abinit
免费Generate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
中文简介正在准备中。当前显示原文说明。
Hello-QM/catgo-LRG2082026年10月23日 更新
免费在 GitHub 公开
electronic-analysis
Use when the user asks to analyze DOS, band structure, COHP bonding, d-band center, or MD trajectory properties (RDF, RMSD, RMSF, hydrogen bonds, clustering, dimensionality reduction, dihedral angles, planar density).
中文简介正在准备中。当前显示原文说明。
Hello-QM/catgo-LRG星标 208(GitHub 208 + cccskills 0)
实测评分 未实测
查看安装方法包含的文件（1）
- SKILL.md3.0 KB
SKILL.md（原文）
安装前可以查看交给 AI 代理的指令内容。
Electronic Structure & MD Trajectory Analysis
Density of States (DOS)
| Tool | Purpose |
|---|---|
catgo_dos_total | Total DOS |
catgo_dos_compute | Projected DOS (PDOS) for atom groups |
catgo_dos_dband | D-band center, width, filling (catalysis) |
catgo_dos_from_dir | Load DOS from remote HPC directory |
PDOS Workflow
- Get
session_idfrom file upload orcatgo_dos_from_dir - Define atom groups:
{"groups": [{"atoms": [0,1,2], "channels": "d", "label": "Surface Pt d"}]} - Call
catgo_dos_computewith session_id and groups
Channel syntax: "d", "s,p", "dxy,dz2"
D-Band Analysis
catgo_dos_dband(session_id, atoms=[surface_indices]) — Returns d-band center, width, filling.
- Higher center = stronger adsorbate binding
occupied_only_center=True(default) for occupied d-band center
Band Structure
| Tool | Purpose |
|---|---|
catgo_bands_data | Band energies, k-path, band gap |
catgo_bands_projections | Projected (fat) bands with orbital weights |
Report: direct/indirect gap, gap value, high-symmetry labels.
COHP (Bonding Analysis)
catgo_cohp_data — Crystal Orbital Hamilton Population from LOBSTER output.
bond_indices: 1-based bond numbers- Negative -COHP below Fermi = bonding; positive = antibonding
- ICOHP = quantitative bond strength
MD Trajectory Analysis
All MD tools accept trajectory_b64 (base64-encoded file) and format (pdb, xyz, extxyz, lammpstrj).
Structural Analysis
| Tool | Purpose | Key Parameters |
|---|---|---|
catgo_md_rdf | Radial distribution g(r) | pairs, r_range, n_bins |
catgo_md_rmsd | RMSD over time (stability) | ref_frame, atom_indices |
catgo_md_rmsf | Per-atom fluctuation | atom_indices |
catgo_md_dihedrals | Dihedral angle evolution | atom_quartets |
Hydrogen Bond Analysis
| Tool | Purpose |
|---|---|
catgo_md_hbonds | Detect H-bonds per frame |
catgo_md_hbond_lifetime | H-bond lifetime autocorrelation |
Methods: baker_hubbard or wernet_nilsson. Default: D-A 3.5 A, D-H-A angle 150 deg.
Conformational Analysis
| Tool | Purpose |
|---|---|
catgo_md_clustering | Cluster frames by structural similarity (kmeans/dbscan) |
catgo_md_dimreduce | PCA/t-SNE/UMAP embedding |
catgo_md_planar_density | 2D density map (diffusion analysis) |
Workflow Recipes
Surface Catalysis DOS
catgo_dos_from_dir(remote_path="...")→ 2.catgo_dos_total→catgo_dos_dband(atoms=[surface])→ 4.catgo_dos_compute(groups=[...])
MD Water/Interface
catgo_md_rdf(pairs=[["O","H"],["O","O"]])→ 2.catgo_md_hbonds→catgo_md_hbond_lifetime→ 4.catgo_md_planar_density(plane="xy")
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同一仓库的技能
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.
中文简介正在准备中。当前显示原文说明。
Hello-QM/catgo-LRG2082026年10月23日 更新
Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.
中文简介正在准备中。当前显示原文说明。
Hello-QM/catgo-LRG2082026年10月23日 更新
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.
中文简介正在准备中。当前显示原文说明。
Hello-QM/catgo-LRG2082026年10月23日 更新
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.
中文简介正在准备中。当前显示原文说明。
Hello-QM/catgo-LRG2082026年10月23日 更新
atom-ops
免费One-shot recipes for adding, deleting, moving, and replacing individual atoms in the active CatGo viewer structure. Use whenever the user asks to "add an atom", "delete atoms", "remove this atom", "move atom N", "replace H with Li", or any single-atom edit — including "add a hydrogen on top of atom 12" / "delete atoms 5–9" / "swap the oxygen at site 3 for fluorine". Skips the discovery loop (no need to list structure tools or check adsorption sites first); goes straight to the matching `catgo_structure` action. Triggers in Chinese on 加原子, 删原子, 减原子, 移动原子, 替换原子, 增加氢, 删除氧, 把 ... 换成 ....
中文简介正在准备中。当前显示原文说明。
Hello-QM/catgo-LRG2082026年10月23日 更新