holes in density plot
The density plotter in kwant.plotter.density
uses a ktree search to find a 2D mask where the system is defined.
The eps
parameter is too lax, and fails for a honeycomb lattice.
Minimal example
import matplotlib
import kwant
import numpy as np
def circle(pos):
x, y = pos
return x**2 + y**2 < 100
lat = kwant.lattice.honeycomb()
syst = kwant.Builder()
syst[lat.shape(circle, (0, 0))] = 0
syst[lat.neighbors()] = 1
fsyst = syst.finalized()
kwant.plotter.density(fsyst, np.zeros(len(fsyst.sites)))