jinzhezenggroupOfficial·43 Agent Skills Included

computational-chemistry-agent-skills

Automated DFT, molecular dynamics, and ML potential workflows

Automates computational chemistry tasks including DFT input preparation for VASP, CP2K, SIESTA, ABINIT, GPAW, and Quantum ESPRESSO, plus LAMMPS molecular dynamics and DeePMD-kit model training. Eliminates manual input file writing, format conversion between 50+ simulation formats, and error-prone HPC job submission. Routes plain-language requests to the right chemistry engine and hands off execution to cluster schedulers automatically.

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npx skills add jinzhezenggroup/computational-chemistry-agent-skills --all -g -y

All Skills in This Repository (43)

Pure Emerald Level Indicators

📦 In Repo

jinzhezenggroup

dpdata-minimizer

Minimize geometries with dpdata minimizer plugins to produce a LabeledSystem.

dpdisp-submit

Convert shell commands into DPDispatcher job configurations for local or HPC schedulers.

dpdata-driver

Label dpdata Systems with driver plugins to compute energies, forces, and virials.

search-species

Retrieve chemical names, formulas, masses, SMILES, and 2D images from OPSIN, PubChem, or Wikidata.

phonopy

Orchestrate phonopy workflows for band structure, DOS, and thermal properties.

reacnetgenerator

Analyze LAMMPS reactive MD trajectories to generate reaction networks and reports.

rdkit-conf

Generate RDKit conformers from SMILES and output SDF or XYZ files.

rdkit-repr

Compute RDKit molecular descriptors and fingerprints from SMILES data.

unimol

Run Uni-Mol embedding, training, and prediction workflows via a CLI wrapper.

lammps-reaxff

Generate and validate annotated LAMMPS ReaxFF input scripts with QEq configuration.

lammps-deepmd

Automate LAMMPS simulations with DeePMD-kit potentials and ensemble selection.

antechamber

Automate atom typing, charge assignment, and prep input generation for AMBER workflows.

Official

Intermediate

Frequently Asked Questions

FAQPage Schema

How to install computational-chemistry-agent-skills?▼

Run `npx skills add jinzhezenggroup/computational-chemistry-agent-skills --all -g -y` in your terminal to install all skills globally.

What chemistry software does this support?▼

It covers DFT engines like VASP, CP2K, SIESTA, ABINIT, GPAW, Quantum ESPRESSO, and DFTB+, plus LAMMPS for molecular dynamics, Gaussian, xTB, and DeePMD-kit for machine learning potentials.

Can it submit jobs to my HPC cluster?▼

Yes. The dpdisp-submit skill converts shell commands into jobs for Slurm, PBS, LSF, and other schedulers, with state tracking and automatic recovery for long-running calculations.

Can it convert between simulation file formats?▼

Yes. The dpdata and Open Babel skills convert between 50+ formats including VASP, LAMMPS, Gaussian, CP2K, and DeePMD-kit training data formats.

Do I need coding experience to run DFT calculations?▼

No. You describe the calculation in plain language, and the agent prepares the input files, validates settings, and submits the job for you.