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 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" }