Dear kwant users, If I want to attach a continuous lead instead of its discrete counterpart to a discrete system, I get the error message 'Use site_family(1, 2) instead of site_family((1, 2))!'. The discrete lead is according to the following 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) 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) Now if I replace the 'if discrete:' part with the following 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) I have to add k_x and k_y with zero coefficient (t00) to solve the symmetry complain (is there a neater way?) where is the error message ('Use site_family(1, 2) instead of site_family((1, 2))!') originated from? Thanks Patrik
Patrik, can you please provide a complete script file that demonstrates your problem?
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?
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?
Thank you Joe for pointing out the mistake! I defined the lead_shape function that return True for sites in the 'lat1'. I have already added the lat1(0, 0, -1) site to the system. 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) I attach the full code at the end of this message. What would be the continuous leads (in the momentum space) equivalent of two discrete leads (vertical 1D chains) attached to my system? Regards Patrik ------------------------------------------------- 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=False #discrete lead continuous=True #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: 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) 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 12:27, Joseph Weston <joseph.weston08@gmail.com> wrote:
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?
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
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
participants (3)
-
Christoph Groth -
Joseph Weston -
Patrik Arvoy