CO on 1D gold chain

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.

../_images/negf_t2_system_cartoon.png

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”.

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 $ADFHOME/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 ADFInput:

Start up ADFInput
1. Switch to BAND: ADFPanel BANDPanel
2. From the main BAND-panel, select Periodicity → Chain
3. Click Click on MoreBtn to switch the Lattice panel
../_images/negf_t2_create_lead_1.png

In the lattice panel we can specify the lattice vector:

Set the lattice vector to 2.9
../_images/negf_t2_create_lead_2.png

We now add the gold atom

1. Click on ‘X’
2. Select ‘Au’
3. Click anywhere in the drawing area to add the gold atom
../_images/negf_t2_create_lead_3.png

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)
../_images/negf_t2_create_lead_4.png

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

Click on File → Export Coordinates...
Save the file as “Au_lead.xyz”
Close ADFInput File → Close

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 BAND-NEGF gold chain calculation:

Start up ADFInput
1. Switch to BAND: ADFPanel BANDPanel
2. In the main BAND panel, select Relativity → Scalar (important for heavy elements)
3. Select Task → NEGF
4. Click on MoreBtn to go to the NEGF panel (or click on Model → NEGF)
../_images/negf_t2_main_panel.png

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:

../_images/negf_t2_Au_chain_ready.png

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

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:

../_images/negf_t2_Au_chain_T.png

CO on gold chain transport calculation

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

Select the ADFInput window: SCM → Input
Add the CO molecule by copy-pasting the following coordinates into ADFInput (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)

Your system should look like this:

../_images/negf_t2_CO-Au_chain_ready.png

Tip

It is good practice to include some buffer lead material in the central region, and test the convergence of the results WRT 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 ADFSpectra:

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.

../_images/negf_t2_CO-Au_chain_T.png

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