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 <mailto:christoph.groth@cea.fr>> wrote:
Patrik, can you please provide a complete script file that demonstrates your problem?