# phonopy-workflows

> Phonopy usage & development helper for finite-displacement phonon jobs, IFC/NAC handling, band/DOS/thermal properties, CLI & setting.conf templates, VASP/QE/ABINIT interfaces, plotting utilities, and repo maintenance (tests, docs, formatting). Trigger when working with phonopy runs, interpreting FORCE_SETS/phonopy.yaml/BORN, or contributing to this repo.

- Author: Siyu Liu
- Repository: IntelligentMat/Materials-Science-Skills-For-LLM
- Version: 20251221161123
- Stars: 0
- Forks: 0
- Last Updated: 2026-02-07
- Source: https://github.com/IntelligentMat/Materials-Science-Skills-For-LLM
- Web: https://mule.run/skillshub/@@IntelligentMat/Materials-Science-Skills-For-LLM~phonopy-workflows:20251221161123

---

---
name: phonopy-workflows
description: "Phonopy usage & development helper for finite-displacement phonon jobs, IFC/NAC handling, band/DOS/thermal properties, CLI & setting.conf templates, VASP/QE/ABINIT interfaces, plotting utilities, and repo maintenance (tests, docs, formatting). Trigger when working with phonopy runs, interpreting FORCE_SETS/phonopy.yaml/BORN, or contributing to this repo."
---

Use this skill whenever a task involves running or debugging phonopy, preparing phonon inputs/outputs, or contributing to the phonopy codebase in this repo.

## What you get
- Minimal end-to-end workflow for finite-displacement phonons (generate displacements → DFT forces → force constants → band/DOS/thermal outputs)
- Pointers to config templates and common file meanings
- Cheats for plotting helpers and common CLI flags
- Dev quick-ref: editable install, tests, formatting, docs

## Quick start (finite-displacement, VASP-style)
1) Start from a relaxed `POSCAR` (or CIF) in the working dir.
2) Create supercells & displacements: `phonopy -d --dim="2 2 2" -c POSCAR` → writes `SPOSCAR`, `supercell-xxx/` (or `POSCAR-001` etc.).
3) Run DFT in each displacement directory to obtain forces (`vasprun.xml` or `OUTCAR` per disp).
4) Build FORCE_SETS: `phonopy -f disp-*/vasprun.xml` (or `phonopy -f supercell-*/OUTCAR`). Adds `FORCE_SETS` and `phonopy_disp.yaml`.
5) (Optional) Include Born charges/dielectric for LO–TO splitting: `phonopy-vasp-born vasprun.xml > BORN` then add `--nac` or `NAC = .TRUE.`.
6) Generate force constants & properties from config: `phonopy --dim="2 2 2" -c POSCAR --readfc --band "0 0 0 0.5 0 0 0.5 0.5 0" --band-points 51 --mesh 20 20 20 --dos --pdos --tmin 0 --tmax 1200 --tstep 50`.
7) Plot: `phonopy-bandplot --gnuplot > band.dat`, `phonopy-bandplot -p band.yaml`, `phonopy-pdosplot -p projected_dos.dat`, `phonopy-propplot -p thermal_properties.yaml`.

## Files to know
- `POSCAR` / `SPOSCAR`: primitive vs supercell structures.
- `phonopy.yaml`: serialized run metadata; inspect instead of re-running.
- `phonopy_disp.yaml`: displacement info used to recreate runs.
- `FORCE_SETS` / `FORCE_CONSTANTS` (or HDF5 variants): input for property calculations.
- `BORN` (or `NAC_PARAMS`): dielectric + Born effective charges for non-analytical term correction.
- `band.conf`, `mesh.conf`, `disp.yaml`: simple config files you can pass with `phonopy --config`.
- Outputs: `band.yaml`, `mesh.yaml`, `projected_dos.dat`, `thermal_properties.yaml`, `total_dos.dat`.

## Plotting helpers
- `phonopy-bandplot`: consume `band.yaml`; use `-p` to plot, `--gnuplot` for text, `-o band.pdf` to save.
- `phonopy-pdosplot`: works with `projected_dos.dat`.
- `phonopy-propplot`: plots thermal properties from `thermal_properties.yaml`.
- `phonopy-gruneisen`, `phonopy-qha`, `phonopy-gruneisenplot`, `phonopy-tdplot` are available for advanced workflows (see references).

## Dev quick-ref (this repo)
- Editable install: `python3 -m pip install -e .` (add `[tools]` for optional deps like seekpath/pypolymlp).
- Fast install for docs/tests: ensure `numpy`, `pytest`, `sphinx`, `myst-parser`, `numpydoc`, `matplotlib` are present (use pip/conda as needed).
- Tests: `pytest` from repo root; targeted modules under `test/`.
- Formatting/lint: `pre-commit run --all-files` (config in `pyproject.toml`).
- Docs: `cd doc && make html` (sources are RST/MD; `_build/html` output).

## References (load on demand)
- `references/quick-start.md`: step-by-step finite-displacement workflows (VASP/QE), NAC handling, band/DOS/thermal examples.
- `references/config-templates.md`: ready-to-copy `setting.conf` snippets for mesh, band, DOS, NAC, Grüneisen, QHA.
- `references/common-files.md`: what each phonopy file means and when to regenerate vs reuse.
- `references/dev.md`: repo-specific dev/CI tips and gotchas.

Use these references instead of re-discovering commands; keep outputs small and reuse `phonopy.yaml` wherever possible.