hello-qm/catgo-lrg
60 skills
$npx skills add hello-qm/catgo-lrgSkillInstalls
abinitGenerate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.adsorption-energyUse when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.antechamberUse AmberTools antechamber for molecular force field parameterization.catgoCatGO materials science assistant. Manipulate crystal structures, build nanostructures, generate DFT/MD inputs, and analyze electronic/vibrational properties…charge-analysisUse when the user asks about Bader charge analysis, charge transfer, oxidation states from DFT, or electron density partitioning.co2rrUse when the user asks about CO2 reduction reaction (CO2RR), CO2 electroreduction intermediates, Faradaic efficiency, or selectivity toward CO, methanol,…cohpUse when the user asks about COHP (Crystal Orbital Hamilton Population), chemical bonding analysis, LOBSTER output, orbital-resolved bonding, or…convergence-testUse when the user asks to test ENCUT convergence, k-point convergence, or any parameter sweep to determine converged computational settings.cp2k-relaxCP2K geometry optimization. Handles bulk, slab, and molecular systems with GPW method. Efficient for large systems (200+ atoms).cp2k-staticCP2K single point energy calculation. Uses GTH pseudopotentials, Gaussian-plane-wave (GPW) method, and DZVP basis sets for periodic DFT.deepmd-inferenceRun DeePMD-kit inference to predict energies, forces, and stresses using a trained DP model. Also covers model evaluation and testing.deepmd-trainTrain DeePMD-kit machine learning potentials. Covers DPA-3 (recommended), se_e2_a (legacy), and fine-tuning from pretrained models.dftbplusGenerate 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.dos-analysisUse when the user asks about density of states (DOS), projected DOS (PDOS), d-band center, spin-resolved DOS, or electronic structure analysis from completed…dpdataConvert between computational chemistry data formats using dpdata. Handles VASP, QE, CP2K, Gaussian, LAMMPS, and DeePMD formats.energy-diagramUse when the user asks to generate a reaction energy diagram, free energy profile, potential energy surface plot, or pathway comparison diagram for catalysis…gaussianGenerate and manage Gaussian calculations. Use when the user requests Gaussian, G16, GJF files, or needs hybrid functionals (B3LYP), MP2, CCSD(T), or molecular…gibbsUse when the user asks for Gibbs free energy, zero-point energy (ZPE), thermal corrections, or thermodynamic properties from DFT + frequency data.gpawGenerate 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.herUse when the user asks about HER (hydrogen evolution reaction), hydrogen adsorption free energy, or volcano plot descriptor for HER catalysts.knowledge-keeperAutomatically logs new discoveries to CLAUDE.md files. Triggers when fixing bugs, discovering pitfalls, finding performance issues, or learning new patterns in…lammpsRoute LAMMPS molecular dynamics requests to force-field-specific sub-skills. Use when the user requests LAMMPS with a specific potential type (DeePMD, ReaxFF).lammps-deepmdRun LAMMPS molecular dynamics with DeePMD-kit machine learning potentials. Use when the user wants MD simulations driven by a trained DP model.lammps-reaxffRun LAMMPS molecular dynamics with ReaxFF reactive force field.lammps-validateWhen to use: Validate LAMMPS input scripts (.in files) for syntax errors and parameter conflicts before running MD simulations.nrrUse when the user asks about NRR (nitrogen reduction reaction), ammonia synthesis, N2 fixation, or the electrochemical reduction of N2 to NH3 on a catalyst…oerUse when the user asks about OER (oxygen evolution reaction) overpotential, water oxidation catalysis, or the 4-electron water splitting pathway on a surface…openbabelConvert molecular file formats using Open Babel. Handles SMILES, mol2, sdf, pdb, xyz, cif, and 100+ other formats.orca-freqORCA frequency calculation. Computes vibrational frequencies, IR intensities, zero-point energy, and thermochemistry at specified temperature/pressure.orca-ircGenerate ORCA input files for IRC (Intrinsic Reaction Coordinate) calculations and post-process the results.orca-neb-tsORCA NEB-TS transition state search. Requires reactant and product structures. Handles NEB parameters, image count, and CI-NEB settings.orca-optORCA geometry optimization. Handles method/basis selection, dispersion corrections, solvent models, and convergence settings.orca-uv-visGenerate ORCA input files for TD-DFT UV-Vis calculations and parse/plot the resulting absorption spectrum.packmolGenerate initial configurations for molecular simulations using Packmol.phonopyRun phonon calculations using Phonopy. Computes phonon band structures, density of states, thermal properties, and checks dynamical stability.qeGenerate and manage Quantum ESPRESSO (pw.x) DFT calculations. Use when the user requests QE, Quantum ESPRESSO, pw.x, or plane-wave pseudopotential calculations…rdkitUse RDKit for molecular conformer generation, SMILES/InChI handling, molecular descriptors, fingerprints, and substructure searching. Python-based toolkit.reacnetgenExtract and visualize reaction networks from reactive MD trajectories using ReacNetGenerator.siestaGenerate and manage SIESTA DFT calculations. Use when the user requests SIESTA, numeric atomic orbital (NAO) DFT, or linear-scaling DFT for large systems.structure-adsorbateUse when the user asks to place an adsorbate molecule on a surface, find adsorption sites, or set up a surface+adsorbate model for DFT.structure-defectUse when the user asks to create point defects such as vacancies, substitutional defects, or interstitial atoms in a crystal structure.structure-dopingUse when the user asks to dope a material, substitute one element for another, create alloy surfaces, or introduce heteroatoms into a structure.structure-fetchFetch crystal structures from Materials Project/OPTIMADE databases and molecules from PubChem. Search, select, and load structures into the CatGO viewer.structure-heterostructureUse when the user asks to build a heterostructure, interface, van der Waals stack, substrate-film system, or lattice-matched bilayer from two different…structure-intercalationUse 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.structure-moireUse when the user asks to create a moire pattern, twisted bilayer structure, magic angle graphene, or any twisted 2D heterostructure.structure-nanotubeUse 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…structure-slabUse when the user asks to generate a surface slab from a bulk crystal, specifying Miller indices, number of layers, vacuum thickness, or supercell size.structure-strainUse when the user asks to apply strain, deformation, lattice distortion, or mechanical loading to a periodic structure (uniaxial, biaxial, hydrostatic, or…structure-substitutionUse when the user asks for systematic element substitution, combinatorial materials screening, high-throughput composition search, or multi-site replacement…troubleshoot-convergenceDiagnose and fix SCF and ionic convergence failures in VASP and ORCA. Covers ALGO, mixing parameters, ISMEAR, NELM, EDIFFG, NSW, and IBRION settings.troubleshoot-vaspDiagnose and fix common VASP errors including ZBRENT, BRMIX, EDDDAV, VERY BAD NEWS, POTCAR mismatch, and memory errors.troubleshoot-workflowDiagnose and fix CatGo workflow engine errors including HPC connection failures, missing POTCARs, stuck tasks, and REMOTE_ERROR states.vasp-bandVASP band structure calculation. Two-step workflow with SCF charge density followed by non-SCF band calculation along high-symmetry k-path.vasp-dosDensity of states (DOS) workflow in VASP. Three-step process for accurate total and projected DOS, d-band center analysis.vasp-freqVASP vibrational frequency calculation. Compute ZPE and thermodynamic corrections. Handles frozen atoms for slab systems with multiple freeze modes.vasp-mdAb initio molecular dynamics (AIMD) with VASP. NVT/NVE ensembles, temperature control, trajectory analysis.vasp-relaxVASP geometry optimization (relaxation). Handles bulk, slab, and adsorbate-on-slab scenarios with correct ISIF, frozen layers, and convergence settings.vasp-staticVASP single-point energy calculation. Used standalone, as a pre-step for DOS/band structure, or to evaluate energy at a fixed geometry.volcano-plotUse when the user asks about volcano plots, catalyst screening, activity descriptors, Sabatier principle, or comparing catalyst performance across a descriptor…