Adsorption energy

Hello, Excuse me, I would like to ask what energy does the energy in each randomxxxx.extxyz file represent? Can you provide the adsorption capability of each step of the optimized trajectory of DFT? Hope you can clear up your confusion.

Hi -

The energy corresponds to the raw DFT energy produced by VASP. If you want the adsorption energy of each step, you must extract the reference energy and subtract that. Specifically, there should be a text file system.txt in the format system_id, reference_energy. system_id corresponds to the randomXXX of the particular .extxyz file. For example, if I wanted to compute per-step adsorption energy for random123456.extxyz, I would find the reference_energy corresponding to random123456 in system.txt then subtract it from each step in the trajectory:


trajectory ="random123456.extxyz", ":") # read all frames
per_step_adsorption_energies = [atoms.get_potential_energy() - reference_energy for atoms in trajectory]

Ok, I see. Thank you very much for your answer.