To setup the atomic coordinates of the device you will use the Custom Builder tool. Open up VNL and start up the Custom Builder tool with a left-click on the icon on the Toolbar.

Within the Custom Builder select the Graphene Junction builder from the Builders menu.

After selecting the Graphene Junction builder, the left side of the tool will have a number of parameters that may be edited and in the right side there is a 3-D view of the structure which corresponds to the current settings of the builder.

The structure is of the DeviceConfiguration type which consists of two electrodes and a central region. The electrodes are periodic structures, and their unit cells are visualized. The central region seamlessly connects the left electrode with the right electrode.

Change the settings of the builder parameters according to the following figure.

The new settings of the parameters have elongated the electrodes and the central region, as well as enabled a dielectric region and a gate potential below the structure. The dielectric region is visualized as a transparent purple region and the gate potential is a metallic region below this.

The required length of the electrode cell depends on the computational model employed. Strictly speaking, the length of the cell in the the C-direction should be longer than the interaction distance of the model. For most models a length of about 7 Å suffices.

The next step is to set up the analysis of e.g. the transmission spectrum for the graphene junction, as well as other properties. First, locate the drag icon positioned in the bottom right-hand corner of the Database window. Left-click and drag-and-drop the icon on to the Script Generator tool located on the VNL Main Window toolbar. The Script Generator tool then opens with the graphene junction displayed in the Script Generator's 3-D viewer indicating that this is the active atomic configuration of the tool.

The Custom Builder tool is no longer needed, so to save space on your desktop, close the tool by pressing Ctrl+W.

Your next task is to set up a calculation for the graphene junction and specify the physical properties that should be calculated. The first step is to create the calculator. To do this, double-click the New Calculator item in the left column. This creates a new calculator block, which is the first block in the input script that is build up in the right column. The Script Generator tool should look like the following

In order to modify the calculator parameters, double-click the newly created item in the right column. This brings up a window where you can change and fine-tune various properties of the calculator. Select the Device Extended Hückel calculator within this new window, and lower the number of k-points in the C direction to 50, as this should be sufficient. The window should look like this

The next step is to change the basis set for the calculation to use parameters specifically fitted to give a good description for Graphite [4]. To this end left-click on the Hückel basis set line in the Calculator settings list and select the Cerda.Carbon [Graphite] and Cerda.Hydrogen [C2H4] basis set.

Uncheck the No SCF iteration box, to perform a self consistent calculation. Electro-static interactions are only included in the self consistent model.

The window should now look like this

The next part is to set up the boundary conditions for the Poisson solver. Left-click on the Poisson solver item of the calculator settings list. In the C-direction the boundary condition for the electrostatic potential is determined by the electrostatic potential in the electrodes, corresponding to a Dirichlet boundary condition. For the two other directions choose a Neumann boundary condition. The Neumann boundary condition corresponds to a zero electric field at the boundary of the computational box, and this gives the best model for studying the effect of the gate potential. This is the last calculator parameter you will need to set and the window should now look like this

Adding analysis objects for calculating physical properties of the system under study is as easy as double-clicking the red Analysis item in the left column of the Script Generator. This brings up a pop-up menu from which you can select different analyses to carry out. Select the ElectronDifferenceDensity, ElectrostaticDifferencePotential, and TransmissionSpectrum analysis objects. As you will learn later in this tutorial, the conductance and current of the device are obtained via the TransmissionSpectrum analysis object.

In order to save results into a more telling filename other than "analysis.nc", rename the default output file to "z-a-z-6-6.nc". This will save all calculations to this single file. Ultimately, the three analysis objects will be listed in the right column of the Script Generator and it should look as follows

Finally, change the default settings for the TransmissionSpectrum analysis object to generate a spectrum with 200 points in the energy range [-2,2] eV. Double-click on the TransmissionSpectrum object in the right column and specify parameters accordingly in the window that will open, as illustrated below

You are now done setting up the calculation. The next step is to save the calculation script itself. You do this by pressing the Save As button in the Script Generators File menu, which saves the defined calculation setting as a Python script on your disk. Select the name “z-a-z-6-6.py” and left-click Save. Now, change to the VNL Main Window. Notice that the file z-a-z-6-6.py you saved is displayed in the browser view of the Main VNL Window.

Once your calculation has been stored as a script on disk, the script can be executed with the Job Manager tool. To do this, locate the file in the browser view of the Main Window, and then drag-and-drop this file onto the Job Manager icon located in the toolbar.

The Job Manager window then appears

To start the execution of the calculation, press the Run Queue button. As a result, a log window appears displaying and updating information regarding the job execution state of each script in the job queue. The job will take 5 to 15 minutes, depending on your computer.

The job will first perform a self-consistent calculation for each of the electrodes. The self-consistent Hartree potential is then used as a boundary condition for a self-consistent calculation for the central region of the device. Finally, the transmission spectrum and other analysis objects of the structure will be calculated. Once the job has finished, the log window will contain the following lines at the end:

NanoLanguageScript finished successfully
+------------------------------------------------------------------------------+
| NanoLanguageScript execution finished                                        |
+------------------------------------------------------------------------------+

You will now examine the outcome of the calculation. In VNL, the Main Window is used for inspecting, analysing, extracting, and visualizing the results of your calculation.

Switch to the VNL Main Window, inspect the browser view, and notice that a NetCDF file z-a-z-6-6.nc has been generated. Then left-click this particular file in the browser view, and observe how the contents of z-a-z-6-6.nc is summarized in the top-right part of the Main Window, where entries for Device Configuration, Electron difference density, Electrostatic difference potential, and Transmission spectrum are displayed.

Then left-click to select the Transmission spectrum item. The bottom-right part of the Main Window now contains two entries, namely plot (for visualizing the transmission spectrum) and export (for generating a text file with the transmission spectrum data). Your VNL Main Window should look like this:

To view the transmission spectrum, press the Show button. This will reveal the following plot of the transmission spectrum.

Note that the transmission spectrum has a low value in the energy range [-0.5, 1.5] eV, corresponding to the energy window within the band gap of the central semi-conducting armchair-edge ribbon. The asymmetric position of the electrode Fermi levels relative to the band edges, i.e. the shift of the valence band edge of the central region towards the electrode Fermi levels, is due to the applied gate potential of 1 V.

You may zoom into details of the plot by moving the mouse while pressing the left-mouse button. To reset the zoom level, use the shortcut Ctrl+R or right-click the plot to access the command via a pop-up menu.

To visualize the effect of the gate potential, select the Electrostatic difference potential item and press its associated Contour Show button. This action launches the 3-D Viewer tool (corresponding to the icon on the VNL Toolbar).

You may manipulate the Viewer camera with the following mouse operations:

Use the above mouse operations to position the contour plot of the electrostatic difference potential similar to the plot shown below

To make the plot more interesting, add a 3-D rendering of the graphene junction by first selecting the Device configuration item in the top-right view of the Main Window. Then click on Device configuration in the bottom-right view, and drag-and-drop the item onto the open 3-D Viewer window.

Next rotate the contour plot. This is done by right-clicking the 3-D Viewer window and choosing the Properties... item. Then select the contour cut plane from plots tree shown in the appearing dialog, and change the angle θ_y to 151°. Finally, apply mouse operations to fine tune the camera of the 3-D Viewer and obtain a plot similar to the plot shown below

If you wish to export a copy of the contour plot, right-click in the 3-D Viewer window, and choose Export… (Ctrl+E). Type in the name of your graphics file in the appearing file dialog browser, for example “contour.png” or “contour.jpg” (the graphics file format is chosen from the file extension you specify). Finally, press the Save button. The plot is now stored on disk and can be used for further processing in any other third party application of your choice.

In the next chapter you will learn how to calculate the temperature dependent conductance from the TransmissionSpectrum analysis object.