jinzhezenggroup/computational-chemistry-agent-skills
68 agent markdown files indexed from jinzhezenggroup/computational-chemistry-agent-skills. Install any of them pinned to an exact hash with mdr add jinzhezenggroup/computational-chemistry-agent-skills/<name>.
create-skill skill
jinzhezenggroup/computational-chemistry-agent-skills · .github/skills/create-skill/SKILL.md · Create new Agent Skills following the agentskills.io specification. Use when the user wants to create, scaffold, or…
v1.0 · audit A · 144 stars
agent-taskboard-manifest skill
jinzhezenggroup/computational-chemistry-agent-skills · agent-workflow/agent-taskboard-manifest/SKILL.md · It is a specification for semantic workflows used by agents to plan, generate, formalize, summarize, and execute…
v0.1.0 · audit A · 144 stars
phonopy skill
jinzhezenggroup/computational-chemistry-agent-skills · analysis/phonopy/SKILL.md · General phonon-workflow skill built around phonopy, independent of force backend. USE WHEN you need to prepare…
v0.1.0 · audit A · 144 stars
reacnetgenerator skill
jinzhezenggroup/computational-chemistry-agent-skills · analysis/reacnetgenerator/SKILL.md · Run ReacNetGenerator on reactive MD trajectories to generate reaction networks and reports. Use when the user wants to…
v2.3 · audit A · 144 stars
ase skill
jinzhezenggroup/computational-chemistry-agent-skills · atomistic-workflows/ase/SKILL.md · Unified ASE router skill with a tree of subskills for static/relax/MD/NEB workflows and backend adapters (GPAW, MACE)…
v0.1.0 · audit A · 144 stars
ase-calculators skill
jinzhezenggroup/computational-chemistry-agent-skills · atomistic-workflows/ase/ase-calculators/SKILL.md · Route ASE calculator-backend requests to adapter subskills based on backend choice. Use when ASE workflows need…
v0.1.0 · audit A · 144 stars
gpaw skill
jinzhezenggroup/computational-chemistry-agent-skills · atomistic-workflows/ase/ase-calculators/gpaw/SKILL.md · Configure ASE GPAW calculator adapter settings for ASE workflows. Use when ASE workflow tasks require GPAW backend…
v0.1.0 · audit A · 144 stars
mace skill
jinzhezenggroup/computational-chemistry-agent-skills · atomistic-workflows/ase/ase-calculators/mace/SKILL.md · Configure ASE MACE calculator adapter settings for ASE workflows. Use when ASE workflow tasks require MACE backend…
v0.1.0 · audit A · 144 stars
ase-workflows skill
jinzhezenggroup/computational-chemistry-agent-skills · atomistic-workflows/ase/ase-workflows/SKILL.md · Route ASE atomistic workflow requests to task-specific subskills based on user intent. Use when the user asks for…
v0.1.0 · audit A · 144 stars
md skill
jinzhezenggroup/computational-chemistry-agent-skills · atomistic-workflows/ase/ase-workflows/md/SKILL.md · Prepare ASE molecular-dynamics workflow tasks with backend-agnostic controls. Use when the user needs…
v0.1.0 · audit A · 144 stars
neb skill
jinzhezenggroup/computational-chemistry-agent-skills · atomistic-workflows/ase/ase-workflows/neb/SKILL.md · Prepare ASE NEB workflow tasks with backend-agnostic controls. Use when the user needs reaction-path optimization…
v0.1.0 · audit A · 144 stars
relax skill
jinzhezenggroup/computational-chemistry-agent-skills · atomistic-workflows/ase/ase-workflows/relax/SKILL.md · Prepare ASE geometry-optimization workflow tasks with backend-agnostic controls. Use when the user needs structural…
v0.1.0 · audit A · 144 stars
static skill
jinzhezenggroup/computational-chemistry-agent-skills · atomistic-workflows/ase/ase-workflows/static/SKILL.md · Prepare ASE static (single-point) workflow tasks with backend-agnostic workflow controls. Use when the user needs…
v0.1.0 · audit A · 144 stars
dpdata-cli skill
jinzhezenggroup/computational-chemistry-agent-skills · data-processing/dpdata-cli/SKILL.md · A command-line utility for converting and manipulating over 50 atomic simulation data formats, including outputs from…
v1.0 · audit A · 144 stars
openbabel skill
jinzhezenggroup/computational-chemistry-agent-skills · data-processing/openbabel/SKILL.md · A versatile CLI tool for converting molecular file formats, generating 3D atomic coordinates from SMILES, rendering 2D…
v1.1 · audit A · 144 stars
packmol-generate-mixture skill
jinzhezenggroup/computational-chemistry-agent-skills · data-processing/packmol-generate-mixture/SKILL.md · A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by…
v1.0 · audit A · 144 stars
pymatgen-structure skill
jinzhezenggroup/computational-chemistry-agent-skills · data-processing/pymatgen-structure/SKILL.md · Structure manipulation and crystal analysis workflows based on pymatgen. USE WHEN you need to read/write common…
v0.1.0 · audit A · 144 stars
deepmd-finetune-dpa3 skill
jinzhezenggroup/computational-chemistry-agent-skills · machine-learning-potentials/deepmd-finetune-dpa3/SKILL.md · Fine-tune a DPA3 model in DeePMD-kit using the PyTorch backend. Use when the user wants to adapt a pre-trained DPA3…
v1.0 · audit A · 144 stars
deepmd-python-inference skill
jinzhezenggroup/computational-chemistry-agent-skills · machine-learning-potentials/deepmd-python-inference/SKILL.md · Run Python inference with DeePMD-kit models using the DeepPot API. Use when the user wants to load a trained/frozen…
v1.0 · audit A · 144 stars
deepmd-train skill
jinzhezenggroup/computational-chemistry-agent-skills · machine-learning-potentials/deepmd-train/SKILL.md · Train DeePMD-kit models with progressive disclosure. Use when the user wants to train a DeePMD-kit potential, prepare…
v1.1 · audit A · 144 stars
dpgen-simplify skill
jinzhezenggroup/computational-chemistry-agent-skills · machine-learning-potentials/dpgen-simplify/SKILL.md · Prepare, explain, validate, and run DP-GEN simplify workflows for reducing repeated or redundant DeepMD datasets. Use…
v0.2.0 · audit A · 144 stars
rdkit-conf skill
jinzhezenggroup/computational-chemistry-agent-skills · molecular-conformer/rdkit-conf/SKILL.md · A standardized CLI wrapper for RDKit 3D/2D conformer generation that samples multiple conformers per molecule (ETKDGv3…
v1.0 · audit A · 144 stars
antechamber skill
jinzhezenggroup/computational-chemistry-agent-skills · molecular-dynamics/antechamber/SKILL.md · A command-line tool in AmberTools for preparing small molecules or non-standard residues within GAFF/AMBER-compatible…
v1.0 · audit A · 144 stars
lammps-deepmd skill
jinzhezenggroup/computational-chemistry-agent-skills · molecular-dynamics/lammps-deepmd/SKILL.md · A tool and knowledge base for running molecular dynamics (MD) simulations in LAMMPS with the DeePMD-kit plugin. It…
v1.0 · audit A · 144 stars
lammps-reaxff skill
jinzhezenggroup/computational-chemistry-agent-skills · molecular-dynamics/lammps-reaxff/SKILL.md · Run reactive molecular dynamics simulations in LAMMPS with the ReaxFF potential, including preparing input scripts…
v1.0 · audit A · 144 stars
rdkit-repr skill
jinzhezenggroup/computational-chemistry-agent-skills · molecular-representation/rdkit-repr/SKILL.md · A standardized CLI wrapper for RDKit molecular featurization workflows that handles physicochemical descriptor…
v1.0 · audit A · 144 stars
unimol skill
jinzhezenggroup/computational-chemistry-agent-skills · molecular-representation/unimol/SKILL.md · A standardized CLI wrapper for Uni-Mol molecular ML workflows that handles representation extraction (embeddings)…
v1.0 · audit A · 144 stars
dft-abinit skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-abinit/SKILL.md · Route ABINIT requests to task-specific subskills based on user intent. Use when the user asks for ABINIT workflows and…
v0.1.0 · audit A · 144 stars
electronic skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-abinit/electronic/SKILL.md · Prepare ABINIT electronic-analysis task inputs from prior converged context. Use when the user requests…
v0.1.0 · audit A · 144 stars
md skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-abinit/md/SKILL.md · Prepare ABINIT molecular-dynamics task inputs from a user-provided structure and MD controls. Use when the user needs…
v0.1.0 · audit A · 144 stars
relax skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-abinit/relax/SKILL.md · Prepare ABINIT geometry-relaxation task inputs from a user-provided structure and optimization settings. Use when the…
v0.1.0 · audit A · 144 stars
static skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-abinit/static/SKILL.md · Prepare ABINIT single-point (static) task inputs from a user-provided structure and essential DFT settings. Use when…
v0.1.0 · audit A · 144 stars
dft-cp2k skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-cp2k/SKILL.md · Route CP2K requests to task-specific subskills based on user intent. Use when the user asks for CP2K workflows and you…
v0.1.0 · audit A · 144 stars
electronic skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-cp2k/electronic/SKILL.md · Prepare CP2K electronic-analysis task inputs from prior converged context. Use when the user requests post-ground-state…
v0.1.0 · audit A · 144 stars
md skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-cp2k/md/SKILL.md · Prepare CP2K molecular-dynamics task inputs from a user-provided structure and MD controls. Use when the user needs…
v0.1.0 · audit A · 144 stars
relax skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-cp2k/relax/SKILL.md · Prepare CP2K geometry-relaxation task inputs from a user-provided structure and optimization settings. Use when the…
v0.1.0 · audit A · 144 stars
static skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-cp2k/static/SKILL.md · Prepare CP2K single-point (static) task inputs from a user-provided structure and essential DFT settings. Use when the…
v0.1.0 · audit A · 144 stars
dft-gpaw skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-gpaw/SKILL.md · Route GPAW DFT requests to task-specific subskills based on user intent. Use when the user asks for GPAW workflows and…
v0.1.0 · audit A · 144 stars
band skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-gpaw/band/SKILL.md · Prepare GPAW band-structure workflow scripts from existing ground-state context and user-specified k-path settings. Use…
v0.1.0 · audit A · 144 stars
dos skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-gpaw/dos/SKILL.md · Prepare GPAW DOS workflow scripts from existing ground-state context and user-specified DOS settings. Use when the user…
v0.1.0 · audit A · 144 stars
relax skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-gpaw/relax/SKILL.md · Prepare GPAW geometry-relaxation task inputs/scripts from a user-provided structure and essential optimization…
v0.1.0 · audit A · 144 stars
static skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-gpaw/static/SKILL.md · Prepare GPAW static SCF task inputs/scripts from a user-provided structure and essential DFT settings. Use when the…
v0.1.0 · audit A · 144 stars
dft-qe skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-qe/SKILL.md · Generate Quantum ESPRESSO DFT input tasks from a user-provided structure plus user-specified DFT settings. Use when the…
v1.0 · audit A · 144 stars
dft-siesta skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-siesta/SKILL.md · Route SIESTA requests to task-specific subskills based on user intent. Use when the user asks for SIESTA workflows and…
v0.1.0 · audit A · 144 stars
electronic skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-siesta/electronic/SKILL.md · Prepare SIESTA electronic-analysis task inputs from prior converged context. Use when the user requests…
v0.1.0 · audit A · 144 stars
md skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-siesta/md/SKILL.md · Prepare SIESTA molecular-dynamics task inputs from a user-provided structure and MD controls. Use when the user needs…
v0.1.0 · audit A · 144 stars
relax skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-siesta/relax/SKILL.md · Prepare SIESTA geometry-relaxation task inputs from a user-provided structure and optimization settings. Use when the…
v0.1.0 · audit A · 144 stars
static skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-siesta/static/SKILL.md · Prepare SIESTA single-point (static) task inputs from a user-provided structure and essential DFT settings. Use when…
v0.1.0 · audit A · 144 stars
dft-vasp skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-vasp/SKILL.md · Route VASP DFT requests to task-specific subskills based on user intent. Use when the user asks for VASP workflows and…
v0.2.0 · audit A · 144 stars
band skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-vasp/band/SKILL.md · Prepare VASP band-structure workflow inputs from existing SCF context and user-specified band-path settings. Use when…
v0.1.0 · audit A · 144 stars
dos skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-vasp/dos/SKILL.md · Prepare VASP DOS workflow inputs from existing SCF artifacts and user-specified DOS settings. Use when the user…
v0.1.0 · audit A · 144 stars
relax skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-vasp/relax/SKILL.md · Prepare VASP geometry-relaxation input tasks from a user-provided structure and essential DFT settings. Use when the…
v0.1.0 · audit A · 144 stars
static skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dft-vasp/static/SKILL.md · Prepare VASP static SCF input tasks from a user-provided structure and essential DFT settings. Use when the user needs…
v0.1.0 · audit A · 144 stars
dftbplus skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dftbplus/SKILL.md · Route DFTB+ requests to task-specific subskills based on user intent. Use when the user asks for DFTB+ workflows and…
v0.1.0 · audit A · 144 stars
electronic skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dftbplus/electronic/SKILL.md · Prepare DFTB+ electronic-analysis task inputs based on prior ground-state context. Use when the user requests…
v0.1.0 · audit A · 144 stars
md skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dftbplus/md/SKILL.md · Prepare DFTB+ molecular-dynamics task inputs from a user-provided structure and MD controls. Use when the user needs…
v0.1.0 · audit A · 144 stars
relax skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dftbplus/relax/SKILL.md · Prepare DFTB+ geometry-relaxation task inputs from a user-provided structure and optimization settings. Use when the…
v0.1.0 · audit A · 144 stars
static skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/dftbplus/static/SKILL.md · Prepare DFTB+ single-point (static) task inputs from a user-provided structure and essential SCC/settings choices. Use…
v0.1.0 · audit A · 144 stars
gjf-flux skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/gjf-flux/SKILL.md · Assemble and extract Gaussian .gjf input file sections (directives, route, title, molecule blocks, appendices) and…
v0.1.0 · audit A · 144 stars
run-gauss skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/run-gauss/SKILL.md · Acts as a knowledge base providing environment checklists, directory/scratch management, and bash command templates…
v0.1.0 · audit A · 144 stars
xtb skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/xtb/SKILL.md · Prepare and explain xTB semiempirical quantum-chemistry workflows for single-point energy, forces, charges, dipole…
v1.0 · audit A · 144 stars
xtbloom-integrate-ase-dpdata skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/xtbloom-integrate-ase-dpdata/SKILL.md · Integrate xTBloom with ASE or dpdata for molecular energy, force, charge, labeling, relaxation, optimizer, or dynamics…
git:20260813.47ae0c6 · audit A · 144 stars
xtbloom-run-python-inference skill
jinzhezenggroup/computational-chemistry-agent-skills · quantum-chemistry/xtbloom-run-python-inference/SKILL.md · Write, review, and run high-level xTBloom Python GFN2-xTB inference with `Calculator`, `Structure`, and…
git:20260810.6a7d139 · audit A · 144 stars
dpdata-cli skill
jinzhezenggroup/computational-chemistry-agent-skills · tools/dpdata-cli/SKILL.md · Convert and manipulate atomic simulation data formats using dpdata CLI. Use when converting between DFT/MD output…
v1.0 · audit A · 144 stars
dpdata-driver skill
jinzhezenggroup/computational-chemistry-agent-skills · tools/dpdata-driver/SKILL.md · Use dpdata Python Driver plugins to label systems (energies/forces/virials) via System.predict(), list available…
v1.0 · audit A · 144 stars
dpdata-minimizer skill
jinzhezenggroup/computational-chemistry-agent-skills · tools/dpdata-minimizer/SKILL.md · Minimize geometries with dpdata minimizer plugins via System.minimize(), including how minimizers relate to drivers…
git:20260318.32fc18f · audit A · 144 stars
dpdisp-submit skill
jinzhezenggroup/computational-chemistry-agent-skills · tools/dpdisp-submit/SKILL.md · Run Shell commands as computational jobs, on local machines or HPC clusters, through Shell, Slurm, PBS, LSF, Bohrium…
v1.0 · audit A · 144 stars
search-species skill
jinzhezenggroup/computational-chemistry-agent-skills · tools/search-species/SKILL.md · USE WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual…
v0.1.0 · audit A · 144 stars
Source
github.com/jinzhezenggroup/computational-chemistry-agent-skills · 144 stars · license LGPL-3.0 · pushed 2026-09-21