I am trying to model an electrochemical reaction (O2 + 4H+ + 4e- = 2H2O) by LAMMPS artificially. It means that I want to consider H2O and O2 in the reaction. Since the reaction happens on the catalyst surface, I want to write a LAMMPS input file in which 1. oxygens get disappeared on the catalyst surface 2. The disappeared oxygen molecules enter the simulation box.
I would be grateful if there are any suggestions.
Perhaps fix bond/react can do what you want. Otherwise, you would need to look into writing your own fix that will remove atoms/molecules and replace with other atoms/molecules. There are fix evaporate and fix deposit that can each do half of it, so there is some kind of template to follow.