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

--

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