lammps-md-executor

name	lammps-md-executor
description	LAMMPS molecular dynamics skill for nanoscale system simulation with force field management
allowed-tools	["Read","Write","Glob","Grep","Bash"]
metadata	{"specialization":"nanotechnology","domain":"science","category":"computational","priority":"high","phase":6,"tools-libraries":["LAMMPS","OVITO","VMD","MDAnalysis"]}

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"
}