Development

Use when the user asks to build a heterostructure, interface, van der Waals stack, substrate-film system, or lattice-matched bilayer from two different materials.

Use when the user asks to dope a material, substitute one element for another, create alloy surfaces, or introduce heteroatoms into a structure.

Use when the user asks to create point defects such as vacancies, substitutional defects, or interstitial atoms in a crystal structure.

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.

Generate and manage Quantum ESPRESSO (pw.x) DFT calculations. Use when the user requests QE, Quantum ESPRESSO, pw.x, or plane-wave pseudopotential calculations outside VASP.

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.

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

Generate ORCA input files for TD-DFT UV-Vis calculations and parse/plot the resulting absorption spectrum. Use when the user asks about UV-Vis spectra, absorption spectra, TD-DFT calculations, excited state calculations in ORCA, or wants to plot results from an ORCA TD-DFT output file. Also trigger when the user mentions oscillator strengths, electronic transitions, or simulated UV-Vis.

ORCA geometry optimization. Handles method/basis selection, dispersion corrections, solvent models, and convergence settings.

ORCA NEB-TS transition state search. Requires reactant and product structures. Handles NEB parameters, image count, and CI-NEB settings.

Generate ORCA input files for IRC (Intrinsic Reaction Coordinate) calculations and post-process the results. Use this skill whenever the user asks about IRC calculations, reaction path following, confirming transition state connectivity, or tracing a minimum energy path from a TS in ORCA. Also trigger when the user mentions IRC endpoints, forward/backward reaction paths, or needs to verify that a TS connects to expected reactants and products.

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

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.

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.

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

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

Automatically logs new discoveries to CLAUDE.md files. Triggers when fixing bugs, discovering pitfalls, finding performance issues, or learning new patterns in the codebase.

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

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.

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

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.

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.

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