.9.0 scipy==0.16.1 seaborn==0.6.0 shiboken==1.2.2 simplegeneric==0.8.1 singledispatch==3.4.0.3 six==1.10.0 ssl-match-hostname==3.4.0.2 supplement==0.5.dev0 sympy==0.7.6.1 tabulate==0.7.3 tinyarray==1.1.0 tornado==4.3 traitlets==4.0.0 traits==4.5.0 traitsui==5.0.0 virtualenv==13.1.2 wxPython==3.0.2.0 zeromq==4.1.3 zipfile2==0.0.8

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New instructions for Windows installation
by Michael Wimmer Jan. 15, 2016

Jan. 15, 2016

Dear kwant users, we have posted new instructions for installing kwant on Windows on the kwant website: http://www.kwant-project.org/install The old instructions do not work any more, as the format of the python packages on Christoph Gohlke's webpage have changed. Best regards, the kwant team

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Green's function for each block
by Sumit Ghosh Jan. 13, 2016

Jan. 13, 2016

I am trying to calculate the Green's function for each layer/slice of a ribbon/wire. I can find the self energy and surface Green's function from which (in principle, I have not tried yet) it is possible find the Green's function for successive layer using RGF algorithm as discussed in this thread (http://thread.gmane.org/gmane.comp.science.kwant.user/647). >From the GreensFunction documentation, it looks like there is a way to specify the slice/block of the system and directly find the Green's function, but I don't find any example of that. Is there any way to do that ? ( http://kwant-project.org/doc/1/reference/generated/kwant.solvers.common.Gre… ) For example consider this graphene ribbon. I added a random impurity to break the translational symmetry so that I can distinguish each slice. I can find the Green's function for the sites which are connected to leads only. How do I calculate the Green's function for each slice? Best, Sumit ------------------------------------------------------ from __future__ import division from math import sqrt from matplotlib import pyplot import kwant import numpy as np sin_30, cos_30 = (1 / 2, sqrt(3) / 2) graphene = kwant.lattice.general([(1, 0), (sin_30, cos_30)], [(0, 0), (0, 1 / sqrt(3))]) a, b = graphene.sublattices L=3;W=3; def box(pos): #scattering region x, y = pos return -L<x<L and -W<y<W def lshape(pos): #lead x,y = pos return -W<y<W def onsite(site): return kwant.digest.uniform(repr(site)) hoppings = (((0, 0), a, b), ((0, 1), a, b), ((-1, 1), a, b)) def scater(): sys = kwant.Builder() sys[graphene.shape(box, (0, 0))] = onsite sys[[kwant.builder.HoppingKind(*hopping) for hopping in hoppings]] = -1 lead = kwant.Builder(kwant.TranslationalSymmetry(graphene.vec((-1, 0)))) lead[graphene.shape(lshape, (0, 0))] = 0 lead[[kwant.builder.HoppingKind(*hopping) for hopping in hoppings]] = -1 sys.attach_lead(lead) sys.attach_lead(lead.reversed()) return sys sys=scater() #def family_colors(site): # return 0 if site.family == a else 1 #kwant.plot(sys, site_color=family_colors, site_lw=0.1, colorbar=False) sys = sys.finalized() # Self energy flead0 = sys.leads[0] flead1 = sys.leads[1] s_en = flead0.selfenergy(0.5) #Green's function g = kwant.greens_function(sys,0.5) gg = g.submatrix(1,0) -- 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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what does ldos compute?
by Sergey Jan. 10, 2016

Jan. 10, 2016

Dear all, sorry for a naive question, but I am confused by ldos function. Two questions: 1) Why it does not work if system has no leads? 2) Imagine I have an infinite homogeneous stripe which I artificially divide into a scattering region and two leads. Why does ldos give different results depending on the length of the scattering region? Is it a numerical error or something physical behind it? Thanks, Sergey

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