jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Run reactive molecular dynamics simulations in LAMMPS with the ReaxFF potential, including preparing input scripts (pairstyle reaxff + fix qeq/reaxff), mapping LAMMPS atom types to elements via paircoeff, choosing ensembles (NVE/NVT/NPT), and adding common ReaxFF diagnostics such as species analysis. Use when the user…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
A standardized CLI wrapper for RDKit molecular featurization workflows that handles physicochemical descriptor computation (outputs .csv) and molecular fingerprint extraction (outputs .npy or .csv), with built-in SMILES validation. USE WHEN you need to compute RDKit molecular descriptors or fingerprints from SMILES…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
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 RDKit SMILES validation. USE WHEN you need to generate molecular embeddings, train machine learning models for chemical…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Route ABINIT requests to task-specific subskills based on user intent. Use when the user asks for ABINIT workflows and you must decide between static, relaxation, molecular dynamics, or electronic-analysis preparation. This orchestration skill dispatches to the correct ABINIT subskill and enforces consistent handoff…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Prepare ABINIT electronic-analysis task inputs from prior converged context. Use when the user requests post-ground-state electronic analyses and needs prerequisite-aware setup.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Route CP2K requests to task-specific subskills based on user intent. Use when the user asks for CP2K workflows and you must decide between static, relaxation, molecular dynamics, or electronic-analysis preparation. This orchestration skill dispatches to the correct CP2K subskill and enforces consistent handoff to…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Route GPAW DFT requests to task-specific subskills based on user intent. Use when the user asks for GPAW workflows and you must decide between static SCF, relaxation, DOS, or band-structure task preparation. This orchestration skill dispatches to the correct GPAW subskill and enforces consistent handoff to submission…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Prepare GPAW band-structure workflow scripts from existing ground-state context and user-specified k-path settings. Use when the user requests electronic band-structure calculations with explicit prerequisite checks and path-definition handling.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Prepare GPAW DOS workflow scripts from existing ground-state context and user-specified DOS settings. Use when the user requests total/projected DOS setup with explicit prerequisite checks against prior converged calculations.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Generate Quantum ESPRESSO DFT input tasks from a user-provided structure plus user-specified DFT settings. Use when the user wants to prepare QE calculations such as SCF, NSCF, relax, vc-relax, MD, bands, DOS, or phonons starting from a structure file or coordinates together with pseudopotentials, functional choice…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Route SIESTA requests to task-specific subskills based on user intent. Use when the user asks for SIESTA workflows and you must decide between static, relaxation, molecular dynamics, or electronic-analysis preparation. This orchestration skill dispatches to the correct SIESTA subskill and enforces consistent handoff…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Route VASP DFT requests to task-specific subskills based on user intent. Use when the user asks for VASP workflows and you must decide between static SCF, relaxation, DOS, or band-structure task preparation. This orchestration skill does not own detailed input generation logic; it dispatches to the correct VASP…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Route DFTB+ requests to task-specific subskills based on user intent. Use when the user asks for DFTB+ workflows and you must decide between static, relaxation, molecular dynamics, or electronic-structure post-ground-state preparation. This orchestration skill dispatches to the correct subskill and enforces consistent…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Assemble and extract Gaussian .gjf input file sections (directives, route, title, molecule blocks, appendices) and build single- or multi-step Link1 jobs from modular component files. USE WHEN needed for generating, refactoring, templating, or scripting Gaussian job files.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Acts as a knowledge base providing environment checklists, directory/scratch management, and bash command templates. USE WHEN you need to guide the execution of Gaussian computational chemistry jobs (.gjf) on local or remote/HPC environments.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Prepare and explain xTB semiempirical quantum-chemistry workflows for single-point energy, forces, charges, dipole, geometry optimization, and molecular dynamics. Use when the user asks for xTB calculations directly, or wants to use xTB through Python/ASE/dpdata bridges while keeping xTB as the primary method rather…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Integrate xTBloom with ASE or dpdata for molecular energy, force, charge, labeling, relaxation, optimizer, or dynamics workflows. Use when an AI coding agent needs to attach the xTBloom ASE calculator, configure dpdata's xtbloom driver or batch minimizer, preserve the adapters' eV/angstrom conventions, choose…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Write, review, and run high-level xTBloom Python GFN2-xTB inference with Calculator, Structure, and BatchCalculator, including single systems, repeated geometry updates, heterogeneous ragged batches, backend selection, units, finite-temperature meaning, and peer-local failure handling. Use for ordinary NumPy-based…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Use dpdata Python Driver plugins to label systems (energies/forces/virials) via System.predict(), list available drivers, and build Driver objects (ase/deepmd/gaussian/sqm/hybrid). Use when working with dpdata Python API (not CLI) and you need driver-based energy/force prediction, plugin registration keys, or examples…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Minimize geometries with dpdata minimizer plugins via System.minimize(), including how minimizers relate to drivers (ASEMinimizer needs a dpdata Driver) and how to list supported minimizers (ase/sqm). Use when doing geometry optimization/minimization through dpdata Python API.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Run Shell commands as computational jobs, on local machines or HPC clusters, through Shell, Slurm, PBS, LSF, Bohrium, etc. USE WHEN the user needs to submit batch jobs to a cluster, run commands on a remote server, execute tasks via job schedulers (Slurm, PBS, LSF), or safely run long-term/background shell commands…
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
USE WHEN requesting core chemical structural data (SMILES, formula, mass, 2D images) via IUPAC, common, or multilingual names. You MUST actively retrieve the data using this skill; DO NOT hallucinate or generate structures yourself. DO NOT USE WHEN asking for physical properties (melting point, solubility)…