The complete source code of this example can be found in
In the following example, we are going to calculate the conductance through a graphene quantum dot with a p-n junction and two non-collinear leads. In the process, we will touch all of the topics that we have seen in the previous tutorials, but now for the honeycomb lattice. As you will see, everything carries over nicely.
We begin by defining the honeycomb lattice of graphene. This is
in principle already done in
kwant.lattice.honeycomb, but we do it
explicitly here to show how to define a new lattice:
graphene = kwant.lattice.general([(1, 0), (sin_30, cos_30)], [(0, 0), (0, 1 / sqrt(3))]) a, b = graphene.sublattices
The first argument to the
general function is the list of
primitive vectors of the lattice; the second one is the coordinates of basis
atoms. The honeycomb lattice has two basis atoms. Each type of basis atom by
itself forms a regular lattice of the same type as well, and those
sublattices are referenced as a and b above.
In the next step we define the shape of the scattering region (circle again)
and add all lattice points using the
def make_system(r=10, w=2.0, pot=0.1): #### Define the scattering region. #### # circular scattering region def circle(pos): x, y = pos return x ** 2 + y ** 2 < r ** 2 sys = kwant.Builder() # w: width and pot: potential maximum of the p-n junction def potential(site): (x, y) = site.pos d = y * cos_30 + x * sin_30 return pot * tanh(d / w) sys[graphene.shape(circle, (0, 0))] = potential
As you can see, this works exactly the same for any kind of lattice. We add the onsite energies using a function describing the p-n junction; in contrast to the previous tutorial, the potential value is this time taken from the scope of make_system, since we keep the potential fixed in this example.
As a next step we add the hoppings, making use of
HoppingKind. For illustration purposes we define
the hoppings ourselves instead of using
hoppings = (((0, 0), a, b), ((0, 1), a, b), ((-1, 1), a, b))
The nearest-neighbor model for graphene contains only
hoppings between different basis atoms. For this type of
hoppings, it is not enough to specify relative lattice indices,
but we also need to specify the proper target and source
sublattices. Remember that the format of the hopping specification
(i,j), target, source. In the previous examples (i.e.
Matrix structure of on-site and hopping elements)
target=source=lat, whereas here
we have to specify different sublattices. Furthermore,
note that the directions given by the lattice indices
(1, 0) and (0, 1) are not orthogonal anymore, since they are given with
respect to the two primitive vectors
[(1, 0), (sin_30, cos_30)].
Adding the hoppings however still works the same way:
sys[[kwant.builder.HoppingKind(*hopping) for hopping in hoppings]] = -1
Modifying the scattering region is also possible as before. Let’s do something crazy, and remove an atom in sublattice A (which removes also the hoppings from/to this site) as well as add an additional link:
del sys[a(0, 0)] sys[a(-2, 1), b(2, 2)] = -1
Note again that the conversion from a tuple (i,j) to site is done by the sublattices a and b.
The leads are defined almost as before:
# left lead sym0 = kwant.TranslationalSymmetry(graphene.vec((-1, 0))) def lead0_shape(pos): x, y = pos return (-0.4 * r < y < 0.4 * r) lead0 = kwant.Builder(sym0) lead0[graphene.shape(lead0_shape, (0, 0))] = -pot lead0[[kwant.builder.HoppingKind(*hopping) for hopping in hoppings]] = -1 # The second lead, going to the top right sym1 = kwant.TranslationalSymmetry(graphene.vec((0, 1))) def lead1_shape(pos): v = pos * sin_30 - pos * cos_30 return (-0.4 * r < v < 0.4 * r) lead1 = kwant.Builder(sym1) lead1[graphene.shape(lead1_shape, (0, 0))] = pot lead1[[kwant.builder.HoppingKind(*hopping) for hopping in hoppings]] = -1
Note the method
vec used in calculating the
TranslationalSymmetry. The latter expects a
real-space symmetry vector, but for many lattices symmetry vectors are more
easily expressed in the natural coordinate system of the lattice. The
vec-method is thus used to map a lattice vector
to a real-space vector.
Observe also that the translational vectors
graphene.vec((-1, 0)) and
graphene.vec((0, 1)) are not orthogonal any more as they would have been
in a square lattice – they follow the non-orthogonal primitive vectors defined
in the beginning.
Later, we will compute some eigenvalues of the closed scattering region without leads. This is why we postpone attaching the leads to the system. Instead, we return the scattering region and the leads separately.
return sys, [lead0, lead1]
The computation of some eigenvalues of the closed system is done in the following piece of code:
def compute_evs(sys): # Compute some eigenvalues of the closed system sparse_mat = sys.hamiltonian_submatrix(sparse=True) evs = sla.eigs(sparse_mat, 2) print(evs.real)
Here we use in contrast to the previous example a sparse matrix and the sparse linear algebra functionality of SciPy.
The code for computing the band structure and the conductance is identical to the previous examples, and needs not be further explained here.
Finally, in the main function we make and plot the system:
def main(): pot = 0.1 sys, leads = make_system(pot=pot) # To highlight the two sublattices of graphene, we plot one with # a filled, and the other one with an open circle: def family_colors(site): return 0 if site.family == a else 1 # Plot the closed system without leads. kwant.plot(sys, site_color=family_colors, site_lw=0.1, colorbar=False)
We customize the plotting: we set the site_colors argument of
plot to a function which returns 0 for
sublattice a and 1 for sublattice b:
def family_colors(site): return 0 if site.family == a else 1
plot shows these values using a color scale
(grayscale by default). The symbol size is specified in points, and is
independent on the overall figure size.
Plotting the closed system gives this result:
Computing the eigenvalues of largest magnitude,
should yield two eigenvalues equal to
The remaining code of main attaches the leads to the system and plots it again:
It computes the band structure of one of lead 0:
showing all the features of a zigzag lead, including the flat edge state bands (note that the band structure is not symmetric around zero energy, due to a potential in the leads).
Finally the transmission through the system is computed,
showing the typical resonance-like transmission probability through an open quantum dot
In a lattice with more than one basis atom, you can always act either on all sublattices at the same time, or on a single sublattice only.
For example, you can add lattice points for all sublattices in the current example using:
sys[graphene.shape(...)] = ...
or just for a single sublattice:
sys[a.shape(...)] = ...
and the same of course with b. Also, you can selectively remove points:
del sys[graphene.shape(...)] del sys[a.shape(...)]
where the first line removes points in both sublattices, whereas the second line removes only points in one sublattice.