Hello-QM/catgo-LRG - Page 2

nrr-overpotential

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.

Langue du texte source : anglais

oer-overpotential

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.

Langue du texte source : anglais

openbabel

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.

Langue du texte source : anglais

orca-freq

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

Langue du texte source : anglais

neb-ts

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

Langue du texte source : anglais

orca-opt

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

Langue du texte source : anglais

orca-uv-vis

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…

Langue du texte source : anglais

packmol

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

Langue du texte source : anglais

phonopy

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.

Langue du texte source : anglais

quantum-espresso

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.

Langue du texte source : anglais

rdkit

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

Langue du texte source : anglais

reacnetgenerator

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.

Langue du texte source : anglais

siesta

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

Langue du texte source : anglais

adsorbate-placement

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.

Langue du texte source : anglais

defect-generation

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

Langue du texte source : anglais

substitutional-doping

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

Langue du texte source : anglais

structure-fetch

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

Langue du texte source : anglais

heterostructure

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.

Langue du texte source : anglais

intercalation

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.

Langue du texte source : anglais

moire-superlattice

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

Langue du texte source : anglais

nanotube-generation

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).

Langue du texte source : anglais

slab-generation

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.

Langue du texte source : anglais

strain-deformation

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

Langue du texte source : anglais

combinatorial-substitution

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

Langue du texte source : anglais

convergence-issues

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

Langue du texte source : anglais

vasp-errors

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

Langue du texte source : anglais

workflow-errors

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

Langue du texte source : anglais

vasp-band

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

Langue du texte source : anglais

vasp-dos

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

Langue du texte source : anglais

vasp-freq

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

Langue du texte source : anglais

vasp-md

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

Langue du texte source : anglais

vasp-relax

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

Langue du texte source : anglais

vasp-static

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

Langue du texte source : anglais

volcano-plot

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

Langue du texte source : anglais

catgo

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

Langue du texte source : anglais

mace-ni-benchmark

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…

Langue du texte source : anglais

analysis-router

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.

Langue du texte source : anglais

data-router

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

Langue du texte source : anglais

deepmd-router

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.

Langue du texte source : anglais

lammps-router

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

Langue du texte source : anglais