Dear Sudin, Your code seems to work fine for me. Why don't you just use an onsite function as below? (you can put a condition as you wish) sys_2[site] returns a function so you need to add the argument of hat function: sys_2[site](site) (be careful, this will not work if the leads add some sites to the central system: in the lead, the potential is given by scalars, in the system by a function. a small modification is required) I hope this helps, Adel ############################################################################# def make_system(W, L, lim): ## scattering region ## def Onsite(site): x,y=site.pos if y< lim: return x else: return 0 sys = kwant.Builder() sys[lat.shape(cross(W,L), (0,0))] = Onsite sys[lat.neighbors(1)] = -1. leads = [create_lead_h(W, xsym1,axis=(0,0)),create_lead_h(W, xsym2,axis=(0,0))] for lead in leads: sys.attach_lead(lead) return sys def main(): sys_2 = make_system(W=3.5, L=3, lim=-1) kwant.plotter.plot(sys_2,site_color=lambda site:sys_2[site](site),colorbar=True, cmap=None) if __name__ == '__main__': main() On Fri, Apr 17, 2020 at 7:06 AM SUDIN GANGULY <sudinganguly@gmail.com> wrote:

Dear Sir,

Thank you for your reply. The problem I am facing is that if I assign the site values like (1,2,3,...) along the bottom line, the colormap of the site values are changing whenever I compile the code. ############################ import kwant from pylab import * import matplotlib.pyplot as plt from random import * import numpy as np

class Honeycomb(kwant.lattice.Polyatomic): def __init__(self, name=''): prim_vecs = [[0.5, sqrt(3)/2], [1, 0]] # bravais lattice vectors # offset the lattice so that it is symmetric around x and y axes basis_vecs = [[-0.5, -1/sqrt(12)], [-0.5, 1/sqrt(12)]] super(Honeycomb, self).__init__(prim_vecs, basis_vecs, name) self.a, self.b = self.sublattices

sys=kwant.Builder() lat = Honeycomb() a,b= lat.sublattices

def cross(W, L): def shape(pos): return ((-W <= pos[1] <= W and -L <= pos[0] <= L)) return shape

pv1, pv2 = lat.prim_vecs

xsym1 = kwant.TranslationalSymmetry((-pv2)) # lattice symmetry in -x direction xsym1.add_site_family(lat.sublattices[0], other_vectors=[(-2, 1)]) xsym1.add_site_family(lat.sublattices[1], other_vectors=[(-2, 1)])

xsym2=kwant.TranslationalSymmetry((pv2)) xsym2.add_site_family(lat.sublattices[0], other_vectors=[(-2, 1)]) xsym2.add_site_family(lat.sublattices[1], other_vectors=[(-2, 1)])

def create_lead_h(W, symmetry, axis): lead = kwant.Builder(symmetry) lead[lat.wire(axis, W)] = 0. lead[lat.neighbors(1)] = -1. return lead

def make_system(W, L, no_of_line):

## scattering region ## sys = kwant.Builder() sys[lat.shape(cross(W,L), (0,0))] = 0 sys[lat.neighbors(1)] = -1.

line=[] for site in sys.expand(lat.shape(cross(W,L), (0, 0))): line.append(site.pos[1])

line=set(line) line=list(line) line=sort(line) my_list=[] i=1 for site in sys.expand(lat.shape(cross(W,L), (0, 0))): for j in range(0,no_of_line+1,2): line_no=j if (site.pos[1]==line[line_no] or site.pos[1]==line[line_no+1]): my_list.append(site) sys[site]=i i=i+1

## leads ##

leads = [create_lead_h(W, xsym1,axis=(0,0))] leads += [create_lead_h(W, xsym2,axis=(0,0))]

for lead in leads: sys.attach_lead(lead)

#============================================================================= return {'sys': sys }

def main(): sys_2 = make_system(W=3.5, L=5, no_of_line=1) kwant.plotter.plot(sys_2['sys'],site_color=lambda site:sys_2['sys'][site],colorbar=True, cmap=None)

if __name__ == '__main__': main() #################################

I can resolve this issue by collecting the site positions from the array named my_list in the given code and then assign the site values accordingly. However, this procedure is a bit lengthy. If there is any other way to do that with less coding, that will be very helpful. With Regards, Sudin

On Fri, Apr 17, 2020 at 1:36 AM Abbout Adel <abbout.adel@gmail.com> wrote:

...

Dear Sudin,

Please post the code giving the error or explain better your concern.

Could you just do it by defining an on site function?

def Onsite(site): x,y=site.pos() i,_=site.tag if y=y0: return Values[i] else: return V0

sys[(........)]=Onsite

I hope this helps, Adel

On Wed, Apr 15, 2020 at 3:45 PM SUDIN GANGULY <sudinganguly@gmail.com> wrote:

...

Dear Sir,

I want to assign a particular sequence of site values on a particular line (a number of lines) of a zigzag graphene nanoribbon. For example, the bottom zigzag line.

let's say, from the left to right there are 10 sites and I want to put the onsite values as [1,2,3,...].

I was able to get the information about the sites that are in the bottom line and have assigned the site values accordingly. But the problem is that each time I finalize the system, I get different onsite values along the bottom line. Is there any way to resolve this? Or maybe this approach is not the right way to do that.

A part of my code is given below ======================== def make_system(W, L, no_of_line):

## scattering region ## sys = kwant.Builder() sys[lat.shape(cross(W,L), (0,0))] = 0 sys[lat.neighbors(1)] = -1. #######INFO of the line######### line=[] for site in sys.expand(lat.shape(cross(W,L), (0, 0))): #print (site.pos[0],site.pos[1]) line.append(site.pos[1])

line=set(line) line=list(line) line=sort(line)

i=1 for site in sys.expand(lat.shape(cross(W,L), (0, 0))): for j in range(0,no_of_line+1,2): line_no=j if (site.pos[1]==line[line_no] or site.pos[1]==line[line_no+1]): sys[site]=i i=i+1 ########################

With Regards, Sudin

-- Abbout Adel

-- সুদিন

-- Abbout Adel