Thank you Joe! In the simple code below (first code), I am adding two sites to the left side of a square lattice and I want to attach the lead to them. Although the starting point is clearly in the lead_shape, but it complains that 'None of the starting sites is in the desired shape' There are of course several ways around this, e.g changing the lead_shape to the following: def lead_shape(site): (x, y) = site.pos return (y==5 and x<=0) Could you please tell me why is that so? I am asking this, because I have the same problem in my original code mentioned before (attached below). The problem is in this section: else: #countinuous lead def lead_shape(site): (x, y, z) = site.pos return (x==-0.7 and y==0 and z<=-a) t00=0.0 params = dict(t00=0., t0=2., e1=0.) Leadham ="(t00*k_x**2)*sigma_0 + (t00*k_y**2)*sigma_0 - (t0*k_z**2)*sigma_0 + (2*t0+e1)*sigma_0" template = kwant.continuum.discretize(Leadham, grid_spacing=a) sym = kwant.TranslationalSymmetry([0, 0, -a]) dn_lead = kwant.Builder(sym, conservation_law=-sigma_z) dn_lead.fill(template, lead_shape, (-0.7, 0, -a)) syst.attach_lead(dn_lead) Although I have manually added the site with this coordinate (-0.7, 0, -a) to the system Regards Patrik #simple example ------------------------------------------------------------------------------------------------------ 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 import scipy.sparse.linalg import scipy.linalg a=1 t = 1.0 W = 10 L = 30 e=4.0 sigma_z = tinyarray.array([[1, 0], [0, -1]]) ct=True if ct: def rec(pos): (x, y) = pos return (0 <= y < W and 0 <= x < L) def lead_shape(site): (x, y) = site.pos return (y==5 and x<=-2) t0=0.0 params = dict(t=1., t0=0.) hamiltonian = "t*k_x**2 * identity(2) + t*k_y**2 * identity(2) + t0 * identity(2)" template = kwant.continuum.discretize(hamiltonian, grid_spacing=a) print(template) syst1 = kwant.Builder() lat = kwant.lattice.square(a, norbs=2) syst1[lat.shape(rec, (0, 0))] = e * identity(2) syst1[lat(-1,5)] = e * identity(2) syst1[lat(-2,5)] = e * identity(2) syst1[lat.neighbors()] = -t * identity(2) sym = kwant.TranslationalSymmetry([-a, 0]) lead1 = kwant.Builder(sym, conservation_law=-sigma_z) lead1.fill(template, lead_shape, (-2, 5)) syst1.attach_lead(lead1) syst1.attach_lead(lead1.reversed()) syst1 = syst1.finalized() system=kwant.plot(syst1) ------------------------------------------------------------------------------------------------------------------------ #my 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 discrete=False #discrete 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) else: #countinuous lead def lead_shape(site): (x, y, z) = site.pos return (x==-0.7 and y==0 and z<=-a) t00=0.0 params = dict(t00=0., t0=2., e1=0.) Leadham ="(t00*k_x**2)*sigma_0 + (t00*k_y**2)*sigma_0 - (t0*k_z**2)*sigma_0 + (2*t0+e1)*sigma_0" template = kwant.continuum.discretize(Leadham, grid_spacing=a) sym = kwant.TranslationalSymmetry([0, 0, -a]) dn_lead = kwant.Builder(sym, conservation_law=-sigma_z) dn_lead.fill(template, lead_shape, (-0.7, 0, -a)) 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 8 August 2017 at 13:12, Joseph Weston <joseph.weston08@gmail.com> wrote:
Dear Patrik,
When I replace the 'if continuous' section with the following section it will complain.
if continuous: def lead_shape(site): (x, y, z) = site.pos return (x == -0.7 and y == 0.0 and z <= -a) 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, lead_shape, lat1(0, 0, -1)) syst.attach_lead(dn_lead)
The error message I got when running the code was:
ValueError: Lead to be attached contains no sites.
This error seems perfectly clear to me; you have defined your "lead_shape" function incorrectly, such that no sites are added to your "dn_lead" system.
Happy Kwanting,
Joe