Development

ORCA frequency calculation. Computes vibrational frequencies, IR intensities, zero-point energy, and thermochemistry at specified temperature/pressure.

Routes ORCA calculation requests to opt, neb_ts, or freq sub-skills. Enforces ORCA-specific policies for method, basis set, charge, and multiplicity.

Run LAMMPS molecular dynamics with DeePMD-kit machine learning potentials. Use when the user wants MD simulations driven by a trained DP model.

Route LAMMPS molecular dynamics requests to force-field-specific sub-skills. Use when the user requests LAMMPS with a specific potential type (DeePMD, ReaxFF).

Generate and manage GPAW Python-based DFT calculations. Use when the user requests GPAW, Python DFT, real-space grid DFT, or LCAO-DFT with ASE integration.

Generate and manage Gaussian calculations. Use when the user requests Gaussian, G16, GJF files, or needs hybrid functionals (B3LYP), MP2, CCSD(T), or molecular quantum chemistry with Gaussian basis sets.

Generate and manage DFTB+ calculations. Use when the user requests DFTB+, tight-binding DFT, SCC-DFTB, or needs fast approximate DFT for large systems or MD.

Run DeePMD-kit inference to predict energies, forces, and stresses using a trained DP model. Also covers model evaluation and testing.

Generate initial configurations for molecular simulations using Packmol. Build liquid boxes, mixtures, solutions, and solvated systems by packing molecules into a defined region.

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.