Babysitter lammps-md-executor

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

install

source · Clone the upstream repo

git clone https://github.com/a5c-ai/babysitter

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/a5c-ai/babysitter "$T" && mkdir -p ~/.claude/skills && cp -r "$T/library/specializations/domains/science/nanotechnology/skills/lammps-md-executor" ~/.claude/skills/a5c-ai-babysitter-lammps-md-executor && rm -rf "$T"

manifest: library/specializations/domains/science/nanotechnology/skills/lammps-md-executor/SKILL.md

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

System Setup
- Build initial configuration
- Assign force field
- Minimize energy
Equilibration
- NVT temperature equilibration
- NPT for density
- Monitor equilibration metrics
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"
}