# Fileset

[README.md](https://mdr.nims.go.jp/filesets/d768bbe5-3f05-4c05-9fe3-52f8190e55ff/download)

## Creator

Terumasa Tadano, Shinji Tsuneyuki

## Rights

[Creative Commons BY Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/)

## Other metadata

[Input and Output Data for "Quartic Anharmonicity of Rattlers and Its Effect on Lattice Thermal Conductivity of Clathrates from First Principles"](https://mdr.nims.go.jp/datasets/373263d3-9de1-4fb5-947e-6b7258561a60)

## Fulltext

# Quartic anharmonicity of rattlers in Ba₈Ga₁₆Ge₃₀ — self-consistent phonon and thermal-conductivity dataInput and output data for:> T. Tadano and S. Tsuneyuki,> *"Quartic Anharmonicity of Rattlers and Its Effect on Lattice Thermal Conductivity of Clathrates> from First Principles"*, **Phys. Rev. Lett. 120, 105901 (2018)** —> [doi:10.1103/PhysRevLett.120.105901](https://doi.org/10.1103/PhysRevLett.120.105901)> — preprint [arXiv:1710.00311](https://arxiv.org/abs/1710.00311)The dataset covers the 54-atom type-I clathrate Ba₈Ga₁₆Ge₃₀ (*Pm-3n*) at **five lattice constants**(−2 %, opt., +2 %, +4 %, +6 %). Anharmonic force constants up to **sixth order** were obtained bycompressive sensing (LASSO); vibrational frequencies were renormalised by **self-consistent phonon(SCPH) theory**; lattice thermal conductivity was then computed from the Peierls–Boltzmann equationwithin the relaxation-time approximation.Software: **VASP** (forces), **ALAMODE** (`alm` / `anphon`, development build `ALAMODE_priv`).**Companion dataset.** The harmonic force constants used here come from the earlier studyT. Tadano, Y. Gohda and S. Tsuneyuki, *Phys. Rev. Lett.* **114**, 095501 (2015); see §2.6.---## 1. Which files reproduce the published numbers| Published quantity | Paper | This dataset | File ||---|---|---|---|| κ_L at 300 K, SCP+BTE, opt. lattice constant | 0.97 W/mK | **0.967085** | `06_bte/results/kl_scph999_cell0_boundary2500_iso.dat` || κ_L at 300 K, conventional BTE | 0.58 W/mK | **0.579661** | `06_bte/results/kl_bte_cell0_boundary2500_iso.dat` || Anharmonic IFCs "up to the sixth order" | — | FC2–FC6 present, FC7 absent | `04_force_constants/lasso_published/*.xml.xz` || Five lattice constants −2 / opt / +2 / +4 / +6 % | — | 10.737 / 10.954 / 11.173 / 11.392 / 11.611 Å | `01_structure/` || SCPH solved at Γ only | — | `KMESH_SCPH = 1 1 1` | `05_scph/*/input_scph2.txt` || κ_L on a 9×9×9 q-grid | — | `*_999.kl`, `&kpoint 2 / 9 9 9` | `06_bte/*/input_BTE*.txt` || 140 training configurations | — | 140 × 54 rows | `03_training_data/disp_random_0.dat` || AIMD sampling temperature | 300 K *(SI typo)* | **800 K** — see §2.7 | `03_training_data/` || ENCUT 320 eV, 4×4×4 MP, PAW-PBE | — | ✓ | `02_dft_reference/` |---## 2. Read this before using the dataThe working directory this came from contains three campaigns — a 2016 pilot, the 2017 productionrun, and a Nov–Dec 2017 revision — plus 2018–2024 follow-on projects. Picking files by name or bydate alone gives the wrong answer in several distinct ways (§2.1–2.4). §2.5–2.7 record three furtherthings a user needs to know before comparing this data against the paper.### 2.1 The published curves include boundary and isotope scatteringTwo variants of every curve exist in `06_bte/results/`. Only the `_boundary2500_iso` files(2500 nm boundary scattering + isotope scattering) reproduce the paper:| At 300 K | plain | `_boundary2500_iso` | paper ||---|---|---|---|| SCP+BTE, cell0 | 1.024 | **0.967** | 0.97 || conventional BTE, cell0 | 0.613 | **0.580** | 0.58 |Both are shipped. Use the `_boundary2500_iso` ones for anything compared against the paper.### 2.2 The 100–1000 K conductivity files were re-run in 2019 — those are NOT the published onesIn the source `BTE/cellV/` directories, the SCPH temperatures 0, 100, 200 … 1000 K were **allrecomputed on 2019-02-25/28 and 2019-03-18** for a later study; only the 10–90 K files survive fromJuly 2017. The 2019 rerun gives κ(300 K) = 1.006 W/mK for cell0, which matches neither publishednumber.**The July-2017 production values survive only in `06_bte/results/*.dat`**, which is therefore theauthoritative record of Fig. 2. This release ships those curves plus the surviving July-2017 `.kl`files, and excludes every 2019 rerun and every `*.kl_coherent` file.### 2.3 Two LASSO fits exist; only the sixth-order one is published| | **Published** | Exploratory ||---|---|---|| File | `BGG_FPMD800K_random*_lasso1.xml` (one per volume) | `BGG_lasso1.xml` || Orders present | FC2–**FC6** — matches the paper | FC4–**FC10** (`NORDER = 9`) || Location here | `04_force_constants/lasso_published/` | not shipped (1.1 GB, superseded) |The cross-validation study in `04_force_constants/lasso_crossval/` (`input_alm*.txt`, `cv1–5.log`,`cvscore.dat`, minimum CV score at α = 5.71638×10⁻⁵) belongs to the **exploratory tenth-order fit**.It documents how the regularisation parameter was chosen, but it is not the fit that produced thepublished force constants — and its α over-shrinks the sixth-order model. The sixth-order model hasbeen recovered by refitting and is documented in`04_force_constants/lasso_published/input_alm_6th_order.reconstructed.txt`; see §6.### 2.4 The +4 % volume uses a different filename`cell+4__BGG_FPMD800K_random_lasso1.xml.xz` — **no `2`** — while the other four volumes are`…random2…`. This matches `FCSXML` in `06_bte/cell+4/input_BTE*.txt`. The names are preservedexactly as used; do not "correct" them.### 2.5 The source tree used symlinks; this release does notIn the source, `BTE/cellV/*.xml` were 94 relative symlinks into `scph/cellV/newfc2/` and`lasso/cellV/`. Everything here was copied with `cp -pL`, so every file is real data.`MANIFEST.tsv` records the resolved source path for each.### 2.6 The harmonic force constants are shared with the 2015 dataset`04_force_constants/harmonic/BGG_cell0_harm.xml` (md5 `e7449a66ed686d5707d749472e8f8959`) is a2016-05-16 refit of the harmonic IFCs of Ba₈Ga₁₆Ge₃₀, produced *for this study*. It is byte-identicalto a file present in the PRL 114, 095501 (2015) working directory — where it is deliberately**excluded**, because that paper used the earlier 2014 fit (`BGG_cell0_harm0.02.xml`,md5 `10b0877d7db3dc71f7236e970bc3e552`). The two deposits are consistent: same file, differentpapers, and each ships the one its own paper used. `INCAR` and `KPOINTS` are likewise byte-identicalbetween the two studies (INCAR md5 `2fca39a52e1951797cf31788c5bacb55`).### 2.7 The AIMD temperature was 800 K — the Supplemental Material says 300 K in errorThe Supplemental Material of the paper states that the training snapshots were sampled from abinitio molecular dynamics at **300 K**. That is a typo. The actual sampling temperature was**800 K**, confirmed by the author. The data are consistent with 800 K in two independent ways:- every file produced by that fit is named `…FPMD800K…`;- the surviving training set has per-species mean-square displacements of  ⟨u²⟩ = 0.277 / 0.118 / 0.104 Ų for Ba / Ga / Ge. Matched against the harmonic ⟨u²⟩(T) curve in  `05_scph/cell0/dos30.msd` this gives T ≈ 760–860 K — near 800 K and nowhere near 300 K.  (That estimate extrapolates a harmonic curve tabulated only to 141 K, so it is indicative  rather than exact, but the discrepancy with 300 K is far larger than the uncertainty.)Everything else in the SI description holds: 140 snapshots from the +4 % cell, an extra 0.1 Å randomdisplacement on every atom, and 140 × 5 = 700 DFT calculations in total. Use **800 K** whendescribing or reproducing this dataset.### Excluded as post-publication`SQS/` (Sep 2018); `disp/cell0/to_Holger*` (Jul 2018 export); all `*.kl_coherent`; the Feb–Mar 2019`.kl` reruns; `scph/*/newfc2` files dated 2020-06; `PM_*.bands`, `No-PM_*.bands`, `Boson_peak_*`,`compute_diff.py` (2019–2024).---## 3. Directory layout```01_structure/          POSCAR / POSCAR.orig / CONTCAR for the five lattice constants02_dft_reference/      INCAR, KPOINTS, POTCAR.spec, PES job script03_training_data/      two 140-configuration displacement-force sets for the LASSO fit                       (AIMD at 800 K on the +4 % cell + 0.1 A random displacements; see §2.7)04_force_constants/    harmonic/          BGG_cell0_harm.xml  - shared with the 2015 dataset (§2.6)    lasso_published/   the five sixth-order IFC files, xz-compressed, + CHECKSUMS.txt, cluster                       patterns, and the reconstructed ALM input recovered by refitting    lasso_crossval/    tenth-order cross-validation study: input_alm*.txt, cv1-5.log, cvscore.dat05_scph/cellV/         SCPH inputs and logs; newfc2/ holds the renormalised FC2 files                       BGG_SCPHV_offdiag_{T}K.xml for T = 0...1000 K that feed the BTE06_bte/cellV/          anphon inputs, run logs, surviving July-2017 *.kl and *.kl_spec06_bte/conventional/   mode-resolved .result behind the conventional-BTE curve (cell0 only;                       see its README.txt - three volumes removed for size, regenerable)06_bte/results/        >> the published Fig. 2 curves <<07_pes_T2g/cellV/      frozen-phonon PES scans along the T2g (and T1g) rattling coordinate08_linewidth/cellV/    Nov-Dec 2017 revision: mode-resolved linewidths, SCPH bands vs temperature90_raw_dft/            vasprun.xml and OUTCAR archives for the PES scans, per volumeMANIFEST.tsv           path, size, md5, original path, original mtime for every file```Total ≈ 914 MB. The five force-constant files are the bulk of the science content: 1.1 GB of XMLcompressed to 65 MB.### Using the force constantsThe bulky files are xz-compressed (`xz -9e`) rather than gzip/bzip2, which roughly halves thedeposit: the five force-constant files go from 11.2 MB each to 5.7 MB, and the raw-DFT archivesfrom 25 MB to 7 MB in total. Every compressed file was verified to decompress to the md5 recordedin `CHECKSUMS.txt` / `MANIFEST.tsv`. Nothing was removed to meet the size limit.```bashcd 04_force_constants/lasso_publishedxz -dk cell0__BGG_FPMD800K_random2_lasso1.xml.xzmd5 -r cell0__BGG_FPMD800K_random2_lasso1.xml   # compare against CHECKSUMS.txt```ALAMODE reads the plain XML. The `cellV__` prefix is added here to keep the five volumes distinct inone directory; strip it if you want the original filename.---## 4. Which files correspond to which figure| Figure | Content | Files ||---|---|---|| **1** | Phonon dispersion along Γ–X, PES of the T2g rattling mode, displacement pattern | `07_pes_T2g/cellV/{disp,force,energy}_pes*.dat` (PES); `05_scph/cellV/*.bands` and `08_linewidth/cellV/BGG_band_*K.bands` (SCPH dispersion vs temperature) || **2** | κ_L versus temperature and volume, SCP+BTE vs conventional BTE, vs experiment | `06_bte/results/kl_scph999_cellV[_boundary2500_iso].dat` and `kl_bte_cellV[_boundary2500_iso].dat` — **use the `_boundary2500_iso` variants** (§2.1) || **3** | Spectral thermal conductivity κ_L(ω) at several temperatures and lattice constants | `06_bte/cellV/*_999.kl_spec` (produced with `KAPPA_SPEC = 1`) |Note on Fig. 2: the conventional-BTE curve exists for four volumes only — `cell+6` was added later(Aug 2017) and has an SCP+BTE curve but no conventional counterpart.---## 5. Reproducing the resultsThe chain, per volume V:```bash# 1. anharmonic IFCs (already provided; the LASSO fit itself is the step documented in §6)xz -dk 04_force_constants/lasso_published/cellV__BGG_FPMD800K_random*_lasso1.xml.xz# 2. SCPH renormalisation of the harmonic force constants, Gamma point, T = 0...1000 Kcd 05_scph/cellVanphon input_scph2.txt > scph.log        # SELF_OFFDIAG = 1  -> BGG_SCPHV_offdiag_{T}K.xml#    (input_scph1.txt is the SELF_OFFDIAG = 0 comparison)# 3. thermal conductivity on a 9x9x9 q-grid, using the SCPH-renormalised FC2 at temperature Tcd ../../06_bte/cellVanphon input_BTE300.txt > BTE_300K_999.log    # FCSXML = LASSO IFCs, FC2XML = SCPH FC2 at 300 K#    -> BGG_SCPHV_offdiag_300K_999.kl# 4. published curve: take the diagonal (kappa at the same T the SCPH was solved at),#    with boundary (2500 nm) and isotope scattering applied  -> 06_bte/results/*.dat````ISOTOPE = 2` in the anphon inputs; the boundary correction was applied with ALAMODE's`analyze_phonons.py` result analyzer (v1.0.4, recorded in the header of each `kl_bte_*.dat`).**Excluded because it is regenerable** — re-run the step shown, do not expect these in the deposit:`*.scph_dymat`, `*.scph_fc2_correction`, `*.scph_bands` (4.8 GB, step 2 restart/output files);the SCPH `*.result` files (≈2.3 GB, step 3). Of the *conventional* `.result` files only cell0'sis shipped, in `06_bte/conventional/` — it is the provenance of the headline published value; theother three volumes' were removed to meet the repository size limit and are regenerable by thestep-3 command (see `06_bte/conventional/README.txt`); `*.V3.*` three-phonon matrix elements (3.3 GB); `*.evec` (782 MB); `*.apr`.---## 6. Known gaps- **The LASSO run that produced the published force constants was not documented — the model has  been recovered by refitting.** No ALM input or log in the source tree carries  `PREFIX = BGG_FPMD800K_random2_lasso1`. The model was reconstructed and validated against the  published XML; see `04_force_constants/lasso_published/input_alm_6th_order.reconstructed.txt`  for the settings and the evidence. In brief: `NORDER = 5`, `NBODY = 2 3 3 2 2`, cutoffs equal to  columns 1–4 of the surviving tenth-order input, harmonic part fixed to `BGG_cell0_harm.xml`.  A refit reproduces the published cubic force constants with r = 0.9991 and a median ratio of  0.998 on significant terms, and reproduces the FC2 and FC3 term counts exactly.  **The regularisation strength is the one thing not recovered**: nothing records it, and the  published file corresponds to the weakly regularised limit (α ≲ 3×10⁻⁸), *not* the  α = 5.71638×10⁻⁵ cross-validation optimum in `lasso_crossval/`, which belongs to the tenth-order  model. Bit-exact reproduction is impossible regardless: no surviving ALM build supports the 2017  `MODE = lasso` syntax (oldest available is 1.3.0; the fit used 1.0.0RC).- **Two of the five training sets survive, not one.** `03_training_data/` holds two independent  140-configuration displacement-force sets — `disp_random_0.dat` and `disp_random.dat` are  different data despite their identical size (no configuration is shared between them). Both  reproduce the published cell0 cubic force constants at r = 0.9991; `disp_random_0` matches  slightly better (median ratio 0.998 vs 0.982), so it is most likely the cell0 set and  `disp_random` the one behind the differently-named `…random_lasso1` fit used for +4 %.  The sets for the remaining volumes are not preserved.- **`06_bte/cellV/` is incomplete by design**: the July-2017 `.kl` files survive only for SCPH  temperatures 10–90 K (§2.2). The full published temperature range lives in `06_bte/results/`.- `cell0_OUTCAR.tar.xz` and the other OUTCAR archives contain one stray entry named plainly  `outcars/OUTCAR`, a leftover from the working directory. The per-configuration files are named  `OUTCAR_T2g.<n>` / `OUTCAR.<n>` and correspond one-to-one with the `vasprun*.xml` files.- **Three of the four conventional-BTE `.result` files were removed to meet the repository size  limit** (22.9 MB each). Only cell0's is kept, since that is the volume the paper quotes. The  published curves derived from all four are shipped in full in `06_bte/results/`, and  `06_bte/conventional/README.txt` gives the exact command to regenerate any of them. This is the  only place where data was dropped for size rather than for provenance reasons — everything else  was kept and simply compressed harder (see §3).- `POTCAR` files are **not** included; see `02_dft_reference/POTCAR.spec`.---## 7. Licence and citationData: **CC BY 4.0** (see `LICENSE`). If you use this dataset, please cite both the paper and thisdeposit — see `CITATION.cff`.ALAMODE is developed by T. Tadano and is available at <https://github.com/ttadano/alamode>.