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Edit and run



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from __future__ import print_function
import sisl
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline

Create the input required for a full TranSiesta calculation. Here you should create your first system with these settings:

A pristine bulk Carbon-chain system.
The Carbon-chain should have a bond-length of $1.5\,\mathrm{Ang}$ and lots of vacuum in the transverse directions (to make it a chain)
You should decide in which direction the semi-infinite directions are.

Please use the script tselecs.sh to create the relevant input for TranSiesta.
Below you will find a skeleton code that only requires editing from your side.



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C = sisl.Atom(6)

Create the electrode. Supply the coordinates and the supercell. Note that you have to decide the semi-infinite direction by ensuring the electrode to be periodic in the semi-infinite direction. You should also ensure nearest neighbour couplings only!



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elec = sisl.Geometry(<fill-in coordinates>,
                     atom=C,
                     sc=<unit-cell size>)
elec.write('ELEC.fdf')

Create the device. The basic unit-cell for a fully periodic device system is 3-times the electrode size.
HINT: If you are not fully sure why this is, please see TS 1.



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device = elec.tile(3, axis=<semi-infinite direction>)
device.write('DEVICE.fdf')

Exercises

Perform the TranSiesta calculation
Create inputs for TBtrans to calculate the Green function density of states, and specify the energy range from $-10$ eV to $10$ eV.
Plot the transmission and DOS