Mailman 3 October 2017 - Kwant-discuss

Current in a closed system
by Abbout Adel Oct. 26, 2017

Oct. 26, 2017

Dear All, I was consulting the example of the current in a *closed system* and I am a little bit confused: The figure showing the current flowing inside a circle [1] is obtained for a magnetic field B=0 ! But we know that for B=0, the Hamiltonian is a real symmetric matrix and thus diagonalized by a real orthogonal matrix, so the eigenvectors are real (any phase is just artificial.) By using the formula giving the current we should find zero ! moreover we can ask why we have a current flowing clockwise and not anticlockwise (I remind that B=0) ! When we put B=0.05, we obtain the figures below for the current and the wave function. the wave function has circular symmetry but not the current. Moreover, x and y play exactly the same role so the current should be the same on x and on y (independently from the used gauge) Am I missing something ? Thank you in advance. Adel [1] https://kwant-project.org/doc/1/tutorial/spectrum

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Colorbar doesn't appear
by Luan Vieira de Castro Oct. 26, 2017

Oct. 26, 2017

Dear all, I am trying to plot the current density using the command: kwant.plotter.current(syst, current, cmap = 'spectral_r',linecolor='black', density = 0.5, colorbar = True). However, when the figure is plotted, the colorbar doesn't appear. I know that this is a simple matter, but can someone indicate to me what am I doing wrong? Best Regards, Luan

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Fwd: problems when plotting the current density map
by Duarte José Pereira de Sousa Oct. 26, 2017

Oct. 26, 2017

Dear all, I'm having problems when formatting the current density map of a system. First, the colorbar doesn't appear even when colobar = True in the arguments of kwant.plotter.current. The other problem is related to the line color of the vectorial field. It seems that the program chooses the color corresponding to the intensities of the chosen color palette in each region of the map, even when the argument linecolor = 'certain color' is selected. For example, if I select cmap = 'jet', linecolor = 'black' in the arguments of kwant.plotter.current, the colors of the arrows will change from region to region according to the colors of the pallete instead of being black throughout the map. Is there an easy way to overcome these difficulties without modifying the plotter.py file? Best regards, Duarte José

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indirect hopping
by Chung Tsai Oct. 24, 2017

Oct. 24, 2017

Dear all, Is there a way to implement indirect hopping in Kwant? I have a cubic system and I want to add to the term describing the direct hopping between site i and j, an indirect hopping term via an intermediate site k, for all the sites in my system. I appreciate any help Bests Chung

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Re: [Kwant] Connecting leads of a different lattice type.
by Anton Akhmerov Oct. 20, 2017

Oct. 20, 2017

On Fri, Oct 20, 2017 at 4:45 PM, Dripto Debroy <driptodebroy(a)gmail.com> wrote: > That makes a lot of sense, would I be correct in assuming that I would need > to define new lattices for each of the rows of square matrices before adding > the hoppings by hand? You only need to define two lattices: one honeycomb, and one square for the lead. Best, Anton > > Much appreciated. > Dripto > > On Oct 20, 2017 5:52 AM, "Anton Akhmerov" <anton.akhmerov+kd(a)gmail.com> > wrote: >> >> Hi Dripto, >> >> The correct approach to implement that is to do the following: >> 1. add a sufficient number of sites from the square lattice to the >> scattering region, so that the lead may be attached to those (this >> should amount to 1 unit cell of the lead). >> 2. manually connect those sites to the honeycomb lattice. Since there >> are too many possibilities to do so, there's no way to make this >> choice automatically. >> 3. attach the lead as usual using Builder.attach_lead. >> >> Best, >> Anton >> >> On Thu, Oct 19, 2017 at 8:31 PM, Dripto Debroy <driptodebroy(a)gmail.com> >> wrote: >> > Hello all, >> > >> > I am hoping to use KWANT to model a graphene flake with two metal leads. >> > The >> > issue I am running in to is figuring out how to connect leads which have >> > a >> > square lattice and graphene which has a honeycomb lattice. Is this >> > something >> > that KWANT can handle? I was unable to find any documentation on mixing >> > lattice types and modeling heterojunctions in general. >> > >> > Thanks for your help, >> > Dripto

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Connecting leads of a different lattice type.
by Dripto Debroy Oct. 20, 2017

Oct. 20, 2017

Hello all, I am hoping to use KWANT to model a graphene flake with two metal leads. The issue I am running in to is figuring out how to connect leads which have a square lattice and graphene which has a honeycomb lattice. Is this something that KWANT can handle? I was unable to find any documentation on mixing lattice types and modeling heterojunctions in general. Thanks for your help, Dripto

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Importing Hamiltonian from file
by Marta Brzezińska Oct. 18, 2017

Oct. 18, 2017

Good afternoon, starting from a tight-binding Hamiltonian saved in external file, how can I import the full matrix to Kwant in order to perform transport calculations? Best regards, Marta Brzezinska

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Mistake on the docstring of `PropagatingModes` ?
by George Datseris Oct. 17, 2017

Oct. 17, 2017

Dear All, (thanks so much for kwant ;) ) I am wondering whether there is a mistake/typo in the docstring of the PropagatingModes object. The reason is the following: In a simple lead (specifically graphene zigzag nanoribbon) at energy that excites 6 modes (only 3 with positive derivative dE/dk), when getting the `PropagatingModes` (either through physics.modes or by the Smatrix), and I get the momenta and velocities, it looks like this: In [35]: modes Out[35]: <kwant.physics.leads.PropagatingModes at 0x2139805ecf8> In [36]: modes.momenta Out[36]: array([-2.12874239, 2.0566145 , 2.06992722, 2.12874239, -2.0566145 , -2.06992722]) In [37]: modes.velocities Out[37]: array([-1.91098658, -2.24527103, -1.66541483, 1.91098658, 2.24527103, 1.66541483]) Now, the docstring of Propagating modes states: > The first half of the > modes have negative velocity, the second half have positive velocity. The > modes with negative velocity are ordered from larger to lower momenta, the > modes with positive velocity vice versa. However, this is not what I see. The first half, with negative velocity, is clearly sorted from smaller to bigger momenta, while the second half (with positive velocity) is sorted from bigger to slower momenta. This is the exact opposite of the docstring. Thus I am writing this mail to see if I have misunderstood something or if this is simply a typo mistake. Best, George

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About the KPM method
by kuangyia lee Oct. 9, 2017

Oct. 9, 2017

Dear Anton and other Kwant users, I am currently using the KPM method to calculate the density of states: spectrum = kwant.kpm.SpectralDensity(fsyst) dos = spectrum(energies) In the tutorial, this method is successfully applied to calculate the dos of a large closed system. But I am wondering that here it can also be applied to the case of an open system (i.e., a system composed of scattering region and leads). Thanks a lot ! Best regards, Kuangyia

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Re: [Kwant] 2D Current Density Streamplot of 3D System
by mitchell.greenberg Oct. 9, 2017

Oct. 9, 2017

Hi Joseph and Anton, Today I had a talk with my supervisor and he wondered if it was possible to plot the raw current data before interpolation, just to see how current travels through each of the hoppings. From previous questions I know that the current array returned from J0 (psi) is in the same from as the system graph, however I was wondering if there was a simple way to plot this array to see the current vectors at each site position. Sorry if this question is naive. Thank You, Mitchell Greenberg Sent from Samsung Mobile <div>-------- Original message --------</div><div>From: "mitchell.greenberg" <mitchell.greenberg(a)my.jcu.edu.au> </div><div>Date:17/09/2017 7:32 PM (GMT+10:00) </div><div>To: Anton Akhmerov <anton.akhmerov+kd(a)gmail.com> </div><div>Cc: kwant-discuss(a)kwant-project.org </div><div>Subject: Re: [Kwant] 2D Current Density Streamplot of 3D System </div><div> </div>This sender failed our fraud detection checks and may not be who they appear to be. Learn about spoofing Feedback Hi Anton, Thanks for that. While my lattice is polyatomic I just switched site.pos to site.tag in the code I posted last message to get the tags for my lattice. Doing that I see the tags for the z axis range from 0 to 9 (makes sense as I have 10 layers), which explains why 5.3 worked when I used it but not 10. My function runs now an accurately deletes the sites without any problems. Thank You, Mitchell Greenberg Sent from Samsung Mobile -------- Original message -------- From: Anton Akhmerov Date:17/09/2017 5:11 AM (GMT+10:00) To: Mitchell Greenberg Cc: Joseph Weston ,kwant-discuss(a)kwant-project.org Subject: Re: [Kwant] 2D Current Density Streamplot of 3D System Hi Mitchel, Deleting and adding sites is done by their lattice coordinates (site.tag), not their real space position (site.pos); if you want to access a site close to a certain position, you can use the method Monatomic.closest (see https://kwant-project.org/doc/1/reference/generated/kwant.lattice.Monatomic…). Best, Anton On Sat, Sep 16, 2017 at 2:34 PM, Mitchell Greenberg <mitchell.greenberg(a)my.jcu.edu.au> wrote: > Hi Joseph and Anton, > > > Thank you for the advice with getting the 2d graph up and running, its now > producing results that look good. Sorry that I haven't replied in over 2 > weeks, uni has gotten into full swing. > > > I wasn't sure if I needed to start a new topic for this (if I need to let me > know) but I am now trying to remove lattice points randomly from my sample. > I have created a function that can remove random lattice points (it is > rather messy) however I have noticed that when I try to delete sites for > layers other than at z=0 and z=5.3 I get the following error.: > > > KeyError: Site(kwant.lattice.Monatomic([[4.3763, 0.0, 0.0], [0.0, 3.3136, > 0.0], [0.0, 0.0, 5.3]], [0.0, 0.0, 0.0], '0', 1), array([50, 50, 10])) > > > This error seems to pop up when I try to delete a site that doesn't exist at > the specified coordinates however when I use: > > Positions=[syst.sites[i].pos for i in range(len(syst.sites))] > > > I see that sites definitely exist for z=10 (should be 10.6 but the error > output seems to round). I was therefore wondering if there is something I am > missing when it comes to deleting sites and if there is an easy way to > delete random sites from a 3d sample. > > > Thank You, > > Mitchell Greenberg > > > ________________________________ > From: Joseph Weston <joseph.weston08(a)gmail.com> > Sent: Wednesday, August 30, 2017 8:33:01 PM > To: Mitchell Greenberg; kwant-discuss(a)kwant-project.org > Subject: Re: [Kwant] 2D Current Density Streamplot of 3D System > > Hi Mitchell, > >> Sorry again for the reply, I've had a look at the documentation and it >> seems that relwidth and abswidth control the size of the arrays. What >> I'm stuck on though is that my system has L = 80, W = 450 and H =52, >> I was expecting field to return something of the form (80,450,52,3), I >> must apologise again, I'm pretty new to all things python so my >> knowledge in the more complex areas is lacking. > > The input to 'interpolate_current' is a current defined on the hoppings > of your system. The output is a current defined over a realspace grid. > First the current defined on the hoppings is convoluted with a bump > function to smooth it out, then the resulting continuous vector field is > sampled on a regular grid. The docstring explains how this is done. The > interpolation grid does not in general coincide with the "grid" of sites > that form your system. Typically there will be several interpolation > points between neighboring sites. > > The 'box' returned by 'interpolate_current' allows you to calculate the > realspace position of the interpolation points. > > Also the modifications to 'interpolate_current' so that it functions > correctly for 3D systems just landed on the most recent development > version of kwant [1]. > > > Happy Kwanting, > > Joe > > > [1]: > https://gitlab.kwant-project.org/kwant/kwant/commit/be364e7c64c316caf86869d… > >

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