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Research & Science · jinzhezenggroup/computational-chemistry-agent-skills
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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 | 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 |
| 10 | 10.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 |
| 11 | 11.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 |
| 12 | 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 |
| 13 | 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 |
| 14 | 14.Dft Abinit Route ABINIT requests to task-specific subskills based on user intent. | jinzhezenggroup/ | 148 | — | ~585 | Automated safety check: Pass | MIT | 2 days ago |
| 15 | 15.Dft Cp2k Route CP2K requests to task-specific subskills based on user intent. | jinzhezenggroup/ | 148 | — | ~578 | Automated safety check: Pass | MIT | 2 days ago |
| 16 | 16.Dft Siesta Route SIESTA requests to task-specific subskills based on user intent. | jinzhezenggroup/ | 148 | — | ~591 | Automated safety check: Pass | MIT | 2 days ago |
| 17 | 17.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 |
| 18 | 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 |
| 19 | 19.Md Prepare ASE molecular-dynamics workflow tasks with backend-agnostic controls. | jinzhezenggroup/ | 148 | — | ~269 | Automated safety check: Pass | MIT | 2 days ago |
| 20 | 20.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 |
| 21 | 21.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 |
| 22 | 22.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 |
| 23 | 23.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 |
