NEGF: Create a Molecular Junction
*********************************

DFTB Organic electronics NEGF (Non-Equilibrium Green's Function) Metal
wire Gate potential Transmission function Current

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

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

[image]


Instructions
============

   Start up **AMSinput**
   Switch to **DFTB**: [image: ADFPanel][image] **→** [image: DFTBPanel][image]
   Select **Task → NEGF**
   Select **Model → SCC-DFTB**
   In the main DFTB panel click on **Parameter directory → QUASINANO2013.1**
   Click on [image: MoreBtn][image] 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**
   Click on **Fill** and 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
 [image]

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**

Your system should now look like this:

[image]

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 (System) → From File(s) ...**
   Open **4_4_bipyridine.xyz** (the .xyz file you just downloaded)

Your system should now look like this:

[image]

Tip:

  It is good practice to test the convergence of the results with
  respect to the **number of lead repetitions and** an amount of
  **buffer lead material in the central region**

We are now ready to run the calculation:

   Click on **File → Save**, and name the job "zero_gate"
   Run the calculation with **File → Run**
   Wait for the calculation to finish


Gate potential
==============

To include a **gate potential** for the 4,4'-bipyridine molecule:

   In the **NEGF panel** in AMSinput
   **1.** **Select** the **4,4'-bipyridine molecule**
   **2.** Click on **+** next to **Gate potential region** in the **NEGF panel**
   **3.** Set the Gate **Voltage** to **0.2 V**
 [image]

We will now run the job and visualize the results:

   Click on **File → Save as...** and save it as **gate_02**
   Run the calculation with **File → Run**
   Wait for the calculation to finish
   Click on **SCM → Spectra...**

To better see the effect of the bias potential on the transmission
function, we can **add** the transmission functions at zero gate we
computed earlier:

   In **AMSspectra** click on **File → Add** and select **negf.rkf** in the **gate_zero.results** folder
 [image]
