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By jinzhezenggroup
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | Turns a user-supplied atomic structure and DFT settings into a runnable Quantum ESPRESSO input file, stopping short of submitting the job. | jinzhezenggroup/ | 148 | — | ~1.8k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 2 | Prepares, validates and runs DP-GEN simplify jobs that thin out repeated or redundant DeepMD datasets, generating param.json and machine.json for local or scheduler runs. | jinzhezenggroup/ | 148 | — | ~2.7k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 3 | Prepares and runs molecular dynamics simulations in LAMMPS with a DeePMD machine-learning potential, writing the input script and choosing NVE, NVT or NPT. | jinzhezenggroup/ | 148 | — | ~2.8k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 4 | Prepares and explains LAMMPS input scripts for reactive molecular dynamics with the ReaxFF potential, including charge equilibration and ensemble choice. | jinzhezenggroup/ | 148 | — | ~1.8k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 5 | Generates 3D molecular conformers from SMILES strings or files with RDKit, keeps the lowest-energy one per molecule, and falls back to 2D coordinates when embedding fails. | jinzhezenggroup/ | 148 | — | ~2.4k | Automated safety check: Pass | LGPL-3.0 | 2 days ago |
| 6 | Computes RDKit physicochemical descriptors and molecular fingerprints from SMILES through a uv-run CLI script that skips and logs invalid molecules. | jinzhezenggroup/ | 148 | — | ~2.3k | Automated safety check: Pass | LGPL-3.0 | 2 days ago |
| 7 | 7.Unimol A standardized CLI wrapper for Uni-Mol molecular ML workflows that handles representation extraction (embeddings), model training (regression/classification), and property prediction with built-in… | jinzhezenggroup/ | 148 | — | ~1.5k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 8 | 8.Xtb Prepare and explain xTB semiempirical quantum-chemistry workflows for single-point energy, forces, charges, dipole, geometry optimization, and molecular dynamics. | jinzhezenggroup/ | 148 | — | ~1.2k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 9 | Integrate xTBloom with ASE or dpdata for molecular energy, force, charge, labeling, relaxation, optimizer, or dynamics workflows. | jinzhezenggroup/ | 148 | — | ~1.7k | Automated safety check: Pass | LGPL-3.0 | 2 days ago |
| 10 | Write, review, and run high-level xTBloom Python GFN2-xTB inference with Calculator, Structure, and BatchCalculator, including single systems, repeated geometry updates, heterogeneous ragged… | jinzhezenggroup/ | 148 | — | ~1.3k | Automated safety check: Pass | LGPL-3.0 | 2 days ago |
| 11 | 11.Antechamber A command-line tool in AmberTools for preparing small molecules or non-standard residues within GAFF/AMBER-compatible chemical space for molecular mechanics simulations, by automating atom/bond… | jinzhezenggroup/ | 148 | — | ~3.2k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 12 | 12.Create Skill Create new Agent Skills following the agentskills.io specification. | jinzhezenggroup/ | 148 | — | ~1.3k | Automated safety check: Pass | MIT | 2 days ago |
| 13 | Fine-tune a DPA3 model in DeePMD-kit using the PyTorch backend. | jinzhezenggroup/ | 148 | — | ~3.1k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 14 | Run Python inference with DeePMD-kit models using the DeepPot API. | jinzhezenggroup/ | 148 | — | ~2.3k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 15 | 15.Deepmd Train Train DeePMD-kit models with progressive disclosure. An agent skill from jinzhezenggroup/computational-chemistry-agent-skills. | jinzhezenggroup/ | 148 | — | ~1.5k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 16 | 16.Dpdata CLI A command-line utility for converting and manipulating over 50 atomic simulation data formats, including outputs from DFT and MD software (VASP, LAMMPS, Gaussian, QE, CP2K, ABACUS, etc.). | jinzhezenggroup/ | 148 | — | ~2.1k | Automated safety check: Pass | LGPL-3.0 | 2 days ago |
| 17 | 17.Dpdata CLI Convert and manipulate atomic simulation data formats using dpdata CLI. | jinzhezenggroup/ | 148 | — | ~2.6k | Automated safety check: Pass | LGPL-3.0 | 2 days ago |
| 18 | Use dpdata Python Driver plugins to label systems (energies/forces/virials) via System.predict(), list available drivers, and build Driver objects (ase/deepmd/gaussian/sqm/hybrid). | jinzhezenggroup/ | 148 | — | ~1k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 19 | Minimize geometries with dpdata minimizer plugins via System.minimize(), including how minimizers relate to drivers (ASEMinimizer needs a dpdata Driver) and how to list supported minimizers (ase/sqm). | jinzhezenggroup/ | 148 | — | ~669 | Automated safety check: Pass | LGPL-3.0 | 2 days ago |
| 20 | Run Shell commands as computational jobs, on local machines or HPC clusters, through Shell, Slurm, PBS, LSF, Bohrium, etc. | jinzhezenggroup/ | 148 | — | ~3.1k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 21 | 21.Gjf Flux Assemble and extract Gaussian .gjf input file sections (directives, route, title, molecule blocks, appendices) and build single- or multi-step Link1 jobs from modular component files. | jinzhezenggroup/ | 148 | — | ~2k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 22 | 22.Openbabel A versatile CLI tool for converting molecular file formats, generating 3D atomic coordinates from SMILES, rendering 2D chemical structure images, and preparing or extracting structures for… | jinzhezenggroup/ | 148 | — | ~850 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 23 | A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input scripts, and executing Packmol. | jinzhezenggroup/ | 148 | — | ~1.4k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 24 | A skill your agent uses WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual names. | jinzhezenggroup/ | 148 | — | ~1.1k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 25 | 25.Dft Abinit Route ABINIT requests to task-specific subskills based on user intent. | jinzhezenggroup/ | 148 | — | ~585 | Automated safety check: Pass | MIT | 2 days ago |
| 26 | 26.Dft Cp2k Route CP2K requests to task-specific subskills based on user intent. | jinzhezenggroup/ | 148 | — | ~578 | Automated safety check: Pass | MIT | 2 days ago |
| 27 | 27.Dft Gpaw Route GPAW DFT requests to task-specific subskills based on user intent. | jinzhezenggroup/ | 148 | — | ~585 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 28 | 28.Dft Siesta Route SIESTA requests to task-specific subskills based on user intent. | jinzhezenggroup/ | 148 | — | ~591 | Automated safety check: Pass | MIT | 2 days ago |
| 29 | 29.Dft Vasp Route VASP DFT requests to task-specific subskills based on user intent. | jinzhezenggroup/ | 148 | — | ~602 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 30 | 30.Dftbplus Route DFTB+ requests to task-specific subskills based on user intent. | jinzhezenggroup/ | 148 | — | ~595 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 31 | 31.Phonopy General phonon-workflow skill built around phonopy, independent of force backend. | jinzhezenggroup/ | 148 | — | ~1.2k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 32 | Structure manipulation and crystal analysis workflows based on pymatgen. | jinzhezenggroup/ | 148 | — | ~1.2k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 33 | 33.Run Gauss Acts as a knowledge base providing environment checklists, directory/scratch management, and bash command templates. | jinzhezenggroup/ | 148 | — | ~398 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 34 | It is a specification for semantic workflows used by agents to plan, generate, formalize, summarize, and execute complex tasks, projects, experiments,and research efforts for agents, requiring… | jinzhezenggroup/ | 148 | — | ~1.1k | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 35 | Route ASE calculator-backend requests to adapter subskills based on backend choice. | jinzhezenggroup/ | 148 | — | ~349 | Automated safety check: Pass | MIT | 2 days ago |
| 36 | Route ASE atomistic workflow requests to task-specific subskills based on user intent. | jinzhezenggroup/ | 148 | — | ~502 | Automated safety check: Pass | MIT | 2 days ago |
| 37 | 37.Ase Unified ASE router skill with a tree of subskills for static/relax/MD/NEB workflows and backend adapters (GPAW, MACE). | jinzhezenggroup/ | 148 | — | ~424 | Automated safety check: Pass | MIT | 2 days ago |
| 38 | 38.Band Prepare GPAW band-structure workflow scripts from existing ground-state context and user-specified k-path settings. | jinzhezenggroup/ | 148 | — | ~379 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 39 | 39.Band Prepare VASP band-structure workflow inputs from existing SCF context and user-specified band-path settings. | jinzhezenggroup/ | 148 | — | ~411 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 40 | 40.Dos Prepare GPAW DOS workflow scripts from existing ground-state context and user-specified DOS settings. | jinzhezenggroup/ | 148 | — | ~347 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 41 | 41.Dos Prepare VASP DOS workflow inputs from existing SCF artifacts and user-specified DOS settings. | jinzhezenggroup/ | 148 | — | ~372 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 42 | 42.Electronic Prepare CP2K electronic-analysis task inputs from prior converged context. | jinzhezenggroup/ | 148 | — | ~333 | Automated safety check: Pass | MIT | 2 days ago |
| 43 | 43.Electronic Prepare DFTB+ electronic-analysis task inputs based on prior ground-state context. | jinzhezenggroup/ | 148 | — | ~340 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
| 44 | 44.Md Prepare ASE molecular-dynamics workflow tasks with backend-agnostic controls. | jinzhezenggroup/ | 148 | — | ~269 | Automated safety check: Pass | MIT | 2 days ago |
| 45 | 45.Md Prepare ABINIT molecular-dynamics task inputs from a user-provided structure and MD controls. | jinzhezenggroup/ | 148 | — | ~296 | Automated safety check: Pass | MIT | 2 days ago |
| 46 | 46.Md Prepare CP2K molecular-dynamics task inputs from a user-provided structure and MD controls. | jinzhezenggroup/ | 148 | — | ~297 | Automated safety check: Pass | MIT | 2 days ago |
| 47 | 47.Md Prepare SIESTA molecular-dynamics task inputs from a user-provided structure and MD controls. | jinzhezenggroup/ | 148 | — | ~300 | Automated safety check: Pass | MIT | 2 days ago |
| 48 | 48.Md Prepare DFTB+ molecular-dynamics task inputs from a user-provided structure and MD controls. | jinzhezenggroup/ | 148 | — | ~291 | Automated safety check: Pass | LGPL-3.0-or-later | 2 days ago |
