Computational Lab 3

Periodic Boundary Conditions-Local Optimization of Bulk Gold and Gold surfaces with DFT

Part 4: Calculating Binding Energies

Lastly, in the dimension exposed to vacuum, we can calculate the binding energy of species such as oxygen in the form of a hydroxyl group.

1. First, create a new directory called Slab111_OH. Copy the INCAR, KPOINTS, CONTCAR and slurm_fri.sub from Slab111 into Slab111_OH. Rename your CONTCAR into POSCAR. Make sure that the CONTCAR you are copying over isn't empty!
2. Then you will need to add a hydroxyl group to the surface with ASE (ase gui):

   Use ase gui to edit your POSCAR or CONTCAR files by using command "ase gui POSCAR" or "ag POSCAR".
   

   Adding the OH group

   Left click is used to select atom(s) and right click will rotate your camera. When an atom is selected, it is outlined with thick dark green lines.
   Select an Au atom. From the menu bar on top, click Edit. In the drop down menu, click Add atoms. Or use the short cut "ctrl + a". A dialog box will pop up. In the first box after "Add:", delete "(selection)" and type "O". Two lines below at "Coordinates:", select the third window and enter "1.5". This determines the coordinates of the added atom relative to your selected atom. Then click button "Add". An oxygen atom will be added on top of your selected Au atom, with a distance of 1.5 Å. The newly added Oxygen atom is automagically highlighted.

   Moving the OH group

   To move the hydroxyl group to your desired location, if different from where you added it, select both O and H. You can do this by either hold down "Ctrl" and left click both atoms, or drag a box by holding down left mouse to capture both atoms. Then go to the menu bar, select Tools. From the drop down menu, select Move selected atoms or use short cut "ctrl + m". The atoms will now be outlined with light green. You can move the atoms with arrow keys. They will always move relative to your camera.

   Visualize bonds and save

   To check the positioning of your atoms are appropriate, click, in the menu bar, View. From the drop down menu, click "Show bonds" or use short cut "ctrl + b" to show bonds. Your oxygen should be bonded to both the H atom and the Au atom. Save your edits by clicking from the menu bar "File". From the drop down menu, click Save or use short cut "ctrl + s". A dialog box will pop up. From the upper right box, find POSCAR and double click it. Another dialog box will pop up asking you if you want to overwrite existing file. Click yes. If you do not already have a POSCAR, you can instead go to the box on the bottom with the current path, append "POSCAR" to its end and click "OK".
   You can find more about ASE and ase gui from their documentation.

3. Create your new POTCAR with sogetsoftpbe.py, edit your .sub file and relax the structure.
4. Next, calculate the binding energy. The reference molecules will be water and hydrogen gas. Since you already made these molecules previously, you can directly use the energies you found. The equation for the binding energy of a hydroxyl group is as follows:
   
   E_bindingOH=E[AuOH] + 0.5 E[H₂] - E[H₂O] - E[Au]