lammps-md-simulator

name	lammps-md-simulator
description	LAMMPS molecular dynamics simulation skill for atomistic simulations, force field setup, and large-scale parallel computations
allowed-tools	["Bash","Read","Write","Edit","Glob","Grep"]
metadata	{"specialization":"physics","domain":"science","category":"numerical-simulation","phase":6}
graph	{"domains":["domain:physics"],"skillAreas":["skill-area:physics-simulation","skill-area:mathematical-reasoning","skill-area:statistical-analysis"],"workflows":["workflow:experiment-design","workflow:peer-review-cycle"],"roles":["role:computational-scientist","role:research-engineer"]}

LAMMPS MD Simulator

Purpose

Provides expert guidance on LAMMPS molecular dynamics simulations, including input script generation, force field selection, and parallel execution optimization.

Capabilities

• Input script generation and validation
• Force field selection (EAM, Tersoff, ReaxFF)
• Boundary condition and ensemble configuration
• Thermodynamic property extraction
• Trajectory file analysis
• Parallel run optimization (MPI/GPU)

Usage Guidelines

1. Input Script Generation: Create LAMMPS input files with proper syntax and structure
2. Force Field Selection: Choose appropriate interatomic potentials for the system
3. Ensemble Configuration: Set up NVT, NPT, or NVE ensembles correctly
4. Output Analysis: Process dump files and thermodynamic output
5. Performance Optimization: Configure parallel execution for HPC environments

Tools/Libraries

• LAMMPS
• OVITO
• MDAnalysis