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
graph:
  domains: [domain:nanotechnology]
  skillAreas: [skill-area:mathematical-reasoning, skill-area:physics-simulation, skill-area:data-analysis]
  workflows: [workflow:experiment-design]
  roles: [role:research-engineer]
---

# 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"
  },
  "trajectory_file": "string",
  "equilibrated": "boolean"
}
```