Dear Christoph,

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])

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

if continuous:
t00=0.0

sym1 = kwant.TranslationalSymmetry([0, 0, a])

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

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