Claude Skills by Hello-QM

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 for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.

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.

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.

CP2K geometry optimization. Handles bulk, slab, and molecular systems with GPW method. Efficient for large systems (200+ atoms).

CP2K single point energy calculation. Uses GTH pseudopotentials, Gaussian-plane-wave (GPW) method, and DZVP basis sets for periodic DFT.

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.

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.

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

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

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 about HER (hydrogen evolution reaction), hydrogen adsorption free energy, or volcano plot descriptor for HER catalysts.

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

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

Run LAMMPS molecular dynamics with ReaxFF reactive force field. Use when the user needs reactive MD for combustion, oxidation, corrosion, or bond breaking/forming.

**When to use:** Validate LAMMPS input scripts (.in files) for syntax errors and parameter conflicts before running MD simulations. Generate LAMMPS input scripts from workflow node parameters. **Prerequisites:** - LAMMPS installed on HPC or local system - Input structure (PDB, MOL2, or LAMMPS data file) - Understanding of potential types and force fields

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

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.

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.

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

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

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

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.

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

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 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.

Use RDKit for molecular conformer generation, SMILES/InChI handling, molecular descriptors, fingerprints, and substructure searching. Python-based toolkit.

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.

Generate and manage SIESTA DFT calculations. Use when the user requests SIESTA, numeric atomic orbital (NAO) DFT, or linear-scaling DFT for large systems.

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.

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 dope a material, substitute one element for another, create alloy surfaces, or introduce heteroatoms into a structure.

Fetch crystal structures from Materials Project/OPTIMADE databases and molecules from PubChem. Search, select, and load structures into the CatGO viewer.

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 intercalate atoms or ions between layers, insert lithium into a cathode, or place species in interlayer gaps of a layered material.

Use when the user asks to create a moire pattern, twisted bilayer structure, magic angle graphene, or any twisted 2D heterostructure.

Use when the user asks to build a nanotube, roll up a 2D sheet into a tube, create a carbon nanotube (CNT), boron nitride nanotube (BNNT), or specify chiral indices (n, m).

Use when the user asks to generate a surface slab from a bulk crystal, specifying Miller indices, number of layers, vacuum thickness, or supercell size.

Use when the user asks to apply strain, deformation, lattice distortion, or mechanical loading to a periodic structure (uniaxial, biaxial, hydrostatic, or shear).

Use when the user asks for systematic element substitution, combinatorial materials screening, high-throughput composition search, or multi-site replacement across different element groups.

Diagnose and fix SCF and ionic convergence failures in VASP and ORCA. Covers ALGO, mixing parameters, ISMEAR, NELM, EDIFFG, NSW, and IBRION settings.