Hi, sorry for the late reply,

Can you point me to the correct direction of where to look at the documentation to figure out how to make a vorticity plot in kwant?

Essentially, I want to attach leads to a graphene flake. I want to find the vorticity around each closed hexagon. Which command of kwant should I look at to figure out the velocity between two adjacent atoms so that I can calculate the vorticity in the end?

Sounds like you want to plot the current flowing across each hopping. This is a feature that will make it into Kwant 1.3
(see https://gitlab.kwant-project.org/kwant/kwant/merge_requests/30), and the plotting of such things (i.e. plotting a
vector field) will also be in the same release. Unfortunately we don't have a concrete timeline for this release, however.
In the mean time, it should be relatively straight forward to calculate the expectation value of the current operator acting
on a wavefunction, e.g. for the current `J_ij` flowing between sites `i` and `j` you can write (give or take a factor -1):

    J_ij = 2 * Im[ ψ^*_i H_ij ψ_j],

where `H_ij` is the Hamiltonian matrix element between the sites `i` and `j`, and `ψ_j` is the wavefunction on site `j`.

kwant.solvers.default.wave_function(some_sys, some_energy)

Where is some_energy a reference to? An excitation energy relative to what?

It's the energy relative to whatever the 0 of energy of your model is! When you write down your Hamiltonian
you are writing it with respect to some reference energy. What this means physically will depend on your model!

Happy Kwanting,