hpc-lammps

name	hpc-lammps
description	Generate, review, debug, and recover LAMMPS molecular dynamics input scripts. Use when working with LAMMPS command ordering, data files, force fields, ensembles, neighbor settings, thermo output, or common runtime errors such as lost atoms and non-numeric pressure.

HPC LAMMPS

Treat LAMMPS input generation as a strict staged workflow.

Start

1. Read references/script-structure.md before editing any in.* file.
2. Read references/units-neighbor-and-timestep.md when choosing units, timestep scale, and neighbor settings.
3. Read references/data-forcefield-and-groups.md when using read_data, multiple atom types, or complex assembly workflows.
4. Read references/forcefield-cookbook.md when choosing between Lennard-Jones, EAM/MEAM, Tersoff, ReaxFF, or hybrid styles.
5. Read references/thermostat-and-barostat-matrix.md when selecting nve, nvt, npt, Langevin, or deforming-box workflows.
6. Read references/input-deck-templates.md when assembling a fresh LJ, EAM, or molecule-style input script.
7. Read references/potentials-and-ensembles.md when choosing force fields, thermostatting, or barostatting.
8. Read references/output-and-restarts.md when designing machine-readable logs, dumps, averaging, or restart behavior.
9. Read references/cluster-execution-playbook.md when staging a LAMMPS deck for scheduler-backed cluster execution.
10. Read references/error-recovery.md when the log shows instability, missing potentials, or neighbor-list failures.

Work sequence

1. Fix the unit system first. Everything downstream depends on it.
2. Keep command ordering strict:
   • initialization
   • system definition
   • force fields and neighbor settings
   • minimization, velocity setup, fixes, output, run
3. Decide whether the structure comes from procedural generation or read_data. Do not mix both box-building paths.
4. Match pair_style and pair_coeff syntax to the actual potential family and atom-type mapping.
5. Minimize before aggressive dynamics unless the user explicitly provides a relaxed starting structure.
6. Keep one time-integration fix per atom group unless the combination is explicitly non-overlapping and intended.

Guardrails

• Do not write read_data before units and atom_style.
• Do not use a timestep copied from another unit system.
• Do not launch NPT on a fragile fresh structure without an equilibration stage.
• Do not ignore neighbor-list settings on hot or highly deforming runs.

Additional References

Load these on demand:

• references/minimization-and-box-relax.md for energy minimization, pressure relaxation, and pre-production setup
• references/computes-chunks-and-analysis.md for RDF, MSD, chunk workflows, and averaging outputs
• references/variables-loops-and-control-flow.md for script automation, loops, branching, and multi-run control
• references/units-fix-compute-matrix.md for unit-system, ensemble-fix, and analysis-command matrices
• references/cluster-execution-playbook.md for launch style, output-volume control, and restart handoff on clusters

Reusable Templates

Use assets/templates/ when a concrete input-deck scaffold is needed, especially:

• lj_fluid_minimal.in
• eam_metal_minimal.in
• lammps-mpi-slurm.sh

Outputs

Summarize:

• unit system
• structure source
• force field and atom-type mapping
• ensemble and damping choices
• log-derived failure mode if the script is under repair