Claude Skills by Hello-QM

Diagnose and fix common VASP errors including ZBRENT, BRMIX, EDDDAV, VERY BAD NEWS, POTCAR mismatch, and memory errors.

Diagnose and fix CatGo workflow engine errors including HPC connection failures, missing POTCARs, stuck tasks, and REMOTE_ERROR states.

VASP band structure calculation. Two-step workflow with SCF charge density followed by non-SCF band calculation along high-symmetry k-path.

Density of states (DOS) workflow in VASP. Three-step process for accurate total and projected DOS, d-band center analysis.

VASP vibrational frequency calculation. Compute ZPE and thermodynamic corrections. Handles frozen atoms for slab systems with multiple freeze modes.

Ab initio molecular dynamics (AIMD) with VASP. NVT/NVE ensembles, temperature control, trajectory analysis.

VASP geometry optimization (relaxation). Handles bulk, slab, and adsorbate-on-slab scenarios with correct ISIF, frozen layers, and convergence settings.

VASP single-point energy calculation. Used standalone, as a pre-step for DOS/band structure, or to evaluate energy at a fixed geometry.

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

CatGO materials science assistant. Manipulate crystal structures, build nanostructures, generate DFT/MD inputs, and analyze electronic/vibrational properties via CatGO MCP tools.

Use when the user asks to generate DFT input files (VASP, Quantum ESPRESSO, LAMMPS), optimize structures with ML potentials (MACE, CHGNet, M3GNet), compute energy, or set up any computational chemistry calculation.

Use when the user asks to analyze DOS, band structure, COHP bonding, d-band center, or MD trajectory properties (RDF, RMSD, RMSF, hydrogen bonds, clustering, dimensionality reduction, dihedral angles, planar density).

Use when the user asks to load, fetch, build, modify, or transform crystal/molecular structures. Covers database import, supercell, defects, doping, intercalation, nanotubes, and atom-level editing.

Use when the user asks about surface slabs, Miller indices, adsorbate placement, adsorption sites, water layers, passivation, heterostructures, lattice matching, moire bilayers, or catalysis workflows.

Use when the user asks to create, build, inspect, validate, or run computational workflows, DAG pipelines, relaxation→static chains, NEB/IRC workflows, or HPC job submission flows.

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.

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

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

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.

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 about Bader charge analysis, charge transfer, oxidation states from DFT, or electron density partitioning.

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 COHP (Crystal Orbital Hamilton Population), chemical bonding analysis, LOBSTER output, orbital-resolved bonding, or bonding/antibonding character between atoms.

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

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

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.

Extract and visualize reaction networks from reactive MD trajectories using ReacNetGenerator. Use after ReaxFF or ab initio MD simulations to identify reaction pathways, species, and kinetics.

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

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...

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.

Authoring conventions for CatGo md-orchestration campaigns — progressive markdown, README+INDEX pairs and keeping them current, logging interventions to LESSONS, human-readable (never-hash) names, and the progressive (top→stage→calc) plan. Use when creating/editing any campaign markdown (plan/README/INDEX/STATUS/LESSONS) so the file tree stays navigable and resumable. Pairs with catgo-campaign.

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.

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.

Compute adsorption/reaction Gibbs free energies, free-energy diagrams, and electrochemical overpotentials (HER/ORR/OER/CO2RR/NRR) with VASP. The per-species pipeline is geo_opt → freq → Gibbs; CHE references; ΔG → η. Use whenever a study's target is a FREE energy (not raw DFT energy) — overpotential, free-energy diagram, ΔG of adsorption/reaction, limiting potential. Pairs with the catgo-campaign skill for orchestration.

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

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

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.

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

Route DeePMD-kit requests to training or inference sub-skills. Use when the user requests machine learning potentials, DeePMD, DPA-3, DP models, or MLIP training.

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

Train DeePMD-kit machine learning potentials. Covers DPA-3 (recommended), se_e2_a (legacy), and fine-tuning from pretrained models.

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.

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