Transmission Pathways

Yes, there is.

In tbtrans (if compiled with NetCDF-4 support) one may calculate the bond-currents (in ATK known as transmission-pathways).

I will highly recommend you to use the Python utility sisl to extract the bond-currents in a reasonable fashion. From sisl you have many options such as extracting the bond-currents for a subset of orbitals or simply the total bond-currents.

Look into the option:
TBT.Current.Orb
and then the sisl manual.

sisl may be found here:

https://github.com/zerothi/sisl

Hello Nick,
Thanks for your reply. I was able to extract the bond currents.
Is there an easy way to render this information?

Regards,
David

There is no "correct" way to visualize the bond-currents. Typically bond-currents are very complex to show and one have to consider a case-by-case visualization of the bond-currents.

See for instance this paper which has bond-currents shown in one way:
https://www.nature.com/articles/ncomms15783#supplementary-information

The method is much similar to this code snippet:

>>>>
import os
import numpy as np
import sisl

# Get the TBT.AV.nc file
if not os.path.exists('siesta.TBT.AV.nc'):
    sisl.get_sile('siesta.TBT.nc').write_tbtav()

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

J_orb = av.orbital_current('Left', E=-0.8, 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('test.png')
plt.show()
>>>>
However, it is probably only good for 2D structures.

Oh, and the code above requires the python package sisl, if used, please cite:

https://doi.org/10.5281/zenodo.495025
and
https://doi.org/10.1016/j.cpc.2016.09.022

Great Thank you so much.

I actually have one more question if you don't mind. I am calculating the bond-currents of a metal as an example. I took the already built example of gold in TranSiesta and try to compute bond-currents via TBT.Current.Orb, but I get this warning:
WARNING: k-averaging orbital currents with time-reversal symmetry will not reproduce
the correct orbital current. Set TBT.Symmetry.TimeReversal F

I set TBT.Symmetry.TimeReversal to false but the warning keep showing up when I run tbtran. I also compared the average transmission when TBT.Current.Orb = true and TBT.Current.Orb=false and they look very different. Do you have any insights into this? Does one need to remove time reversal symmetry even for the transiesta calculation?

I appreciate your help.

Best Regards,
David

No, time-reversal symmetry should not change the k-averaged transmission function.

Could you please download this version:

http://bazaar.launchpad.net/~siesta-maint/siesta/rel-4.1/tarball/714

If the same thing occurs, send me the complete set of files needed to perform your calculation.

And please know that transiesta and tbtrans is not the same program, they do two distinct things.

So no, you shouldn't remove time-reversal symmetry in transiesta (only tbtrans).

Hello Nick,

I didn't have time to try this earlier, but now I have an update.
I downloaded the subversion you pointed out and compile Siesta but TranSiesta gives me an error in siesta_forces.F. you can find the log file here https://www.dropbox.com/s/lc9s45hbc46bnsr/transiesta.log?dl=0 and Makefile here https://www.dropbox.com/s/p2kv6qxqzxc4wnv/arch.make?dl=0 . I have been using the same makefile for multiple version of siesta/transiesta and this error has never showed up.

Anyway, I thought I would just go ahead and compile TBtran and run it with the output of my working version of Transiesta (4.1_b2) and turns out that everything works fine. I haven't test it very carefully but the transmission with and without TBT.Current.Orb are the same. Moreover, I quickly checked the bond currents and compared with an example ran in ATK and the look very similar.

Do you see an issue if I run my production calculations with Siesta/TranSiesta 4.1_b2 but use TBtran from the subversion you suggested?

Thanks much for all your help,
David

Ok, great.

I have fixed the issue you said.

And no, it should be fine to use the new tbtrans on the 4.1-b2 output.

So when 4.1-b3 is released the problem is solved.

Thanks. I consider this solved then.

Solved.