Mailman 3 March 2017 - Kwant-discuss

How the spin is positioned in the Smatrix?
by Qingtian Zhang 06 Mar '22

06 Mar '22

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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Spin polarized transport calculation
by L.M J 06 Mar '22

06 Mar '22

Dear Kwant users and developers I have two questions related to the spin calculation using kwant. 1. I'm wondering if we can do spin-polarized transport in kwant? For example, can we can get the separate Conductance Vs Energy diagram for spin up and spin down terms. I'm thinking one way of doing this is to set up the Rashba Hamiltonian as a whole. And then manually extract the spin up and spin down hamiltonian and do the transport calculation separately. But this will eliminate some extra terms that I don't know whether this is correct anymore. Any suggestions? 2. How can we set up the spin polarization for a particular site? For example, in some of the topological insulator, can we set up spin polarization on the edge as up and the other side of the edge as down, and then do the transport? Or this question is completely wrong? Thanks for advance. Sincerely, Liming

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How to caculate hall resistance
by ZHANG Bing 12 Sep '21

12 Sep '21

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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lead_info
by Prof. CHAN Kwok Sum 20 Sep '17

20 Sep '17

Dear Kwant developer, Thank you for your effort in developing Kwant. I have a question about the definition of the direction of momentum in the smatrix.lead_info. Assume a lead lies along the y direction with primitive vector (0,1). The symmetry operation of a lead is (0,1) if the lead goes towards the positive direction and is (0,-1) if the lead goes towards the negative direction. For the momenta contained in smatrix.lead_info for these two leads , do they use the same coordinate system? Positive momenta mean the direction (0,1), negative momenta mean the direction (0,-1). For velocity, in smatrix.lead_info, it has nothing to do with the coordinate system. Positive means outgoing, negative means incoming in the lead. Thank you KS Chan 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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forking smatrix.transmission
by Sergey Slizovskiy 31 Mar '17

31 Mar '17

Dear all, I have tried a primitive forking of kwant computation with joblib package. This worked well for bands computation, here's the code, but it fails for smatrix.transmission. I would be grateful for any hints and examples. Thank you, Sergey from joblib import Parallel, delayed def plot_bandstructure(flead, momenta, args, max=0.05): global processors switch=False cutoff=0.001 bands = kwant.physics.Bands(flead, args=args) energies = Parallel(n_jobs=processors)(delayed(bands)(k) for k in momenta) pyplot.figure() pyplot.plot(momenta, energies) pyplot.ylim([-max,max]) pyplot.xlabel("momentum [(lattice constant)^-1]") pyplot.ylabel("energy [t]") pyplot.show(block=False) def transm(sys, energy, lead1,lead2,args): print("Smatrix for energy ", energy) smatrix = delayed(kwant.smatrix)(sys, energy,args=args) return smatrix.transmission(lead1, lead2) def plot_conductance(sys, lead1,lead2, energies,args,label): # Compute transmission as a function of energy global processors data = Parallel(n_jobs=processors)(delayed(transm)(sys, energy,lead1, lead2, args=args) for energy in energies) print(data) pyplot.figure() pyplot.plot(energies, data) pyplot.xlabel("energy [t]") pyplot.ylabel("conductance [e^2/h]") pyplot.title(label) return data

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Query for Kwant Software
by Biswadeep Upadhyay 30 Mar '17

30 Mar '17

Respected Sir, It's Biswadeep Upadhyay from India. I'm a engineering student recently studying in 3rd year. I'm pursuing a study of Nano Device under the guidance of my professor specialized in Electronic devices. In that regard I consistently use the Kwant software. Recently my area of focus is Carbon Nano Tubes(CNTs). I have done several simulations on 2D structures earlier with ease. But I have question can i simulate CNTs using Kwant. More precisely will I be able to solve CNT related problem using Kwant ; for example to plot the system , band structure, plot of conductance. So I request you to have a look upon my query and enlighten me in this regard. Your active operation is highly solicited. Regards, Biswadeep

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transmission through a barrier of zero height
by Jambulat Basaev 29 Mar '17

29 Mar '17

Hi Everyone! I want to solve basic problem of transmission of electron through a potential barrier without taking into account any effects contacts. But the influence of leads in all the examples provided in kwant documentation definitely exists. For example, in the quantum wire case leads are set the same way as the scattering region, that why I expect the transmission should be obtained identically one (for any energy of incident electron). This means that kwant takes into account also some regions outside the leads e.g. bulk metal contacts. Also I modified the quantum well example like this: def plot_transmission(syst, energies, welldepth): data = [] for energy in energies: smatrix = kwant.smatrix(syst, energy, args=[-welldepth]) data.append(smatrix.transmission(1, 0)) data = np.array( data ) pyplot.figure() pyplot.plot(energies, data) pyplot.xlabel("Energy [t]") pyplot.ylabel("Transmission") pyplot.show() and in the main function make a call plot_transmission(syst, [0.01 * i for i in range(1,100)], 0.0) As a result some dependence on E is obtained even for the case of zero depth of the potential whell and it is not identically one. So, is it possible to obtain in Kwant the transmission coefficient through the defined in the scattering region structures which is not affected by anything else? Sincerely, Jambulat Basaev

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Using args in hamiltonian-function
by Camilla Espedal 27 Mar '17

27 Mar '17

Dear Kwant team, (am using the development version, 1.3) I am trying to plot the potential of my system and I want to use the hamiltonian(ind,ind,*args) function, but I don't understand how to use the args. Normally, I would give a vector with the values of the args as input, but this doesn't work in the case of hamiltonian (it does with hamiltonian_submatrix). What am I doing wrong? I also have a problem using the kwant.plot(sys) after I switched to Linux, I get the error message "NameError: name 'mplot3d' is not defined", is there something I need to install? Sincerely, Camilla

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function for current density calculation
by Prof. CHAN Kwok Sum 26 Mar '17

26 Mar '17

In the discussion thread about calculation of current density, it is mentioned for the function defined for current as follows only work for 1 orbital per site. Does the expression work for system with spin? I guess the Hamiltonian matrix element for sites I and j will be a matrix for a system with spin and the wavefunction for a site is a vector. If this is the case, the function still works for systems with spin degree of freedom (or other internal degree of freedom) Ks chan def current(psi): H_ij = sys.hamiltonian(i, j, args=(B,)) return -2 * (psi[i].conjugate() * H_ij * psi[j]).imag 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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transmission though a barrier of zero height
by Вячеслав Семененко 23 Mar '17

23 Mar '17

Hi Everyone! I want to solve basic problem of transmission of the electron through a potential barrier without taking into account any effects contacts. But the influence of leads in all the examples provided in kwant documentation definitely exists. For example, in the quantum wire case leads are set the same way as the scattering region, that why I expect the transmission should be obtained identically zero. This means that kwant takes into account also some regions outside the leads e.g. bulk metal contacts. Also I modified the quantum well example like this: def plot_transmission(syst, energies, welldepth): data = [] for energy in energies: smatrix = kwant.smatrix(syst, energy, args=[-welldepth]) data.append(smatrix.transmission(1, 0)) data = np.array( data ) pyplot.figure() pyplot.plot(energies, data) pyplot.xlabel("Energy [t]") pyplot.ylabel("Transmission") pyplot.show() and in the main function make a call plot_transmission(syst, [0.01 * i for i in range(1,100)], 0.0) As a result some dependence on E is obtained even for the case of zero depth of the potential whell and it is not identically zero. So, is it possible to obtain in Kwant the transmission coefficients through the defined in the scattering region structures which is not affected by anything else? Sincerely, Jambulat

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periodic boundary conditions on the lead
by Sergey Slizovskiy 21 Mar '17

21 Mar '17

Dear Colleagues, There has already been a discussion on this subject back in 2014, (https://www.mail-archive.com/kwant-discuss@kwant-project.org/msg00124.html) but I am not quite sure I understand the proper solution. I made a lead with rectangular unit cell and naive attempt to make periodic boundary conditions gives a error: "Further-than-nearest-neighbor cells are connected by hopping". The only solution I can think of, is to introduce an auxiliary 1-D lattice made of the atoms along the edge and introduce hopping from this 1D chain to the edge atoms of 2D lead. Hope it will work. Are there any better solutions? Thanks, Sergey

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lead periodic boundary conditions
by Sergey Slizovskiy 20 Mar '17

20 Mar '17

Dear all, Can anyone send an example of setting periodic boundary conditions on a lead, please. E.g. on a simplest square lattice. Is defining a long unit cell the only solution? Thanks, Sergey

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How to reduce memory requirement
by Li Mingkai 16 Mar '17

16 Mar '17

Dear all, I try to build a bulk transport system with periodic boundary condition by 40 * 40 * 40 sites. It requests over 2 GB memory during transmission calculation. I curious why it produces so large memory requirement. Since I'm going to expand the system up to 50 times, I want to know any way to reduce the memory requirement and increase calculation speed. I'm using kwant 1.1.2 and MUMPS with default PORD ordering. The system building code is syst = kwant.Builder(kwant.TranslationalSymmetry(lat.vec((0, cube.NY, 0)), lat.vec((0, 0, cube.NZ)))) for i in range(cube.NX): for j in range(cube.NY): for k in range(cube.NZ): syst[(lat(i, j, k))] = -cube.data[i, j, k] + 6 * t syst[lat.neighbors(1)] = -t lead = kwant.Builder(kwant.TranslationalSymmetry(lat.vec((-1, 0, 0)), lat.vec((0, cube.NY, 0)), lat.vec((0, 0, cube.NZ)))) lead[lat.shape(lead_shape, (0, 0, 0))] = 6 * t lead[lat.neighbors(1)] = -t syst=wraparound(syst) syst.attach_lead(wraparound(lead,keep=0)) syst.attach_lead(wraparound(lead,keep=0).reversed()) -- Mingkai Li

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update Kwant to newer versions.
by Prof. CHAN Kwok Sum 16 Mar '17

16 Mar '17

Dear Kwant developers, I have a version of Kwant 1.02 installed for python 2.7 in a window computer. If I want to update it, do I need to uninstall it? Or Just download the new version and install the new version using the python 2.7. What happens if I want to change it to python 3.X, do I need to uninstall the python 2.7 and all the old Kwant? KS Chan 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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updation to Kwant 1.3
by kamal ghosh 15 Mar '17

15 Mar '17

Dear Kwant Developers, We use Kwant 1.2.2 in the background of Python 3.4. We now understand that the Kwant package is updated to 1.3. The Kwant official website (https://kwant-project.org/install) recommends to download the packages from the website of Christoph Gohlke (http://www.lfd.uci.edu/~gohlke/pythonlibs/). But we are unable to find the updated Kwant package in the site mentioned above. Please help to solve the matter. Regards. Dr. K.K.Ghosh

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Graphene band structure with more than 3 nearest-neighbors
by Juan Manuel Marmolejo-Tejada 14 Mar '17

14 Mar '17

Hi, I have been trying to get band structure for graphene with more than 3 nearest-neighbors using the following: graphene = kwant.lattice.general([[1, 0], [1/2, np.sqrt(3)/2]], # lattice vectors [[0, 0], [0, 1/np.sqrt(3)]]) # Coordinates of the sites a, b = graphene.sublattices zigzag_ribbon = kwant.Builder(kwant.TranslationalSymmetry([1, 0])) zigzag_ribbon[graphene.shape((lambda pos: abs(pos[1]) < 9), (0, 0))] = 0 zigzag_ribbon[graphene.neighbors(1)] = 1 zigzag_ribbon[graphene.neighbors(2)] = 0.2 zigzag_ribbon[graphene.neighbors(3)] = 0.18 zigzag_ribbon[graphene.neighbors(4)] = 0.1 kwant.plot(zigzag_ribbon); kwant.plotter.bands(zigzag_ribbon.finalized()); When I plot the system, I see the hoppings have been added successfully, but the band structure calculation returns the following error: ValueError: Further-than-nearest-neighbor cells are connected by hopping Can you please give me some advice on how to fix this error? Thanks for your help, Juan Marmolejo

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problem with the wave_function calculation
by Luan Vieira de Castro 13 Mar '17

13 Mar '17

Dear Kwant team and community, I am trying to calculate the current density for a infinite system with kwant and, therefore, I have to use the the kwant.wave_function function. However, I always get a different result when I use this function, for example, with wf = kwant.wave_function(sys, energy=E), wf(0)[0][0] always gets a different value for every time I run my code. Am I misunderstanding the meaning of this function? Regards, Luan

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Re: [Kwant] Transport across infinite plane with wraparound module
by Li Mingkai 10 Mar '17

10 Mar '17

Hi Kristjan, I'm working on 3D periodic boundary problem recently. Your code really helps me a lot. I tested your code. It seems working with nanowire leads instead of a periodic repeat in y direction. I changed the leads setting a little as following. A translational symmetry along y direction was added on lead. Then wraparound it with keep=0 lead = kwant.Builder(kwant.TranslationalSymmetry((-a, 0),lat.vec((0, W)))) lead[(lat(0,j) for j in range(W))] = 4*t lead[lat.neighbors(1)] = -t sys.attach_lead(wraparound(lead,keep=0)) sys.attach_lead(wraparound(lead,keep=0).reversed()) It seems working as a periodic boundary condiction. I judge it by settiing all potential to 0 in the scatting region. Then the tramsmittion with energy above 0 should be 1. Without above changes, the transmission at a little positive energy is 0 and the it will jump to 1 at a little higher energy. It implies the transversal energy quantization. I tested the ky under the above flat potential condition. The period of ky is 2Pi instead of 2Pi/L. I don't know why. Maybe some expert can explain it. Anyway, I'm just a newbie with kwant and trying to solve some bulk problem with it. I'm not sure about the above opinion. Let's discuss and figure out how it works in peroidic boundary condiction. -- Mingkai Li

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Problems with memory allocation (?) in KWANT 1.3
by Camilla Espedal 10 Mar '17

10 Mar '17

Dear KWANT team, I am currently trying to write a program to try to calculate the spin Hall angle in a 4-terminal normal metal using Kwant 1.3 and the conservation law module. The scattering region is a square 40x40. I run in to a problem when trying to run it. The error message I get is: *** Error in `python3': malloc(): memory corruption: 0x00000000034f0de0 *** ======= Backtrace: ========= and then a bunch of stuff, and in the end [Finished in 29.6s with exit code -6] It seems to crash when I make the system too big or for too many energies. But, I don't understand why it doesn't work to solve the problem at one energy, store the result (which is just one number), and then for another. It seems the results from the other runs are somehow stored? I am not that experienced when it comes to programming, so I don't know if the problem is at my end or not. Thanks in advance, Camilla ------------------------------ Here is my code as well: import kwant import tinyarray as ta import numpy as np from scipy import sparse import matplotlib from matplotlib import pyplot s0 = ta.array([[1, 0], [0, 1]]) sx = ta.array([[0, 1], [1, 0]]) sy = ta.array([[0, -1j], [1j, 0]]) sz = ta.array([[1, 0], [0, -1]]) def calculate_sh_conductance(smatrix, leadIn, leadOut): con = -smatrix.transmission((leadOut, 0),(leadIn, 0)) + smatrix.transmission((leadOut, 1),(leadIn, 1)) return con def make_system(t=1.0, W=40, L=40, lead_W = 40): # Now we must specify the number of orbitals per site. lat = kwant.lattice.square(norbs=2) syst = kwant.Builder() """ We define the system below. The s-parameters are site parameters. The onsite has 1 site-parameter, while the hopping has two. The form of the functions must be like this, because Kwant requires it. """ syst[(lat(x, y) for x in range(L) for y in range(W))] = \ lambda s, alpha, phi: 0*4 * t * s0 # The last term here is the AF onsite coupling. syst[kwant.builder.HoppingKind((1, 0), lat, lat)] = \ lambda s1, s2, alpha, phi: -t * s0 - 1j * alpha * sy syst[kwant.builder.HoppingKind((0, 1), lat, lat)] = \ lambda s1, s2, alpha, phi: -t * s0 + 1j * alpha * sx ### Make the leads ### # Side leads lead = kwant.Builder(kwant.TranslationalSymmetry((-1, 0)), conservation_law=-sz, time_reversal=s0) lead[(lat(0, j) for j in range(W))] =0* 4 * t * s0 lead[lat.neighbors()] = -t * s0 # Note: no spin-orbit in the lead. # Top/bottom leads lead_tb = kwant.Builder(kwant.TranslationalSymmetry((0,-1)), conservation_law =-sz, time_reversal=s0) # We define the start and end fo the lead start = int(L/2 - lead_W/2) end = int(L/2 + lead_W/2) lead_tb[(lat(j,0) for j in range(start,end))] = 0*4 * t * s0 lead_tb[lat.neighbors()] = -t * s0 syst.attach_lead(lead) syst.attach_lead(lead.reversed()) syst.attach_lead(lead_tb) syst.attach_lead(lead_tb.reversed()) syst = syst.finalized() return syst def main(): syst = make_system(t=1.0, W=40, L=40, lead_W = 40) energies = np.linspace(-4,4, 200) socos = 0.5 fig = pyplot.figure(figsize=(13,8)) ax = fig.add_subplot(1, 1, 1) print("Starting spin calculation") conductance = [] # Calculate spin Hall conductance for energy in energies: smatrix= kwant.smatrix(syst, energy=energy, args=(socos, 0)) addi = calculate_sh_conductance(smatrix, 0, 3) conductance.append(addi) print(energy) ax.plot(energies, conductance, label="SOC %s" % socos) ax.legend(fontsize='x-large'); pyplot.show() if __name__ == '__main__': main()

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(no subject)
by enrique colomes 09 Mar '17

09 Mar '17

Hello, My name is Enrique and first of all, thanks for the developping of such a useful tool. My question is related to that one of the edge potentials. I am trying to reproduce the Haldane model with disorder in a rectangular scattering region. My goal is to introduce edge disorder as well as compute the local current density. I have two problems: a) Regarding the edge disorder, I cannot remove the disorder in the edges with the leads (I saw your recent previous discussion) b) Is it possible already to compute directly from Kwant the local current density? If yes, how? Thanks again, Enrique from __future__ import division # so that 1/2 == 0.5, and not 0 from scipy.sparse import spdiags from math import pi, sqrt, tanh, e import numpy as np import kwant import random import math # For computing eigenvalues import scipy.sparse.linalg as sla # For plotting from matplotlib import pyplot # Define the graphene lattice graphene = kwant.lattice.honeycomb() a, b = graphene.sublattices edge_potential=10 def make_system(L=10, W=10, pot=0.001): t=1 tt= 0.04 * t phi=1*pi/2 edge=1 # 1 if there is edge disorder bulk=0 # 1 if there is bulk disorder nnn_hoppinga=tt*e**(1j*phi) nnn_hoppingb=tt*e**(1j*phi) #### Define the scattering region. #### def rec(pos): x, y = pos return 0 < x < L and 0 < y < W sys = kwant.Builder() # w: width and pot: potential maximum of the p-n junction def potential(site): (x, y) = site.pos d = y * 2 + x * 3 return 0 sys[graphene.shape(rec, (1, 1))] = potential # specify the hoppings of the graphene lattice nn_hoppings = (((0, 0), a, b), ((0, 1), a, b), ((-1, 1), a, b)) nnn_hoppings_a = (((-1, 0), a, a), ((0, 1), a, a), ((1, -1), a, a)) nnn_hoppings_b = (((1, 0), b, b), ((0, -1), b, b), ((-1, 1), b, b)) sys[[kwant.builder.HoppingKind(*hopping) for hopping in nn_hoppings]] = -t sys[[kwant.builder.HoppingKind(*hopping) for hopping in nnn_hoppings_a]] = -nnn_hoppinga sys[[kwant.builder.HoppingKind(*hopping) for hopping in nnn_hoppings_b]] = -nnn_hoppingb # Modify the scattering region if edge==1: # change the values of the potential at the edge for site in sys.expand(graphene.shape(rec, (0, 1))): if sys.degree(site)<=9 and abs(site.pos[0])!=L-4: #abs(site.pos[0])!=19 execludes the interfaces with the leads sys[site]=edge_potential elif bulk==1: # change the values of the potential at the edge for site in sys.expand(graphene.shape(rec, (0, 1))): if sys.degree(site)==9 and abs(site.pos[0])!=19: #abs(site.pos[0])!=19 execludes the interfaces with the leads sys[site]=edge_potential #### Define the leads. #### # left lead sym0 = kwant.TranslationalSymmetry(graphene.vec((-1, 0))) sym0.add_site_family(graphene.sublattices[0], other_vectors=[(-1, 2)]) sym0.add_site_family(graphene.sublattices[1], other_vectors=[(-1, 2)]) def lead0_shape(pos): x, y = pos return (0 < y < W) lead0 = kwant.Builder(sym0) lead0[graphene.shape(lead0_shape, (0, 0))] = -pot lead0[[kwant.builder.HoppingKind(*hopping) for hopping in nn_hoppings]] = -t lead0[[kwant.builder.HoppingKind(*hopping) for hopping in nnn_hoppings_a]] = -nnn_hoppinga lead0[[kwant.builder.HoppingKind(*hopping) for hopping in nnn_hoppings_b]] = -nnn_hoppingb # right lead sym1 = kwant.TranslationalSymmetry(graphene.vec((1, 0))) sym1.add_site_family(graphene.sublattices[0], other_vectors=[(-1, 2)]) sym1.add_site_family(graphene.sublattices[1], other_vectors=[(-1, 2)]) def lead1_shape(pos): x, y = pos return (0 < y < W) lead1 = kwant.Builder(sym1) lead1[graphene.shape(lead1_shape, (0, 0))] = pot lead1[[kwant.builder.HoppingKind(*hopping) for hopping in nn_hoppings]] = -t lead1[[kwant.builder.HoppingKind(*hopping) for hopping in nnn_hoppings_a]] = -nnn_hoppinga lead1[[kwant.builder.HoppingKind(*hopping) for hopping in nnn_hoppings_b]] = -nnn_hoppingb sys.attach_lead(lead1) sys.attach_lead(lead0) return sys # Call the main function if the script gets executed (as opposed to imported). if __name__ == '__main__': main()t.show() def main(): sys = make_system() # Check that the system looks as intended. def family_color(site): #print(sys[site]) if sys[site]==edge_potential: return 'green' else: return 'black' def site_size(site): if sys[site]==edge_potential: return 0.35 else:return 0.2 kwant.plot(sys,site_color=family_color,site_size=site_size) # Finalize the system. sys = sys.finalized() # Compute number of neighbors i=sys.sites.index(graphene(5,6)) all_the_neighbors=sys.graph.out_neighbors(i) # Call the main function if the script gets executed (as opposed to imported). # See <http://docs.python.org/library/__main__.html><http://docs.python.org/library/__main__.html>. if __name__ == '__main__': main()

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Kwant 1.3
by Ali Asgharpour 06 Mar '17

06 Mar '17

Hello all, I was wondering if you'd mind explaining more about conservation law and operators you have added to Kwant 1.3. Would you please explain what conservation law does? Is it for just leads or it can be used for systems too? I have seen an example which stated in previous emails where you used conservation_law=-sz and time_reversal=s0. I want to know what happened if I use sx instead of sz numerically. In addition, I want to know more about Current and Source operators. It would be great if you implement them in a small code like conservation law one as an example. Your time and consideration are greatly appreciated. Best regards, Ali

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Wavefunction inside scattering region + spin
by Sverre Gulbrandsen 05 Mar '17

05 Mar '17

Hi, I am interested in calculating the wavefunction at sites inside the scattering region in systems with one or more leads. My goal is to calculate spin currents between sites, which requires to find expressions on the form \psi^{\dagger}(x,y) \vect{\sigma} \psi(x+1,y) and so on. As far as I understand one can use kwant.solvers.default.wave_function() and specify lead number, mode and a position (by inserting the site index) to get out a wave function (a complex number). My questions are then: - What is the wave function at a site when there are several leads and propagating modes at a given energy ? Is it a sum of all contributions from all leads and all propagating modes ? - Can one get out the spin components of the wavefunction (not just a single number) ? (Maybe this is related to what modes we put in) I use the dev version of kwant 1.3 where it is possible to specify a conservation_law in the lead. I included a simple example below of a two-dimensional NFN-system where I try to get out the wavefunction at the site (1,2). Best, Sverre Gulbrandsen import kwant from matplotlib import pyplot import tinyarray # Define 2x2-matrices to span spin space: sigma_0 = tinyarray.array([[1, 0], [0, 1]]) sigma_z = tinyarray.array([[1, 0], [0, -1]]) def make_system(a=1, t=1.0, W=10, L=30): lat = kwant.lattice.square(a, norbs=2) sys = kwant.Builder() sys[(lat(x, y) for x in range(L) for y in range(W))] = 4 * t * sigma_0 + 0.2 * t * sigma_z sys[lat.neighbors()] = -t * sigma_0 lead = kwant.Builder(kwant.TranslationalSymmetry((-a, 0)), conservation_law=-sigma_z) lead[(lat(0, j) for j in range(W))] = 4 * t * sigma_0 lead[lat.neighbors()] = -t * sigma_0 sys.attach_lead(lead) sys.attach_lead(lead.reversed()) return sys def print_wave_function_at_site(sys, energy, position_vector): site_index = [sys.sites[i].pos for i in range(len(sys.sites))].index(position_vector) wf_at_site = kwant.solvers.default.wave_function(sys, energy)(0)[0][site_index] print(wf_at_site) def main(): sys = make_system() kwant.plot(sys) sys = sys.finalized() print_wave_function_at_site(sys, energy=1, position_vector=(1, 2)) if __name__ == '__main__': main()

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performance issue with Kwant on CentOS with mpi4py
by Fatih Dogan 02 Mar '17

02 Mar '17

Hello, I have recently installed Kwant using miniconda onto my own account (no root access). I installed Python and all its dependencies as well with your help. Thank you!! When I run a code on a single processor, it works fine. When I add more CPUs, each calculation takes longer time. Code builds a system with hopping, on-site repulsion and SOC, with leads, then I calculate the scattering matrix of it. I ran a check with no-Kwant function (a simple summation), calculation takes almost same time independent of number of CPUs. I understand Kwant itself is not a parallel program, but given the same task, it should take same time to finish regardless of how many times it has been called. The code I am using builds 2 systems and calculates 2 smatrices. I paste below the times it takes for each set of CPUs. I am guessing this is an issue with sharing the library, but I am not certain. The time increases faster than linear. Any ideas? Thanks Fatih Single CPU ----------------- hello world from process 0 done system 1 0 0.05028367042541504 done smatrix 1 0 0.23258066177368164 done system 2 0 3.244915723800659 done smatrix 2 0 13.960146427154541 Two CPUs --------------- hello world from process 1 done system 1 1 0.04906630516052246 done smatrix 1 1 0.23961257934570312 done system 2 1 3.5525107383728027 done smatrix 2 1 16.66365075111389 hello world from process 0 done system 1 0 0.045102834701538086 done smatrix 1 0 0.20883417129516602 done system 2 0 2.842400550842285 done smatrix 2 0 14.466880559921265 Four CPUs --------------- hello world from process 1 done system 1 1 0.09960174560546875 done smatrix 1 1 0.630927324295044 done system 2 1 3.514568328857422 done smatrix 2 1 119.35529565811157 hello world from process 2 done system 1 2 0.09219717979431152 done smatrix 1 2 0.8386905193328857 done system 2 2 4.74960732460022 done smatrix 2 2 119.06909513473511 hello world from process 3 done system 1 3 0.13100957870483398 done smatrix 1 3 0.860680341720581 done system 2 3 3.4969165325164795 done smatrix 2 3 120.44963669776917 hello world from process 0 done system 1 0 0.1307511329650879 done smatrix 1 0 0.8210744857788086 done system 2 0 4.6470348834991455 done smatrix 2 0 120.91561484336853 8 CPUs -------------- hello world from process 3 done system 1 3 0.08914065361022949 done smatrix 1 3 1.9215054512023926 done system 2 3 12.615397214889526 done smatrix 2 3 264.25777077674866 hello world from process 1 done system 1 1 0.05163288116455078 done smatrix 1 1 1.5547888278961182 done system 2 1 7.847089767456055 done smatrix 2 1 264.47394609451294 hello world from process 4 done system 1 4 0.05323219299316406 done smatrix 1 4 1.8263118267059326 done system 2 4 8.452224254608154 done smatrix 2 4 258.97272992134094 hello world from process 6 done system 1 6 0.0951833724975586 done smatrix 1 6 1.7297015190124512 done system 2 6 9.489607334136963 done smatrix 2 6 258.52338123321533 hello world from process 7 done system 1 7 0.052448272705078125 done smatrix 1 7 1.3691565990447998 done system 2 7 8.31990361213684 done smatrix 2 7 260.8307328224182 hello world from process 2 done system 1 2 0.0588071346282959 done smatrix 1 2 1.5174744129180908 done system 2 2 5.244871377944946 done smatrix 2 2 242.011638879776 hello world from process 5 done system 1 5 0.05212259292602539 done smatrix 1 5 1.5607316493988037 done system 2 5 5.980914831161499 done smatrix 2 5 251.20327258110046 hello world from process 0 done system 1 0 0.05146503448486328 done smatrix 1 0 1.4909172058105469 done system 2 0 5.17970871925354 done smatrix 2 0 246.73624682426453

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Starting reference and multilayer system
by Mohammed Ghadiyali 01 Mar '17

01 Mar '17

Hi All, I am using DFT simulations for purposing Quantum well structures, to be used as 2D topological insulator (TI) i.e. Quantum well as 2D TI. I wanted to perform the transport calculations on my system which is multi layer setup. I wanted to know if it is possible to do so? And if possible can a reference can be provided? Also, as I use DFT approach I am not well versed with the tight binding formulation, a starting reference to both would be great. Finally can some one point me to the paper of 3-d system: Majorana states. Regards, Ghadiyali Mohammed Kader, Dept. of Physics, University of Mumbai.

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