Hpc Lammps

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