WuGroup-XJTLU/cc-skills-ZhenghaoWu-Group

ase

Use when manipulating atomistic structures, converting between file formats (CIF, POSCAR, XYZ, LAMMPS data), building supercells and surfaces, or running small geometry optimizations with ASE-supported calculators.

原文语言：英语

bayes-opt

Use when optimizing material compositions, polymer sequences, molecular structures, or any expensive-to-evaluate property where each evaluation requires simulation or experiment. Also use when the user mentions Bayesian optimization for materials, black-box…

原文语言：英语

cp2k

Use when writing, reviewing, or debugging CP2K input files, choosing DFT methods (GPW, GAPW, functionals, basis sets), setting up calculations (geometry optimization, AIMD, cell optimization, NEB, single-point energy), validating parameters (cutoff, SCF…

原文语言：英语

freud

Use when code imports `freud` or `freud-analysis`, or user asks to analyze molecular simulation trajectories (RDF, MSD, order parameters, structure factor, PMFT, Voronoi, clustering). Also use when reading LAMMPS dump/data files for freud analysis via…

原文语言：英语

gromacs

Use when setting up and running biomolecular MD simulations with GROMACS. Generate topologies, write MDP input files, execute simulations, and perform basic analysis.

原文语言：英语

lammps

Use when writing, reviewing, or debugging LAMMPS input scripts, choosing simulation methods (deformation, equilibration, transport), validating physics parameters (timestep, thermostat, units), or encountering LAMMPS runtime errors (lost atoms, DOF conflicts,…

原文语言：英语

lammpsio

Use when importing `lammpsio`, reading/writing LAMMPS data/dump files, or converting between LAMMPS and GSD formats.

原文语言：英语

mace

Use when running machine-learning potential calculations with MACE. Load pretrained MACE-MP models, compute energies and forces, and run geometry optimizations on atomistic structures.

原文语言：英语

materials-project

Use when querying the Materials Project database for crystal structures, material properties, or generating phase diagrams. Requires the MP_API_KEY environment variable to be set.

原文语言：英语

matplotlib

Use when creating matplotlib plots from scratch, customizing plot elements at a low level, or building novel visualization types that seaborn does not support.

原文语言：英语

ovito

Use when code imports `ovito`, or user asks to render molecular snapshots / animations from LAMMPS, XYZ, GSD, PDB, CIF or POSCAR files. Covers headless rendering (Tachyon/OSPRay), coloring, PBC handling, bonds, camera setup, and publication-ready output.

原文语言：英语

packmol

Use when writing, reviewing, debugging, or explaining packmol input files and packing strategies for molecular dynamics simulations.

原文语言：英语

polymer-build

Use when creating polymer systems, generating LAMMPS data files from SMILES, building atomistic or coarse-grained bead-spring models, setting up polymer simulations (homopolymer, copolymer, ring polymer, polymer solutions), or when user mentions AutoPoly,…

原文语言：英语

pymatgen

Use when working with crystal structures in Python, converting materials file formats (CIF, POSCAR, XYZ), querying the Materials Project database, or computing phase diagrams and electronic structure properties.

原文语言：英语

pyscf

Use when running molecular quantum chemistry calculations in Python. Computes single-point energies, optimized geometries, vibrational frequencies, and population analysis using HF, DFT, or MP2 methods.

原文语言：英语

rdkit

Use when parsing SMILES/SDF files, calculating molecular descriptors or fingerprints, performing substructure searches with SMARTS, or generating 2D/3D coordinates in Python.

原文语言：英语

scientific-plotting

Use when creating publication-quality matplotlib figures in Python — scientific line plots, scatter, error bars, heatmaps, contour, bar, histogram, 3D, multi-panel, log-scale, twin/inset axes, and colorbars. Applies APS journal styling (Helvetica, 8pt, inward…

原文语言：英语

scikit-learn

Use when training classification or regression models, performing clustering or dimensionality reduction, tuning hyperparameters, or building preprocessing pipelines in Python.

原文语言：英语

seaborn

Use when creating statistical visualizations from pandas DataFrames, exploring distributions or categorical comparisons, or producing multi-panel relational plots with minimal code.

原文语言：英语

shap

Use when computing SHAP values, generating explanation plots (waterfall, beeswarm, bar), or debugging feature importance for tree-based, neural-network, or linear models.

原文语言：英语

umap-learn

Use when reducing high-dimensional data to 2D/3D for visualization, preprocessing embeddings before clustering with HDBSCAN, or training parametric dimensionality-reduction models.

原文语言：英语