jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Create new Agent Skills following the agentskills.io specification. Use when the user wants to create, scaffold, or design a new skill for AI agents. Handles SKILL.md generation, directory structure setup, and validation.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
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 explicit structure, lazy loading,scoped context, evidence-grounded routing, and human review at critical checkpoints. USE WHEN…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
General phonon-workflow skill built around phonopy, independent of force backend. USE WHEN you need to prepare finite-displacement phonon calculations, build force constants, and analyze phonon properties (band structure, DOS, thermal quantities) while obtaining forces from different engines such as VASP, Quantum…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Run ReacNetGenerator on reactive MD trajectories to generate reaction networks and reports. Use when the user wants to analyze LAMMPS dump/xyz/bond trajectories with ReacNetGenerator. Handles LAMMPS dump quirks like x/y/z vs xs/ys/zs by converting to x/y/z (orthorhombic + triclinic supported via reacnet-md-tools). Can…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Unified ASE router skill with a tree of subskills for static/relax/MD/NEB workflows and backend adapters (GPAW, MACE). Use when you need backend-agnostic workflow orchestration while keeping calculator-specific setup isolated in adapter subskills, with reproducible task preparation as output.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Route ASE calculator-backend requests to adapter subskills based on backend choice. Use when ASE workflows need backend-specific calculator setup (for example GPAW or MACE) while keeping workflow logic backend-agnostic.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Configure ASE GPAW calculator adapter settings for ASE workflows. Use when ASE workflow tasks require GPAW backend setup including mode, k-point, convergence, and restart policies.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Configure ASE MACE calculator adapter settings for ASE workflows. Use when ASE workflow tasks require MACE backend setup including model path/version, device/precision, stress availability, and inference controls.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Route ASE atomistic workflow requests to task-specific subskills based on user intent. Use when the user asks for ASE-based static, relaxation, MD, or NEB workflows and you must apply consistent workflow controls independent of calculator backend.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Prepare ASE molecular-dynamics workflow tasks with backend-agnostic controls. Use when the user needs finite-temperature trajectories with explicit ensemble, timestep, thermostat, and output policies.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Prepare ASE NEB workflow tasks with backend-agnostic controls. Use when the user needs reaction-path optimization between initial/final states with explicit image construction, spring settings, and convergence controls.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Prepare ASE geometry-optimization workflow tasks with backend-agnostic controls. Use when the user needs structural relaxation while selecting optimizer, convergence target, constraints, and output trajectory policy independently of calculator backend.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Prepare ASE static (single-point) workflow tasks with backend-agnostic workflow controls. Use when the user needs one-shot energy/force/stress evaluation through an ASE calculator adapter.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
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.). USE WHEN you need to convert structural or trajectory files between different computational chemistry formats, or when parsing raw…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
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 computational workflows. USE WHEN you need to convert between chemical file formats (e.g., xyz, pdb, mol, smi, gjf), generate 3D…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
A tool for generating initial packed molecular configurations (XYZ format) from single-molecule structures by calculating box dimensions, writing input scripts, and executing Packmol. USE WHEN you need to randomly pack a specific number of molecules into a simulation box (defined by target density or fixed lengths) to…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Structure manipulation and crystal analysis workflows based on pymatgen. USE WHEN you need to read/write common atomistic formats (CIF, POSCAR, XYZ), build supercells, perform site substitution/doping, inspect symmetry (space group), or compute local structure descriptors for materials tasks.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Fine-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. Supports fine-tuning from a self-trained DPA3 model (.pt checkpoint), from a multi-task pre-trained model, or from a built-in pretrained model downloaded via dp…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Run Python inference with DeePMD-kit models using the DeepPot API. Use when the user wants to load a trained/frozen DeePMD model (.pth or .pb) or a built-in pretrained model (e.g., DPA-3.2-5M) in Python, predict energy/force/virial for atomic configurations, evaluate descriptors, or calculate model deviation between…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Train DeePMD-kit models with progressive disclosure. Use when the user wants to train a DeePMD-kit potential, prepare an input.json, choose between model families such as see2a/DeepPot-SE and DPA3, run dp train, monitor learning curves, freeze checkpoints, or test trained models. Start with model selection and read…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Prepare, explain, validate, and run DP-GEN simplify workflows for reducing repeated or redundant DeepMD datasets. Use when the user wants to generate or modify param.json and machine.json, run dpgen simplify param.json machine.json, organize repeated simplify experiments, or inspect simplify outputs.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
A standardized CLI wrapper for RDKit 3D/2D conformer generation that samples multiple conformers per molecule (ETKDGv3, default 10), optimizes each with a force field (MMFF94s/UFF), keeps the lowest-energy conformer, automatically falls back to 2D layout on total embedding failure with a printed warning, and writes…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
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 typing, charge generation or import, and force-field–compatible input generation. USE WHEN you are working in AMBER, dealing…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
A tool and knowledge base for running molecular dynamics (MD) simulations in LAMMPS with the DeePMD-kit plugin. It handles input script preparation, ensemble selection (NVE/NVT/NPT), and job execution via uv or offline binaries. USE WHEN you need to set up, write, explain, or execute a LAMMPS molecular dynamics…