fl-sean03/agentic-science-worker

Analyze simulation data and compute properties. Use when asked to parse LAMMPS/QE output, calculate diffusion coefficients, RDF, MSD, energies, or generate plots and visualizations.

Run jobs on CU Boulder CURC HPC cluster (Alpine). Use when simulations need more compute than the local workstation, for large-scale parallel jobs, or when GPU resources are needed beyond local availability. You have full SSH access - work like a researcher.

Run LAMMPS molecular dynamics simulations. Use when asked to run MD simulations, energy minimization, equilibration, production runs, or calculate properties like diffusion, RDF, MSD. Supports both CPU and GPU execution.

Search and retrieve scientific literature. Use when asked to find papers, research a topic, find citations, get paper abstracts, or conduct literature reviews. Accesses Semantic Scholar, arXiv, and other academic databases.

Query materials databases for structures and properties. Use when asked to get crystal structures, material properties, phase diagrams, or thermodynamic data. Primary source is Materials Project, with NIST, PubChem as secondary.

Run Quantum ESPRESSO DFT calculations. Use when asked to perform first-principles calculations, SCF, structural relaxation, band structure, DOS, phonons, or any ab initio quantum mechanical calculation.