Dear Patrik,

The line that fails is

dn_lead.fill(template, lat1, lat1(0, 0, -2))

did you read the documentation for the "fill" method of builders? The documentation says that the second argument, called "shape", should be a function that takes a site and returns true or false depending on whether or not the site should be added. Instead of providing such a function, you have just provided the lattice itself.

Happy Kwanting,

Joe

On 08/07/2017 11:35 AM, Patrik Arvoy wrote:

Dear Christoph,

Thank you for the reply!

The code works fine with the switch (discrete=True and continuous=False).

Now if I change (discrete=False and continuous=True), I want to attach a continuous lead instead of its discrete counterpart to the system,

I get the error.

Regards

Patrik

Here is the code
-----------------------------------
from mpl_toolkits.mplot3d import Axes3D
from scipy.spatial import *
from matplotlib import rcParams
from numpy import *      
from numpy.linalg import *
import pickle
import sys
import os
import string
import heapq
import kwant
import tinyarray
from matplotlib import pyplot





chiral=True
if chiral:
    p = pi/5    #phi
    t = 0.66    #theta
    a = 0.34
    x = 1.4
    e1 = 0
    e2 = 0.3
    t2=0.1
    t1=-x*t2
    t0 = 2
    lam=-0.08
    t_so1 = 0.01 #spin-orbit coupling param
    t_so2 = x*t_so1 #spin-orbit coupling param
    tl=tr=0.3
    N = 30
    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]])
    no=2            #number of orbitals
    def sigma_v1(ap):         # pauli metrix along the vertical axis
        value=sigma_z*cos(t)+sin(t)*(sigma_x*sin(ap)-sigma_y*cos(ap))
        return value

    def sigma_v2(ap):         # pauli metrix along the vertical axis
        value=sigma_z*cos(t)-sin(t)*(sigma_x*sin(ap)-sigma_y*cos(ap))
        return value

    def family_color(sites):
        return 'black' #if site.family == sites

    def hopping_lw(site1, site2):
        return 0.08

  
    class Amorphous(kwant.builder.SiteFamily):
        def __init__(self, coords):
            self.coords = coords
            super(Amorphous, self).__init__("amorphous", "",no)

        def normalize_tag(self, tag):
            try:
                tag = int(tag[0])
            except:
                raise KeyError

            if 0 <= tag < len(coords):
                return tag
            else:
                raise KeyError

        def pos(self, tag):
            return self.coords[tag]

    coords=[(0.0000000000, 0.0000000000, 0.0000000000), (-0.1336881039, 0.4114496766, 0.3400000000), (-0.4836881039, 0.6657395614, 0.6800000000), (-0.9163118961, 0.6657395614, 1.0200000000), (-1.2663118961, 0.4114496766, 1.3600000000), (-1.4000000000, 0.0000000000, 1.7000000000), (-1.2663118961, -0.4114496766, 2.0400000000), (-0.9163118961, -0.6657395614, 2.3800000000), (-0.4836881039, -0.6657395614, 2.7200000000), (-0.1336881039, -0.4114496766, 3.0600000000), (0.0000000000, -0.0000000000, 3.4000000000), (-0.1336881039, 0.4114496766, 3.7400000000), (-0.4836881039, 0.6657395614, 4.0800000000), (-0.9163118961, 0.6657395614, 4.4200000000), (-1.2663118961, 0.4114496766, 4.7600000000), (-1.4000000000, 0.0000000000, 5.1000000000), (-1.2663118961, -0.4114496766, 5.4400000000), (-0.9163118961, -0.6657395614, 5.7800000000), (-0.4836881039, -0.6657395614, 6.1200000000), (-0.1336881039, -0.4114496766, 6.4600000000), (0.0000000000, -0.0000000000, 6.8000000000), (-0.1336881039, 0.4114496766, 7.1400000000), (-0.4836881039, 0.6657395614, 7.4800000000), (-0.9163118961, 0.6657395614, 7.8200000000), (-1.2663118961, 0.4114496766, 8.1600000000), (-1.4000000000, 0.0000000000, 8.5000000000), (-1.2663118961, -0.4114496766, 8.8400000000), (-0.9163118961, -0.6657395614, 9.1800000000), (-0.4836881039, -0.6657395614, 9.5200000000), (-0.1336881039, -0.4114496766, 9.8600000000), (-1.4000000000, 0.0000000000, 0.0000000000), (-1.2663118961, -0.4114496766, 0.3400000000), (-0.9163118961, -0.6657395614, 0.6800000000), (-0.4836881039, -0.6657395614, 1.0200000000), (-0.1336881039, -0.4114496766, 1.3600000000), (0.0000000000, -0.0000000000, 1.7000000000), (-0.1336881039, 0.4114496766, 2.0400000000), (-0.4836881039, 0.6657395614, 2.3800000000), (-0.9163118961, 0.6657395614, 2.7200000000), (-1.2663118961, 0.4114496766, 3.0600000000), (-1.4000000000, 0.0000000000, 3.4000000000), (-1.2663118961, -0.4114496766, 3.7400000000), (-0.9163118961, -0.6657395614, 4.0800000000), (-0.4836881039, -0.6657395614, 4.4200000000), (-0.1336881039, -0.4114496766, 4.7600000000), (0.0000000000, -0.0000000000, 5.1000000000), (-0.1336881039, 0.4114496766, 5.4400000000), (-0.4836881039, 0.6657395614, 5.7800000000), (-0.9163118961, 0.6657395614, 6.1200000000), (-1.2663118961, 0.4114496766, 6.4600000000), (-1.4000000000, 0.0000000000, 6.8000000000), (-1.2663118961, -0.4114496766, 7.1400000000), (-0.9163118961, -0.6657395614, 7.4800000000), (-0.4836881039, -0.6657395614, 7.8200000000), (-0.1336881039, -0.4114496766, 8.1600000000), (0.0000000000, -0.0000000000, 8.5000000000), (-0.1336881039, 0.4114496766, 8.8400000000), (-0.4836881039, 0.6657395614, 9.1800000000), (-0.9163118961, 0.6657395614, 9.5200000000), (-1.2663118961, 0.4114496766, 9.8600000000)]
    amorphous_lat = Amorphous(coords)

    syst = kwant.Builder()

    for i in range(N):
        syst[amorphous_lat(i)] = e1*sigma_0
        syst[amorphous_lat(N+i)] = e2*sigma_0
        syst[amorphous_lat(i), amorphous_lat(N+i)] = lam*sigma_0
        if i > 0:
            syst[amorphous_lat(i), amorphous_lat(i-1)] = t1*sigma_0 + 1j*t_so1*(sigma_v1(i*p)+sigma_v1((i-1)*p))
            syst[amorphous_lat(N+i),amorphous_lat(N+i-1)] = t2*sigma_0 + 1j*t_so2*(sigma_v2(i*p)+sigma_v2((i-1)*p))
                   
    prim_vecs=tinyarray.array([(a,0.,0.),(0.,a,0.),(0.,0.,a)])

    offset1=tinyarray.array((-0.7, 0.0, 0.0))   
    lat1=kwant.lattice.Monatomic(prim_vecs, offset1, norbs=no)


    syst[lat1(0, 0, -1)] = e1*sigma_0
    syst[amorphous_lat(0), lat1(0, 0, -1)] = tl*sigma_0
    syst[amorphous_lat(N), lat1(0, 0, -1)] = tl*sigma_0

    sym = kwant.TranslationalSymmetry([0, 0, -a])
    dn_lead = kwant.Builder(sym, conservation_law=-sigma_z)
   
   
   
   
    discrete=True           #discrete lead
    continuous=False     #countinuous lead


    if discrete:
        sym = kwant.TranslationalSymmetry([0, 0, -a])
        dn_lead = kwant.Builder(sym, conservation_law=-sigma_z)

        dn_lead[lat1(0, 0, -2)] = e1*sigma_0
        dn_lead[lat1.neighbors()] = t0*sigma_0
        syst.attach_lead(dn_lead)              
       
    if continuous:
        t00=0.0
        Leadham ="t00*sigma_0*k_x**2+t00*sigma_0*k_y**2-t0*sigma_0*k_z**2+(2*t0+e1)*sigma_0"
        template = kwant.continuum.discretize(Leadham, grid_spacing=a)
        dn_lead.fill(template, lat1, lat1(0, 0, -2))
        syst.attach_lead(dn_lead)
       
       
       
       
       
       
       
    sym1 = kwant.TranslationalSymmetry([0, 0, a])
    up_lead = kwant.Builder(sym1, conservation_law=-sigma_z)
   
   
    syst[lat1(0, 0, N)] = e1*sigma_0
    syst[amorphous_lat(N-1), lat1(0, 0, N)] = tr*sigma_0
    syst[amorphous_lat(2*N-1), lat1(0, 0, N)] = tr*sigma_0


    up_lead[lat1(0, 0, N+1)] = e1*sigma_0
    up_lead[lat1.neighbors()] = t0*sigma_0   
    syst.attach_lead(up_lead)
   
    system=kwant.plot(syst, site_lw=0.1, site_color=family_color, hop_lw=hopping_lw)


    trans=True      
    if trans:
        syst = syst.finalized()
        energies = []
        datau = []

        for ie in range(-320,520):
            energy = ie * 0.001
            smatrix = kwant.smatrix(syst, energy=energy)
            energies.append(energy)
            Gu=smatrix.transmission((1, 0), 0)
            Gd=smatrix.transmission((1, 1), 0)
            datau.append(Gu)    

        fig = pyplot.figure()      
        pyplot.plot(energies, datau, 'b--')
        pyplot.legend(['Gu'], loc='upper left')
        pyplot.xlim([-0.32,0.52])
        pyplot.ylim([-0.03,1.05])
        pyplot.show()

On 7 August 2017 at 10:15, Christoph Groth <christoph.groth@cea.fr> wrote:

Patrik, can you please provide a complete script file that demonstrates your problem?