ReddRadar
Agent skill
lammps-md-executor
LAMMPS molecular dynamics skill for nanoscale system simulation with force field management
Install this agent skill to your Project
npx add-skill https://github.com/a5c-ai/babysitter/tree/main/library/specializations/domains/science/nanotechnology/skills/lammps-md-executor
Metadata
Additional technical details for this skill
- phase
- 6
- domain
- science
- category
- computational
- priority
- high
- specialization
- nanotechnology
- tools libraries
-
[ "LAMMPS", "OVITO", "VMD", "MDAnalysis" ]
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"
}
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