Hello, Thanks both of you for the quick answers. I have Phyton3. It was an old line from another code.
a) Clearly I didn't explain myself correctly about the edges and leads. But everything is solved now, following Adel's instructions. b) When I asked about computing it directly from Kwant it was because I read in another thread that it was going to be in Kwant1.3, but I was not sure if it was already avalaible. I will "fight" then with the code and will try to use your guidelines Joseph. Definetively doing it with neighbors will be much faster than itering the whole system. Will this new version be ready soon? :-) I will let you know my progress and will attach the code if successful. Thanks again, Enrique El 08/02/2017 a las 5:19, Abbout Adel escribió: Dear Enrique, What I see in your program is that you put a potential ''edge_potential=10'' to help you to color the sites at the edge where you want to put disorder. In your case, the width is uniform. So you can achieve your goal just by putting a constraint on the coordinates of your sites: Ex: W-1>site.pos[1]>1. The most interesting case, is when the shape of your system is arbitrary. To choose the edge , you do: for site in sys.expand(graphene.shape(rec, (0, 1))): if sys.degree(site)<9 : sys[site]=edge_potential Please, notice that I used <9 and not <=9 as you did in your program (this is why everything is green in your plot). To get rid of the sites at the edge, in front of the leads, just do, after attaching the leads : for site in sys.leads[0].interface+sys.leads[1].interface: sys[site]=0 This way, your program will work for arbitrary shape, and you can think how to put disorder after this. I hope that this helps. Adel On Wed, Feb 8, 2017 at 5:31 AM, enrique colomes <kc3...@hotmail.com<mailto:kc3...@hotmail.com>> wrote: 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() -- Abbout Adel