lammps-preparation

name	lammps-preparation
description	Use this skill for source-grounded LAMMPS force-field validation and preparation of minimization, MD, and restart stages.
allowed-tools	lammps_forcefield_validate lammps_prepare remote_submission remote_submission_batch get_avail_remote_task lammps_log_summary md_trajectory_summary execute

lammps-preparation

Overview

Use this skill for LAMMPS stages in dynamics_worker. LAMMPS requires an explicit validated force-field card before input generation.

Quick Start

1. Validate the force-field card with lammps_forcefield_validate.
2. Prepare a stage with lammps_prepare(recipe="minimize" | "nve" | "nvt" | "npt" | "anneal" | "restart").
3. Verify in.lammps, system.data or restart file, manifest.json, and potential files.
4. Submit with remote_submission(task_name="lammps_execute").
5. Summarize with lammps_log_summary and md_trajectory_summary when outputs are collected.

Allowed tools

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

Workflow

1. Validate before prepare

• The force-field card must declare units, atom_style, pair_style, and pair_coeff.
• Referenced potential files must exist in the workspace.
• Do not choose or invent a force field from chemistry alone.

2. Prepare one stage per simulation

• lammps_prepare writes in.lammps, system.data when starting from a structure, and manifest.json.
• Use recipe="minimize" for force-field minimization.
• Use nve, nvt, npt, or anneal for MD stages.
• Use restart only when the intended restart file is present and verified.

3. Submit through the generic execute task

• Use only task_name="lammps_execute".
• The boot script runs lmp and may use GPU/KOKKOS/GPU-package acceleration when available, with CPU fallback if acceleration fails.

Method-critical defaults

• Report units, atom_style, pair_style, thermostat/barostat recipe, timestep, steps, thermo stride, dump stride, and restart stride.
• Do not hide force-field assumptions; they are part of the scientific model.
• RDF/MSD are generic only when species or group selections are explicit. Use task-specific scripts for residence time, adsorption events, or reaction analysis.

Output Contract

Return:

• normalized force-field card path
• LAMMPS stage path
• submitted receipt/context
• lammps_log_summary and trajectory summary paths when generated
• any force-field or parser limitation

References

• Local source note: references/lammps_input_reference.md
• LAMMPS units: https://docs.lammps.org/units.html
• LAMMPS read_data: https://docs.lammps.org/read_data.html
• LAMMPS pair_style: https://docs.lammps.org/pair_style.html
• LAMMPS fix nvt/npt: https://docs.lammps.org/fix_nh.html
• LAMMPS minimize: https://docs.lammps.org/minimize.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 read_restart: https://docs.lammps.org/read_restart.html
• LAMMPS compute rdf: https://docs.lammps.org/compute_rdf.html
• LAMMPS compute msd: https://docs.lammps.org/compute_msd.html
• pymatgen LAMMPS module: https://pymatgen.org/pymatgen.io.lammps.html
• lammpsio docs: https://lammpsio.readthedocs.io/