Use this skill for thermodynamic and free-energy post-processing, result normalization, explicit adsorbate-only frequency-job SOP, and concise reporting standards for catalyst comparison.
Use this skill to convert raw electronic-structure results into comparable thermodynamic conclusions.
For MACE-derived vibrational post-processing, treat frequencies as the vibrational-analysis stage only, then evaluate thermodynamics with ASE HarmonicThermo for adsorbates/slabs or IdealGasThermo for gas molecules. The local implementation reference is references/ase_vibrational_thermo_reference.md.
fix_atoms_by_indicesidentify_structure_fragmentsvaspkit_adsorbate_thermo_correctionvaspkit_gas_thermo_correctionIBRION=5, POTIM=0.015, NFREE=2, and ISYM=0.ISYM=0 as mandatory for these jobs; leaving symmetry on can conflict with parallel settings such as NCORE and fail before frequencies are evaluated.mace_analyze_frequencies as the vibrational-analysis stage only, then follow the ASE thermochemistry implementation pattern in references/ase_vibrational_thermo_reference.md.CONTCAR already has the correct selective-dynamics mask for adsorbate-only thermochemistry. A relax-stage mask that still leaves surface atoms mobile is not acceptable for adsorbate-only vibrational treatment.ads_indices are known, explicitly refreeze the relaxed structure before writing the frequency job. Use fix_atoms_by_indices(indices=ads_indices, reverse=true) on the relaxed adsorbate-slab structure so only the adsorbate atoms remain T T T and every slab atom is F F F.identify_structure_fragments. Prefer the default jmolnn probe and compare the fragment/reference-index overlap against existing ads_indices. Use this as a physisorption sanity check only; do not treat it as a robust chemisorption detector.ENCUT, EDIFF, smearing, spin treatment, DFT+U, D3, dipole correction, and related reference-sensitive toggles.Return:
references/ase_vibrational_thermo_reference.md.band-and-dos-analysis, reaction-neb-analysis, or md-diffusion-analysis as the upstream workflow skill before final thermochemistry reporting.