An error occurs when I follow the AdsorbML Tutorial

[LeehansoL-123]

Python version

3.12.3

fairchem-core version

2.13.0

pytorch version

2.8.0

cuda version

12.8

Operating system version

No response

Minimal example

# The exact code from fairchem/docs/catalysts/examples_tutorials/adsorbml_walkthrough.md

from __future__ import annotations

import pandas as pd
from fairchem.data.oc.core import Adsorbate, Bulk, Slab

bulk_src_id = "mp-30"
adsorbate_smiles = "*CO"

bulk = Bulk(bulk_src_id_from_db=bulk_src_id)
adsorbate = Adsorbate(adsorbate_smiles_from_db=adsorbate_smiles)
slabs = Slab.from_bulk_get_specific_millers(bulk=bulk, specific_millers=(1, 1, 1))

# There may be multiple slabs with this miller index.
# For demonstrative purposes we will take the first entry.
slab = slabs[0]


from ase.optimize import LBFGS
from fairchem.core import FAIRChemCalculator, pretrained_mlip
from fairchem.core.components.calculate.recipes.adsorbml import run_adsorbml

predictor = pretrained_mlip.get_predict_unit("uma-s-1p1")
calc = FAIRChemCalculator(predictor, task_name="oc20")
print(adsorbate.atoms)
outputs = run_adsorbml(
    slab=slab,
    adsorbate=adsorbate,
    calculator=calc,
    optimizer_cls=LBFGS,
    fmax=0.1,
    steps=20,  # Increase to 200 for practical application, 20 is used for demonstrations
    num_placements=10,  # Increase to 100 for practical application, 10 is used for demonstrations
    reference_ml_energies=True,  # True if using a total energy model (i.e. UMA)
    relaxed_slab_atoms=None,
    place_on_relaxed_slab=False,
)

# visualizing the bug
print(adsorbate)
print(outputs["adslabs"][0]["atoms"])

from ase.visualize import view
aaa = outputs["adslabs"][0]["atoms"]

view(aaa)

Current behavior

as output, Adsorbate changed as N2H4

Expected Behavior

Adsorbate should be CO

Relevant files to reproduce this bug

fairchem/docs/catalysts/examples_tutorials/adsorbml_walkthrough.md

In the run_adsorbml() function, replacing adsorbate=adsorbate with adsorbate=adsorbate_smiles resolves the issue and ensures the code runs correctly.

Please update the tutorial code to prevent confusion for other users.

[mshuaibii]

Thanks for catching this! Fix landing soon - #1810