jinzhezenggroup/computational-chemistry-agent-skills
38 skills
$npx skills add jinzhezenggroup/computational-chemistry-agent-skillsSkillInstalls
agent-taskboard-manifestIt is a specification for semantic workflows used by agents to plan, generate, formalize, summarize, and execute complex tasks, projects, experiments,and…antechamberA command-line tool in AmberTools for preparing small molecules or non-standard residues within GAFF/AMBER-compatible chemical space for molecular mechanics…aseUnified ASE router skill with a tree of subskills for static/relax/MD/NEB workflows and backend adapters (GPAW, MACE).ase-calculatorsRoute ASE calculator-backend requests to adapter subskills based on backend choice.ase-workflowsRoute ASE atomistic workflow requests to task-specific subskills based on user intent.bandPrepare GPAW band-structure workflow scripts from existing ground-state context and user-specified k-path settings.create-skillCreate new Agent Skills following the agentskills.io specification. Use when the user wants to create, scaffold, or design a new skill for AI agents.deepmd-finetune-dpa3Fine-tune a DPA3 model in DeePMD-kit using the PyTorch backend. Use when the user wants to adapt a pre-trained DPA3 model to a new downstream dataset.deepmd-python-inferenceRun Python inference with DeePMD-kit models using the DeepPot API.deepmd-trainTrain DeePMD-kit models with progressive disclosure. Use when the user wants to train a DeePMD-kit potential, prepare an input.json, choose between model…dft-abinitRoute ABINIT requests to task-specific subskills based on user intent.dft-cp2kRoute CP2K requests to task-specific subskills based on user intent.dft-gpawRoute GPAW DFT requests to task-specific subskills based on user intent.dft-qeGenerate Quantum ESPRESSO DFT input tasks from a user-provided structure plus user-specified DFT settings.dft-siestaRoute SIESTA requests to task-specific subskills based on user intent.dft-vaspRoute VASP DFT requests to task-specific subskills based on user intent.dftbplusRoute DFTB+ requests to task-specific subskills based on user intent.dosPrepare GPAW DOS workflow scripts from existing ground-state context and user-specified DOS settings.dpdata-cliA command-line utility for converting and manipulating over 50 atomic simulation data formats, including outputs from DFT and MD software (VASP, LAMMPS,…dpgen-simplifyPrepare, explain, validate, and run DP-GEN simplify workflows for reducing repeated or redundant DeepMD datasets.electronicPrepare ABINIT electronic-analysis task inputs from prior converged context.gjf-fluxAssemble and extract Gaussian .gjf input file sections (directives, route, title, molecule blocks, appendices) and build single- or multi-step Link1 jobs from…gpawConfigure ASE GPAW calculator adapter settings for ASE workflows.lammps-deepmdA tool and knowledge base for running molecular dynamics (MD) simulations in LAMMPS with the DeePMD-kit plugin.lammps-reaxffRun reactive molecular dynamics simulations in LAMMPS with the ReaxFF potential, including preparing input scripts (pair_style reaxff + fix qeq/reaxff),…maceConfigure ASE MACE calculator adapter settings for ASE workflows.mdPrepare ASE molecular-dynamics workflow tasks with backend-agnostic controls.nebPrepare ASE NEB workflow tasks with backend-agnostic controls.openbabelA versatile CLI tool for converting molecular file formats, generating 3D atomic coordinates from SMILES, rendering 2D chemical structure images, and preparing…packmol-generate-mixtureA tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input…phonopyGeneral phonon-workflow skill built around phonopy, independent of force backend.pymatgen-structureStructure manipulation and crystal analysis workflows based on pymatgen.rdkit-confA standardized CLI wrapper for RDKit 3D/2D conformer generation that samples multiple conformers per molecule (ETKDGv3, default 10), optimizes each with a…rdkit-reprA standardized CLI wrapper for RDKit molecular featurization workflows that handles physicochemical descriptor computation (outputs .csv) and molecular…reacnetgeneratorRun ReacNetGenerator on reactive MD trajectories to generate reaction networks and reports.relaxPrepare ASE geometry-optimization workflow tasks with backend-agnostic controls.staticPrepare ASE static (single-point) workflow tasks with backend-agnostic workflow controls.unimolA standardized CLI wrapper for Uni-Mol molecular ML workflows that handles representation extraction (embeddings), model training (regression/classification),…