lammps-md-execution

name	lammps-md-execution
description	Use this skill for LAMMPS NVE/NVT/NPT/annealing preparation, execution, restart output, and generic MD health analysis.
allowed-tools	lammps_forcefield_validate lammps_prepare remote_submission remote_submission_batch get_avail_remote_task lammps_log_summary md_trajectory_summary analyze_trajectory execute

lammps-md-execution

Overview

Use this skill for LAMMPS equilibration, annealing, and production MD stages in dynamics_worker.

Quick Start

1. Validate or reuse an explicit force-field card.
2. Prepare with lammps_prepare(recipe="nve" | "nvt" | "npt" | "anneal").
3. Submit with remote_submission(task_name="lammps_execute").
4. Summarize with lammps_log_summary and md_trajectory_summary.

Allowed tools

• lammps_forcefield_validate
• lammps_prepare
• remote_submission
• remote_submission_batch
• get_avail_remote_task
• lammps_log_summary
• md_trajectory_summary
• analyze_trajectory
• execute

Workflow

1. Choose the ensemble deliberately

• Use nve for microcanonical production only after appropriate preparation.
• Use nvt/anneal for temperature-controlled stages.
• Use npt only when pressure control is physically meaningful for the model.

2. Preserve output controls

• Set timestep, steps, thermo, dump_stride, and restart_stride explicitly for production runs.
• Enable in-run rdf or msd only when the requested observable is generic enough for all atoms/groups represented by the stage.

3. Analyze health before interpretation

• Use lammps_log_summary for thermo segments, drift, warnings/errors, and run completion.
• Use md_trajectory_summary for frame count, final frame export, restart files, and RDF/MSD table presence.
• Write focused scripts for residence time, adsorption/desorption, reactions, or region-specific observables.

Method-critical defaults

• Do not hide thermostat/barostat settings in prose; they are method choices.
• Do not infer equilibrated production data from a completed run without drift and sampling checks.

Output Contract

Return:

• force-field card and stage paths
• submitted receipt/context
• log summary and trajectory summary paths
• ensemble, timestep, steps, thermo/dump/restart strides
• warnings, errors, and observable limitations

References

• Local source note: references/lammps_md_reference.md
• LAMMPS fix nvt/npt: https://docs.lammps.org/fix_nh.html
• LAMMPS fix: https://docs.lammps.org/fix.html
• LAMMPS thermo_style: https://docs.lammps.org/thermo_style.html
• LAMMPS dump: https://docs.lammps.org/dump.html
• LAMMPS write_restart: https://docs.lammps.org/write_restart.html
• LAMMPS compute rdf: https://docs.lammps.org/compute_rdf.html
• LAMMPS compute msd: https://docs.lammps.org/compute_msd.html