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.
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 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
system.txt then subtract it from each step in the trajectory:
import ase.io trajectory = ase.io.read("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.