Au-(4,4’-bipyridine)-Au molecular junction

In this tutorial we will use the NEGF geometry building tools to create a Au-(4,4’-bipyridine)-Au molecular junction:

/scm-uploads/doc.2019/Tutorials/_images/negf_t3_final_geo.png

Using tips

Start up ADFInput
Switch to BAND
In the main BAND panel, select Relativity → Scalar (important for heavy elements)
Select Task → NEGF
Click on ... to go to the NEGF panel (or click on Model → NEGF)

Import the leads and fill the central region with 4 layers of lead material:

Click here to download the lead file Au3x3_lead.xyz
Import the lead file Au3x3_lead.xyz by clicking on the folder icon next to Lead
Fill the central region with 4 layers of lead material

We now carve two tips out of the central gold wire:

Select the gold atoms as shown in the picture below
Delete the selected atoms by pressing delete on your keyboard
/scm-uploads/doc.2019/Tutorials/_images/negf_t3_carve_out.png

We need to make space in the central region for the 4,4’-bipyridine molecule; to this aim we define a left tip and a right tip:

1. Select the gold atoms on the left-hand side
2. Click on + next to Left Tip in the NEGF panel
Clear the selection by clicking anywhere in the molecule-drawing area
3. Select the gold atoms on the right-hand side
4. Click on + next to Right Tip in the NEGF panel
/scm-uploads/doc.2019/Tutorials/_images/negf_t3_assign_tip.png

Your system should now look like this:

/scm-uploads/doc.2019/Tutorials/_images/negf_t3_tips_ready.png

Tip

You can remove atoms from a tip by selecting them and clicking on - next to Left/Right Tip in the NEGF panel

The tips are now anchored to their respective leads. If we move the two leads via the Left/Right lead offset, the tips will follow them.

Make space for 4,4’-bipyridine molecule:

Set the Left lead offset to -10.0 Angstrom
Set the Right lead offset to 10.0 Angstrom

and import it:

Click here to download the .xyz file 4_4_bipyridine.xyz
Click on File → Import Coordinates
Open 4_4_bipyridine.xyz (the .xyz file you just downloaded)

Your system should now look like this:

/scm-uploads/doc.2019/Tutorials/_images/negf_t3_mol_imported.png

Warning

This calculation is computationally demanding; running this job on a 4-cores desktop machine might take one hour or more.