lammps-md-executor

# LAMMPS MD Executor ## Purpose The LAMMPS MD Executor skill provides molecular dynamics simulation capabilities for nanoscale systems, enabling investigation of structural, mechanical, and thermal properties through classical simulations. ## Capabilities - Force field selection and parameterization - System equilibration protocols - NVT/NPT ensemble simulations - Trajectory analysis - Thermal conductivity calculation - Mechanical property simulation ## Usage Guidelines ### MD Simulation Workflow 1. **System Setup** - Build initial configuration - Assign force field - Minimize energy 2. **Equilibration** - NVT temperature equilibration - NPT for density - Monitor equilibration metrics 3. **Production** - Run appropriate ensemble - Calculate properties on-the-fly - Save trajectories ## Process Integration - Molecular Dynamics Simulation Workflow - Multiscale Modeling Integration ## Input Schema ```json { "structure_file": "string", "force_field": "string (ReaxFF|MEAM|Tersoff|LJ)", "ensemble": "nvt|npt|nve", "temperature": "number (K)", "pressure": "number (atm, for npt)", "timestep": "number (fs)", "total_time": "number (ns)" } ``` ## Output Schema ```json { "thermodynamic_properties": { "temperature": "number (K)", "pressure": "number (atm)", "total_energy": "number (eV)", "volume": "number (Angstrom^3)" }, "structural_properties": { "rdf_file": "string", "msd_file": "string" }, "traject...