Draw Bond-Currents with sisl

Hi Nick,

I got a tutorial on calculating the bond-current from your answer here. And I tried to draw the bonding current of graphene. But the atom is not shown in the graph, and the image does not seem to be correct.

This is the code:

import os
import numpy as np
import sisl

# Now read in the AV file
av = sisl.get_sile('graphene_scat.TBT.AV.nc')
geom = av.geom


J_orb = av.orbital_current('Left', E=2, isc=[None] * 3)
J_a = av.atom_current_from_orbital(J_orb, activity=False)

#J_v = av.vector_current_from_orbital(J_orb)

# Now create plot
from matplotlib.colors import Colormap
from matplotlib.mlab import griddata
import matplotlib.pyplot as plt

def mmlinspace(a, axis, N):
    m, M = np.min(a[:, axis]), np.max(a[:, axis])
    return np.linspace(m, M, N)

N_x, N_y = 2000, 2000
x = mmlinspace(geom.xyz, 0, N_x)
y = mmlinspace(geom.xyz, 1, N_y)

xi, yi = np.meshgrid(x, y)
zi = griddata(geom.xyz[:, 0], geom.xyz[:, 1], J_a, xi, yi, interp='linear')

cm = Colormap('inferno')
plt.contourf(xi, yi, zi, cmap=plt.cm.plasma)
plt.savefig('test2.png')

plt.show()

My question is how to set “J_orb” correct in the code, and If I expect to get both the atom and bond-current, What changes should I make for this code?

Best Regards~

[Mr-Bey]

Yes，it resolved. And thanks a lot for your help！Cheers！XD

[zerothi]

I will consider this issue resolved 😃