Use when the user asks to analyze computational results: Gibbs free energy, OER/HER/CO2RR overpotentials, adsorption energy, convergence tests, DOS/d-band analysis, or Bader charge analysis.
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This skill routes analysis requests to the correct sub-skill based on what the user is asking for.
| User Intent | Sub-Skill | Key Indicators |
|---|---|---|
| Gibbs free energy, ZPE, thermal corrections | gibbs/ | "free energy", "ZPE", "entropy", "thermal" |
| OER overpotential | oer/ | "OER", "oxygen evolution", "water splitting anode" |
| HER overpotential | her/ | "HER", "hydrogen evolution", "water splitting cathode" |
| CO2 reduction | co2rr/ | "CO2RR", "CO2 reduction", "carbon dioxide" |
| Adsorption energy | adsorption/ | "adsorption energy", "binding energy", "E_ads" |
| ENCUT/KPOINTS convergence | convergence/ | "convergence", "ENCUT test", "k-point test" |
| DOS, d-band center, PDOS | dos_analysis/ | "DOS", "d-band", "PDOS", "density of states" |
| Bader charge | charge/ | "Bader", "charge transfer", "charge analysis" |
| MACE Ni benchmark (Kreitz 2021) | mace_ni_benchmark/ | "Kreitz", "MACE Ni benchmark", "MLP vs DFT-D3 on Ni" |
All analysis actions use the catgo_analyze tool with an action parameter.
{"tool": "catgo_analyze", "arguments": {"action": "convergence", ...}}
{"tool": "catgo_analyze", "arguments": {"action": "frequencies", ...}}
{"tool": "catgo_analyze", "arguments": {"action": "forces", ...}}
Most analysis workflows are built as DAGs using the workflow tool.
{"tool": "catgo_workflow_engine", "arguments": {"action": "create", "name": "Analysis WF"}}
{"tool": "catgo_workflow_engine", "arguments": {"action": "add_task", "workflow_id": "...", "task_type": "gibbs_energy", ...}}
All analysis workflows follow the same skeleton:
from catgo.workflow import Workflow
wf = Workflow("Analysis name")
# 1. Input structure
inp = wf.add_task("structure_input", structure=structure_json)
# 2. Compute (geo_opt, single_point, freq, etc.)
opt = wf.add_task("geo_opt", structure=inp.output.structure, software="vasp")
frq = wf.add_task("freq", structure=opt.output.structure, software="vasp",
freeze_mode="layers", freeze_layers=4)
# 3. Analyze (gibbs_energy, dos_analysis, charge_analysis, etc.)
gib = wf.add_task("gibbs_energy", energy=opt.output.energy,
frequencies=frq.output.frequencies, phase="adsorbed")
wf.submit()
her/, adsorption/oer/, co2rr/convergence/dos_analysis/, charge/gibbs/geo_opt before freq -- frequencies on unrelaxed structures are meaningless.freeze_mode="layers" in freq to avoid
imaginary frequencies from slab bottom atoms.energy (from geo_opt) and frequencies (from freq) --
these come from separate tasks connected via output references.single_point (not geo_opt) to isolate the parameter effect.No reviews yet. Tell others what you thought.
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Generate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
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Use when the user asks to place an adsorbate molecule on a surface, find adsorption sites, or set up a surface+adsorbate model for DFT.
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Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.
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Use AmberTools antechamber for molecular force field parameterization. Generates GAFF/GAFF2 parameters and AM1-BCC or RESP charges for use in AMBER or LAMMPS classical MD simulations.
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One-shot recipes for adding, deleting, moving, and replacing individual atoms in the active CatGo viewer structure. Use whenever the user asks to "add an atom", "delete atoms", "remove this atom", "move atom N", "replace H with Li", or any single-atom edit — including "add a hydrogen on top of atom 12" / "delete atoms 5–9" / "swap the oxygen at site 3 for fluorine". Skips the discovery loop (no need to list structure tools or check adsorption sites first); goes straight to the matching `catgo_structure` action. Triggers in Chinese on 加原子, 删原子, 减原子, 移动原子, 替换原子, 增加氢, 删除氧, 把 ... 换成 ....
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Diagnose and fix the CatGo backend. Use whenever the user asks to "check the backend", "diagnose the backend", "fix the backend", "why isn't X working", reports connection problems, a blank/failing UI, "router not loaded", "deps missing", or "can't reach the server". Reads GET /api/diagnostics, explains each issue from its fix_hint, auto-applies SAFE fixes (reconnect HPC, pip install a missing dep via the terminal), confirms risky actions first, and — if diagnostics itself is unreachable — tells the user how to start the backend instead of pretending to fix one that is down.
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