chem-sorption-relax

Goal

To process porous frameworks (e.g., MOFs, COFs) for downstream molecular sorption calculations. It checks if the unit cell's interplanar distances are large enough (usually ≥ 12 Å for typical gases) to avoid self-interaction of gas molecules across periodic boundaries. If not, it builds an appropriate supercell. Finally, it uses a standard Machine Learning Interatomic Potential (MLIP) workflow to relax the structure.

Prerequisites

• Input: A framework structure in CIF (or XYZ) format.
• MLIP MCP Tool: A relaxation tool such as mcp_fairchem_relax_structure, mcp_mace_relax_structure, or mcp_matgl_relax_structure.
• Conda environment: base-agent for the supercell builder logic, followed by the specific environment for the chosen MLIP (e.g., fairchem-agent).

Instructions

1. Build Supercell (if necessary): Determine if the input framework needs to be expanded. Use the provided utility to read the input CIF, check interplanar distances, build a supercell if they are below the threshold, and save the result.