Hello: Im simulating a nanotube with this hamiltonian: ns = {'hdiag':[[1,0,0,0],[0,-1,0,0],[0,0,1,0],[0,0,0,-1]], 'hA1':[[0,1,0,0],[1,0,0,0],[0,0,0,-1],[0,0,-1,0]], 'hA2r':[[0,0,0,1],[0,0,1,0],[0,0,0,0],[0,0,0,0]], 'hA2s':[[0,0,0,0],[0,0,0,0],[0,1,0,0],[1,0,0,0]] } ham=""" (C_0+C_1*k_z**2+C_2*(k_x**2+k_y**2))*identity(4)+(M_0+M_1*k_z**2+M_2*(k_x**2+k_y**2))*hdiag + (B_0*k_z)*hA1 + (1/sqrt(2)*(1+1j)*A_0*(k_x-1j*k_y))*hA2r + (1/sqrt(2)*(1-1j)*A_0*(k_x+1j*k_y))*hA2s """ ham= kwant.continuum.sympify(ham,ns) and this shape: def cuboid_shape(pos): x, y, z = pos return 0 <= x < Lx/2 and abs(y) <= R and abs(z) <= np.sqrt(R**2-y**2) When using : lat = kwant.lattice.general([(1, 0, 0),(0, 1, 0),(0, 0, 1)], norbs=4) syst = kwant.Builder() template = kwant.continuum.discretize(ham, coords =['x','y','z'], grid=a) syst.fill(template, cuboid_shape,(0,0,0)) I get this weird error that all the sites have been deleted because an exception with fill(); and i can't seem to find a similar error anywhere on the internet. Any ideas? Kind Regards Alejandro Álvarez Chico