adsorb-screen

Automated, general-purpose AdsorbML configuration screening of molecules, radicals, and atoms on any catalytic surface using FAIRChem v2 / UMA and VASP input generation.

Key Features

• Any Adsorbate: Screen built-in radicals (CH2I2, CH2I, CH2, CH2OO), any single atom (H, O, N, I, Pt), any molecule in the ASE G2 database (CO, CO2, NH3, CH3OH, H2O, C2H4), SMILES strings (smiles:CC(=O)O), or custom structure files (.xyz, POSCAR, .sdf).
• Any Catalytic Surface: Provide your own slab (--slab-file), cleave any bulk crystal file (--bulk my_oxide.cif --millers 1 1 0), use built-in oxide presets (alpha-quartz, rutile-TiO2, MgO), use any ASE metal/crystal (--bulk Pt --millers 1 1 1), or fetch directly from the Materials Project (--bulk mp-126 --millers 1 1 1).
• Symmetry-Aware Binding Modes: Automatically identifies symmetry-unique monodentate and bidentate binding sites and orients lone pairs/radical lobes toward the surface (down), pi-systems parallel to the surface (flat), or bidentate bridges (pair).
• Anomaly Filtering & VASP Export: Rejects dissociated, desorbed, intercalated, or reconstructed trajectories and exports ready-to-run VASP directories (POSCAR, INCAR, KPOINTS, POTCAR_ORDER) with open-shell MAGMOM/NUPDOWN and metallic/insulator smearing.

Installation

pip install -e .
# Optional extras for SMILES and Materials Project support:
pip install -e ".[smiles,mp,dev]"
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