Guide To Using Adsorber

There are four parts (Part A, Part B, Part C + Part D) + a prelude step to using the Adsorber program. These parts are described in the sections below:

Prelude Step

In this step, we will step up the general.py and adsorbate.py scripts, which include all the inputs that are required across the whole Adsorber program. Information about how to set up these two python script are given in Prelude 1: Setting your general.py and adsorbate.py scripts. Extra details about how to set up the adsorbates in your adsorbate.py script are given in Prelude 2: How to obtain some of the settings for the adsorber.py script.

Part A

This part creates the VASP files to locally optimise your system, as well as lone adsorbates and any other molecules that you need to reference your VASP energies to. The guide to perform this set is given in Part A: How to optimise your system, as well as optimise adsorbates and other molecules. If you already have the system locally optimised with your functional, feel free to move on to Part B.

Part B

In this part, your VASP optimised system will have all adsorbates attached to it in all the various top sites, bridging sites, three fold sites, and four fold sites found across the surface of your system. From these you can select which models your want to include for further optimisation by VASP. The guide to perform this part is given in Part B1: Adsorbing Adsorbates to your System, with further information in Part B1: How to Mark Surface Atoms in your Cluster/Surface model in Adsorber and Part B2: How to choose which xyz files to optimise in VASP.

Part C

In this part, Adsorber will take the models of adsorbates on various sites on your system and create the files required to locally optimise these models in VASP. The guide to perform this part is given in Part C1: Preparing Selected Adsorbed Systems For VASP Optimisation, with further information in Part C1: How to submit VASP jobs to Slurm: Adsorber submit and Part C2: What To Do If Some Jobs Have Not Finished/Converged.

Part D

In this part, a subsidiary program is used to gather information about your VASP local optimisations, including the energy of absorbate+system as well as adsorbates and system alone, as well as if the VASP local optimisation converged or not. The guide to perform this part is given in Part D: Gathering Information from VASP Calculations.

Final Notes about this process

You may want to move backwards and forwards between these parts as you progress in your study. Parts B - D can be performed multiple times if you want to include extra adsorbates in your study. I performed Part C multiple times as I like to focus on obtaining and understanding the energetics of an adsorbates on various top, bridging, three-fold, and four-fold sites and understand which of these site are preferable for binding before moving on to the next adsorbate.