# lammps-analysis-and-output

> This skill should be used when users ask about analysis and output 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-analysis-and-output:20260207223556

---

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

# lammps: Analysis and Output

## High-Signal Playbook
### Route the request
- Use `lammps-simulation-workflows` to decide equilibration vs production segmentation first.
- Use `lammps-troubleshooting` if output reveals instability (lost atoms, NaN, exploding pressure).
- Use `lammps-api-and-scripting` for Python-native extraction and programmatic control.

### Triage questions
- Which observables are required: thermo, per-atom trajectories, chunk averages, restart state?
- Is downstream parsing done in OVITO/VMD, shell tools, or Python/pandas?
- Is compact structured output (YAML/JSON) preferred over plain text?
- What output cadence balances statistical resolution and I/O cost?

### Canonical workflow
- Define thermo fields with `thermo_style custom` (or `yaml`) (`doc/src/thermo_style.rst`).
- Apply `thermo_modify` only after `thermo_style` (it resets defaults) (`doc/src/thermo_modify.rst`).
- Define dump schema with atom IDs (or explicit sorting) (`doc/src/dump.rst`, `doc/src/dump_modify.rst`).
- Add averaged channels via `fix ave/time` or `fix ave/chunk` when needed (`doc/src/Howto_output.rst`).
- For machine parsing, use YAML thermo/dump outputs (`doc/src/Howto_structured_data.rst`).

### Minimal working examples
- Thermo + trajectory baseline (`doc/src/thermo_style.rst`, `doc/src/dump.rst`):
```LAMMPS
thermo 100
thermo_style custom step temp press pe ke etotal vol nbuild ndanger
thermo_modify flush yes
dump trj all custom 500 dump.lammpstrj id type x y z vx vy vz
dump_modify trj sort id pbc yes
```
- YAML thermo for scripting pipelines (`doc/src/thermo_style.rst`):
```LAMMPS
thermo_style yaml
thermo 200
```

### Pitfalls
- Setting `thermo_modify` before `thermo_style` and expecting it to persist (`doc/src/thermo_style.rst`).
- Dumping without `id` and without sorting, breaking per-atom frame tracking (`doc/src/dump.rst`).
- Assuming dumped coordinates are always wrapped inside box without `pbc yes` (`doc/src/dump.rst`, `doc/src/dump_modify.rst`).
- Writing output too frequently and bottlenecking performance.
- Ignoring warning trends (`ndanger`, missing topology warnings) in thermo/log outputs.

### Convergence and validation checklist
- Include at least `step`, `temp`, `press`, `pe`, `etotal`, and neighbor diagnostics in thermo.
- Validate at least one dump frame in the intended visualization/analysis tool.
- Check time-windowed averages (not just instantaneous values) for reported observables.
- Confirm output cadence is sufficient for target correlation/transport analyses.

## Scope
- Handle questions about output formats, analysis, and post-processing.
- Keep responses abstract and architectural for large codebases; avoid exhaustive per-function documentation unless requested.

## Primary documentation references
- `doc/src/Howto_output.rst`
- `doc/src/Howto_structured_data.rst`
- `doc/src/Run_output.rst`
- `doc/src/thermo_style.rst`
- `doc/src/thermo_modify.rst`
- `doc/src/dump.rst`
- `doc/src/dump_modify.rst`
- `examples/peptide/in.peptide`

## 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/write_dump.h`
- `src/write_dump.cpp`
- `src/thermo.h`
- `src/thermo.cpp`
- `src/read_dump.h`
- `src/read_dump.cpp`
- `src/output.h`
- `src/output.cpp`
- Prefer targeted source search (for example: `rg -n "<symbol_or_keyword>" fortran lib python src`).