create OC22 dataset

[mingyue605]

Hi,

I have a question regarding the function get_random_clean_slabs from the termination_generator.py script in the Open Catalyst Dataset (OC22). Specifically, I’m trying to create metal oxide structures myself following the OC22 dataset format. However, I encounter an issue on line 163 where I get the error 'O'.

I'm unsure whether the problem is related to how I’m creating the bulk structure. Below is the script I’m using to generate the bulk structure for Al₂O₃:

python
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from pymatgen.core import Structure, Lattice

Define the lattice for Al2O3 (corundum structure - hexagonal/trigonal lattice)

lattice = Lattice.hexagonal(a=4.759, c=12.991) # Lattice constants for Al2O3 in angstroms

Define the atomic basis (positions of atoms in the unit cell for Al2O3)

species = ["Al", "Al", "Al", "Al", "Al", "Al", "O", "O", "O", "O", "O", "O"]
coords = [
[0.3522, 0.0000, 0.2500],
[0.6478, 0.0000, 0.7500],
[0.0000, 0.3522, 0.7500],
[0.0000, 0.6478, 0.2500],
[0.6478, 0.6478, 0.2500],
[0.3522, 0.3522, 0.7500],
[0.3060, 0.0000, 0.2500],
[0.6940, 0.0000, 0.7500],
[0.0000, 0.3060, 0.7500],
[0.0000, 0.6940, 0.2500],
[0.6940, 0.6940, 0.2500],
[0.3060, 0.3060, 0.7500]
]

Create the bulk structure as a Structure object

bulk_structure = Structure(lattice, species, coords)

Import the slab generator

from termination_generator import get_random_clean_slabs

Set parameters for slab generation

n_slabs = 3
max_index = 2
min_slab_size = 10 # in Å
min_vacuum_size = 15 # in Å

Generate random clean slabs

random_slabs = get_random_clean_slabs(bulk=bulk_structure,
n_slabs=n_slabs,
max_index=max_index,
min_slab_size=min_slab_size,
min_vacuum_size=min_vacuum_size)
Could you please help me identify whether the bulk structure is being created correctly, or if there might be an issue causing the error during slab generation? I’d appreciate any guidance or advice you can offer on how to resolve this issue.

Thank you!