Part A: How to optimise your system initially

To begin, we need to obtain the locally optimise version of the system you want to adsorb adsorbates onto. To do this, you will want to set the Step_to_Perform variable in the Run_Adsorber.py script to 'Part A':

Step_to_Perform = 'Part A'

You also need to create a folder called VASP_Files that contains the following files and folders:

  • INCAR: This is a VASP file that contains all the information required to run the VASP job (https://www.vasp.at/wiki/index.php/INCAR and https://cms.mpi.univie.ac.at/vasp/vasp/INCAR_File.html).

  • KPOINTS: The KPOINTS file is used to specify the Bloch vectors (k-points) that will be used to sample the Brillouin zone in your calculation (https://www.vasp.at/wiki/index.php/KPOINTS).

  • POTCARs: This is a folder that contains all of the POTCAR files for all of the different elements in your models. Each of the POTCAR files in this folder need to be labelled as POTCAR_XX, where XX is the symbol for the particular element. For example, for the POTCAR to describe Cu, you want to name the POTCAR as POTCAR_Cu, the POTCAR for C should be called POTCAR_C, the POTCAR for H should be called POTCAR_H, ….

You want to also include any other files that will be needed. For example, if you are running VASP with the BEEF functional, you need to include the vdw_kernel.bindat file in the VASP_Files folder.

An example of VASP_Files folders can be found in Adsorber Examples on Github.

You can then run the Run_Adsorber.py script in the terminal:

python Run_Adsorber.py

This will create a folder called Part_A_Non_Adsorbed_Files_For_VASP. In this folder is another folder called system that contains all the VASP files required to locally optimise your system in VASP.

This Part_A_Non_Adsorbed_Files_For_VASP folder also contains all the VASP files of your adsorbates that you can also locally optimise in VASP. This is often required to determine in the adsorption energy of your adsorbate onto your system

\[E_{abs} = E(system+adsorbate) - (E(system) + E(adsorbate))\]

or if you are defining your adsorption energy with reference species, such as C from graphene, H from H 2 , and O from H 2 O:

\[E_{abs} = E(system+adsorbate) - (E(system) + E(each\;element\;in\;the\;adsorbate\;in\;stiochiometic\;amounts))\]

Once you have run VASP on your system and all your adsorbates, proceed to Part B (Part B: Adsorbing Adsorbates to your System).