# lammps-getting-started

> This skill should be used when users ask about getting started in lammps; it prioritizes documentation references and then source inspection only for unresolved details.

- Author: Tao E. Li
- Repository: TEL-Research-Group/lammps
- Version: 20260207223556
- Stars: 0
- Forks: 0
- Last Updated: 2026-02-08
- Source: https://github.com/TEL-Research-Group/lammps
- Web: https://mule.run/skillshub/@@TEL-Research-Group/lammps~lammps-getting-started:20260207223556

---

---
name: lammps-getting-started
description: This skill should be used when users ask about getting started in lammps; it prioritizes documentation references and then source inspection only for unresolved details.
---

# lammps: Getting Started

## High-Signal Playbook
### Route the request
- Use `lammps-build-and-install` for compiler, package, and binary build issues.
- Use `lammps-inputs-and-modeling` for force-field setup, topology, and data files.
- Use `lammps-simulation-workflows` for equilibration/production/restart sequencing.
- Use `lammps-parallel-hpc` for MPI/OpenMP/GPU launch tuning and scaling.
- Use `lammps-troubleshooting` for lost atoms, NaN/Inf thermodynamics, and crashes.

### Triage questions
- Which executable are you launching (`lmp`, `lmp_mpi`, `lmp_<machine>`)?
- Which `units` and `atom_style` are required by the model?
- Is the box created via `create_box`, `read_data`, or `read_restart`?
- Are long-range electrostatics required (`kspace_style`)?
- Which ensemble/integrator is intended (`fix nve`, `fix nvt`, `fix npt`)?
- What minimum outputs are required (thermo fields, dumps, restart cadence)?

### Canonical workflow
- Verify feature availability with `lmp -help` (`doc/src/Run_options.rst`).
- Start scripts with `units`, `atom_style`, and `boundary` before box creation (`doc/src/units.rst`, `doc/src/atom_style.rst`, `doc/src/boundary.rst`).
- Define the system with `create_box`/`read_data`/`read_restart` (`doc/src/Run_formats.rst`).
- Configure pair/bonded styles and coefficients (`doc/src/pair_style.rst`, `doc/src/pair_coeff.rst`).
- Set neighbor policy and timestep (`doc/src/neighbor.rst`, `doc/src/neigh_modify.rst`, `doc/src/timestep.rst`).
- Initialize velocities and integrator fix (`doc/src/velocity.rst`, `doc/src/fix_nve.rst`, `doc/src/fix_nh.rst`).
- Run a short sanity segment before long production (`doc/src/run.rst`, `doc/src/Run_output.rst`).

### Minimal working examples
- Launch pattern (`doc/src/Run_basics.rst`):
```bash
mpirun -np 4 lmp -in in.lj
```
- Small starter input (`doc/src/Run_formats.rst`):
```LAMMPS
units lj
atom_style atomic
boundary p p p
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
velocity all create 1.0 4928459 mom yes rot yes dist gaussian
fix int all nve
thermo 100
run 1000
```

### Pitfalls
- Using shell redirection (`< in.file`) under MPI; prefer `-in` (`doc/src/Run_basics.rst`).
- Changing `units` or `atom_style` after box creation (not allowed) (`doc/src/units.rst`, `doc/src/atom_style.rst`).
- Mixing potential/data files with incompatible units (`UNITS:` tags) (`doc/src/units.rst`, `doc/src/pair_coeff.rst`).
- Missing package-enabled styles causing "invalid ... style" (`doc/src/Run_options.rst`, `doc/src/Build_package.rst`).
- Overly aggressive timestep during initialization causing lost atoms (`doc/src/Errors_details.rst`).

### Convergence and validation checklist
- Confirm no lost atoms and no NaN/Inf thermo values (`doc/src/Errors_details.rst`).
- Check `Dangerous builds` is zero or rare (`doc/src/Run_output.rst`).
- Verify short NVE segment has acceptable energy drift for chosen `dt`.
- Compare key averages across different MPI counts for statistical consistency (`doc/src/Errors_common.rst`).

## Scope
- Handle questions about initial setup, quickstarts, and core concepts.
- Keep responses abstract and architectural for large codebases; avoid exhaustive per-function documentation unless requested.

## Primary documentation references
- `doc/src/Run_basics.rst`
- `doc/src/Run_options.rst`
- `doc/src/Run_formats.rst`
- `doc/src/Run_output.rst`
- `doc/src/Build_basics.rst`
- `doc/src/Build_cmake.rst`
- `doc/src/units.rst`
- `doc/src/atom_style.rst`
- `doc/src/boundary.rst`
- `doc/src/Errors_common.rst`
- `doc/src/Errors_details.rst`
- `examples/melt/in.melt`

## Workflow
- Start with the primary references above.
- If details are missing, inspect `references/doc_map.md` for additional topic documents (generated inventory plus curated anchors).
- Use tutorials/examples as executable usage patterns when available.
- Use tests as behavior or regression references when available.
- If ambiguity remains after docs, inspect `references/source_map.md` and start with the ranked source entry points.
- Cite exact documentation file paths in responses.

## Tutorials and examples
- `examples`

## Test references
- None discovered.

## Optional deeper inspection
- `fortran`
- `lib`
- `python`
- `src`

## Source entry points for unresolved issues
- `src/main.cpp`
- `src/lammps.h`
- `src/lammps.cpp`
- `src/input.h`
- `src/input.cpp`
- `src/run.h`
- `src/run.cpp`
- `src/modify.h`
- `src/modify.cpp`
- `src/read_restart.h`
- `src/read_restart.cpp`
- `src/write_restart.h`
- `src/write_restart.cpp`
- Prefer targeted source search (for example: `rg -n "<symbol_or_keyword>" fortran lib python src`).