Some questions

Hello,
I have two questions. I would be grateful if you could teach me.(1)In the tutorial( Zacros Tutorial ), calculations were performed to determine that C2H5 occupies only one site. Even if the molecule is enlarged with C3 or C4, if it adsorbs to only one catalytic atom, is it not necessary to set it to occupy two sites?(2)Does the energy obtained from DFT and written in the energy file have to contain the zero-point and free energy corrections? I couldn't find where to input frequency in Zacros' input file, so is it necessary to use the values converted to free energy beforehand as input for energy?Thank you.

To answer your questions:

1) The tutorial you mentioned was just a simple example. Certainly for realistic simulations one can use bidentate species, and the model developer has to make a choice that should be informed by ab initio calculations (which actually show how the species bind to the surface). In general, I would recommend trying simple models first and then building up complexity, otherwise KMC models can quickly become diffucult to handle. Simplications can be neglecting high-energy binding configurations, treating species as monodentate in the first instance, and incorporating the lowest energy pathways in the reaction mechanism.

2) It's up to the user how the energies are expressed, Zacros "doesn't care" where the values come from and how they were calculated. Having said that, you need to be careful to make sure you don't double-count things. So if you add the ZPE correction to your species formation energies and the reaction barriers, you should not include it in the vibrational quasi-partition function, Qvib, i.e. you should then use the form of Qvib that takes the ground state (not the bottom of the well) as the reference energy (E_ground_state = 0 eV). Regarding the thermal (free energy) corrections, it is recommended to have these in the preexponentials, since Zacros allows you to have a temperature-dependent form of the pre-exponential, but only a fixed (temperature-independent) activation energy.