Calculating Adsorbtion and relaxation energies of Aqueos state Catalysis

1

Hi,

I am struggling to calculate the adsorbtion energies for my system which has palladium slab on which I intend to get the adsorbtion energies of -OOH ( ORR reaction intermediate of water reduction). I followed the tutorial to find out we use ASE to setup the slab. Since everything provided in the tutorials is gas phase adsorbtion, it would be helpful if you could direct me or give a headsup with how to set up the ASE ( since the OOH and other intermediates are not in the Atoms mooduleI I cannot setup the problem) environment for the aqueos system explained above. Also thank you for this amazing platform and I am using the .traj file of H , OH ,OOH from OC22 which i assume has no fixed atom constraints. If I can make sure I am on right page whether or how to run a aqueos phase visualisation it will be a big piece of puzzle solved when I implement in the lab. Thanks again.

Felix

2

Hey -

Yeah some of the pre-defined adsorbates/molecules in ASE don’t really contain intermediates. However, you aren’t limited to the exact molecules contained with ASE and you should be able to create whatever environment you’re interested in. If I were to simulate an aqueous environment I would place a bunch of H2O molecules on top of the surface. For instances, the Atoms module:

atoms_environment = Atoms(["O", "O", "H"], positions=[(0,0,0), (0, 0, 1), (0.5, 0, 1.5)])

Alternatively, ASE provides support for a large range of inputs. Are you creating inputs in a different format? If so, you should be able to convert that into an ASE Atoms object and use it with our models. Let me know if I’m misunderstanding your question though!

3

Sorry for the late reply,

Thank you so much.

I figured out setting up of the adsorbate and slab and the dataset everything to be used. As said I am trying to predict the trajectories of intermediates.

I set up all the simulation environment, once I visualise my trajectories I get the following error

IndexError Traceback (most recent call last)

in <cell line: 11>()
9 radii=0.8,
10 rotation=(“-75x, 45y, 10z”))
—> 11 ase.visualize.plot.plot_atoms(traj[25].repeat((2,2,1)),
12 ax[1],
13 radii=0.8,

IndexError: list index out of range

IndexError Traceback (most recent call last)

in <cell line: 11>()
9 radii=0.8,
10 rotation=(“-75x, 45y, 10z”))
—> 11 ase.visualize.plot.plot_atoms(traj[25].repeat((2,2,1)),
12 ax[1],
13 radii=0.8,

IndexError: list index out of range

I can only see the initial state of my catalysis process, but not when the slab is at the different time steps ( from my understanding in the code) .

Thank you already for the help, Figuring this will be great step when I do the catalysis in the lab this week.

Felix