Development

Convert molecular file formats using Open Babel. Handles SMILES, mol2, sdf, pdb, xyz, cif, and 100+ other formats. Also performs 3D coordinate generation and hydrogen addition.

Convert between computational chemistry data formats using dpdata. Handles VASP, QE, CP2K, Gaussian, LAMMPS, and DeePMD formats. Essential for preparing ML potential training data.

Route data processing requests to the appropriate tool. Covers format conversion (dpdata, OpenBabel), structure packing (Packmol), and data manipulation.

Run a CatGo file-first md-orchestration "campaign" — a multi-step / high-throughput computational-materials study (e.g. SAA HER screening) driven from a human-readable folder + markdown tree, not the DB workflow engine. Use when the user says "跑一个 campaign", "md 模式跑", "high-throughput screening", or wants an agent-in-the-loop study with stages/funnel/analysis/report. Requires `catgo` on PATH.

Run and resume the CatGo md-orchestration poll loop — delegate each poll to a subagent (keep main context lean), verify convergence by force, auto-advance each converged species per-species (pipeline, not barrier), and resume a campaign from disk after context compaction / new session. Use when driving or resuming a campaign's job-watch loop. Pairs with catgo-campaign.

Drive a file-first, agent-in-the-loop computational campaign via a folder + markdown tree (no DB). Use when the user opts out of the visual workflow engine.

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 — te...

Use when the user asks about volcano plots, catalyst screening, activity descriptors, Sabatier principle, or comparing catalyst performance across a descriptor space.

Run phonon calculations using Phonopy. Computes phonon band structures, density of states, thermal properties, and checks dynamical stability. Works with VASP, QE, ABINIT, and other DFT codes as the force calculator.

Use when the user asks about OER (oxygen evolution reaction) overpotential, water oxidation catalysis, or the 4-electron water splitting pathway on a surface catalyst.

Use when the user asks about NRR (nitrogen reduction reaction), ammonia synthesis, N2 fixation, or the electrochemical reduction of N2 to NH3 on a catalyst surface.

Use when the user asks to reproduce the Kreitz 2021 Ni surface benchmark, run the MACE Ni benchmark, or compare a machine-learning potential (MACE, CHGNet, M3GNet) against DFT-D3 surface-science references. Invokes the "UMA Catalysis Tutorial" preset (template key `uma_catalysis_screening`).

Use when the user asks about HER (hydrogen evolution reaction), hydrogen adsorption free energy, or volcano plot descriptor for HER catalysts.

Use when the user asks for Gibbs free energy, zero-point energy (ZPE), thermal corrections, or thermodynamic properties from DFT + frequency data.

Use when the user asks to generate a reaction energy diagram, free energy profile, potential energy surface plot, or pathway comparison diagram for catalysis or reaction mechanism studies.

Use when the user asks about density of states (DOS), projected DOS (PDOS), d-band center, spin-resolved DOS, or electronic structure analysis from completed DFT calculations.

Use when the user asks to test ENCUT convergence, k-point convergence, or any parameter sweep to determine converged computational settings.

Use when the user asks about CO2 reduction reaction (CO2RR), CO2 electroreduction intermediates, Faradaic efficiency, or selectivity toward CO, methanol, methane, formic acid, etc.

Use when the user asks about Bader charge analysis, charge transfer, oxidation states from DFT, or electron density partitioning.

Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.

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.

Generate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.

Route computational chemistry requests to the correct software and task skill. Entry point for all CatGo agent interactions.

Create and manage computational chemistry workflows with CatGo. Supports VASP, CP2K, ORCA, MLP, LAMMPS. Build OER/HER/CO2RR workflows, geometry optimization, frequency analysis, Gibbs energy calculations.