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lammps-md-executor

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LAMMPS molecular dynamics skill for nanoscale system simulation with force field management

QUICK START

How to use this skill

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Source SKILL.md: https://github.com/a5c-ai/babysitter/blob/HEAD/library/specializations/domains/science/nanotechnology/skills/lammps-md-executor/SKILL.md

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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

{
  "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

{
  "thermodynamic_properties": {
    "temperature": "number (K)",
    "pressure": "number (atm)",
    "total_energy": "number (eV)",
    "volume": "number (Angstrom^3)"
  },
  "structural_properties": {
    "rdf_file": "string",
    "msd_file": "string"
  },
  "trajectory_file": "string",
  "equilibrated": "boolean"
}