Electronic transport in a 1D gold chain
***************************************

BAND DFTB NEGF (Non-Equilibrium Green's Function) Metal wire Lead
Transmission function Current


Introduction
============

The system studied in this tutorial is discussed in **Electronic and
Transport Properties of Artificial Gold Chains** PhysRevLett.93.096404
and **Benchmark density functional theory calculations for nano-scale
conductance** The Journal of Chemical Physics 128, 114714 (2016).

We will simulate the electronic transport through an atomic gold
chain, and study the effect that an adsorbed CO molecule has on the
conductance.

[image]

According to PhysRevLett.93.096404 "a single CO group [...] modulates
the electronic wave functions, acting as a ‘‘chemical scissor’’ along
the gold chain, to strongly modify the coherent transport properties
of the system".

See also: DFTB-NEGF manual and BAND-NEGF manual


Creating the lead file
======================

Let's begin by **creating a lead file**. A lead file is a simple .xyz
file with an extra lattice vector.

Tip:

  The folder **$AMSHOME/atomicdata/Molecules/NEGF/Leads** contains
  some pre-defined lead files

For this tutorial the lead will be a single gold atom with a lattice
of 2.9 Å (in the x-direction). Let us create this with AMSinput:

   Start up **AMSinput**
   **1.** Switch to **BAND**: [image: ADFPanel][image] **→** [image: BANDPanel][image]
   **2.** From the main BAND-panel, select **Periodicity → Chain**
   **3.** Click Click on [image: MoreBtn][image] to switch the **Lattice** panel
 [image]

In the lattice panel we can specify the lattice vector:

   Set the lattice vector to 2.9
 [image]

We now add the gold atom

   **1.** Click on 'X' in the bar below the molecule drawing area
   **2.** Select 'Au'
   **3.** Click anywhere in the drawing area to add the gold atom
 [image]

and set the coordinates of the gold atom to **(0,0,0)**:

   **1.** Click on **Model → Coordinates**
   **2.** Set the xyz coordinates on the Au atom to (0,0,0)
 [image]

We now export this 1D gold chain as an .xyz file:

   **1.** Click on **File → Export Coordinates (System) → .xyz...**
   **2.** Save the file as "Au_lead.xyz"
   **3.** Close AMSinput: **SCM → Quit**

The .xyz file, defining our lead, should look like this:

   1

   Au       0.00000000       0.00000000       0.00000000
   VEC1     2.90000000       0.00000000       0.00000000


Gold chain transport calculation
================================

We are now ready to set up the NEGF calculation for the gold chain.
The simulation in this tutorial can be performed with either the DFTB
engine or the BAND engine. DFTB is computationally faster than BAND,
but the results will generally be less accurate.

-[ DFTB ]-

   Start up a **new AMSinput**
   **1.** Switch to **DFTB**: [image: ADFPanel][image] **→** [image: DFTBPanel][image]
   **2.** Select **Task → NEGF**
   **3.** Select **Model → SCC-DFTB**
   **4.** Select **Parameter directory → QUASINANO2013.1**
   **5.** Click on [image: MoreBtn][image] next to **Task: NEGF** to switch to the NEGF panel (or click on **Model → NEGF**)

-[ BAND ]-

   Start up a new **AMSinput**
   **1.** Switch to **BAND**: [image: ADFPanel][image] **→** [image: BANDPanel][image]
   **2.** Select **Task → NEGF**
   **3.** Click on [image: MoreBtn][image] next to **Task: NEGF** to switch to the NEGF panel (or click on **Model → NEGF**)

In the **NEGF panel**, import the lead file we just created
('Au_lead.xyz'):

   Click on the folder icon next to **Lead**: this will prompt a file dialog window
   Open **Au_lead.xyz** (the .xyz file you just created)

**Fill the central region** with 9 gold atoms using the "Fill central
region" option:

   Click on **Fill**
   Enter **9** in the prompted dialog window and click on **OK**

Let us also change the range for the Transmission energy grid to
**[-3.5,3.0]**, to match the energy range of PhysRevLett.93.096404:

   Set the **Transmission energy grid** to **-3.5 ... 3.0**

This is what your set-up should look like:

[image]

We are now ready to **run the calculation** and visualize the results
with **AMSspectra**:

   Click on **File → Save as...**
   Run the calculation with **File → Run**
   Wait for the calculation to finish
   Click on **SCM → Spectra...**

This is the computed transmission function through a 1D gold chain:

-[ DFTB ]-

[image]

-[ BAND ]-

[image]


CO on gold chain transport calculation
======================================

We now modify our previous system by adding a CO molecule in the
central region:

   Select the AMSinput window: **SCM → Input**
   Add the **CO** molecule by **copy-pasting** the following coordinates into AMSinput (**CTRL+V** in molecule drawing area)

   O     0.0   0.0   3.12
   C     0.0   0.0   1.96

The gold atom on which CO is adsorbed is "pulled" towards the CO
molecule by 0.2 Angstrom:

   In the **Coordinates panel** adjust the position of the central gold atom to **(0.0, 0.0, 0.2)**
   Change the View Direction to Along Y-axis either via the View Menu or via pressing CTRL+2.

Your system should look like this:

[image]

Tip:

  It is good practice to include some *buffer* lead material in the
  **central region**, and test the convergence of the results with
  respect to the *buffer* size (in this tutorial we have 4 *buffer*
  gold atoms on each side of the central Au-CO).

**Run the calculation** and visualize the results with **AMSspectra**:

   Click on **File → Save**
   Run the calculation with **File → Run**
   Wait for the calculation to finish
   Click on **SCM → Spectra...**

This is the computed transmission function when CO is adsorbed on a
gold chain.

-[ DFTB ]-

[image]

-[ BAND ]-

[image]

As expected, the conductivity around the Fermi energy is suppressed by
the adsorbed CO molecule.
