# Fileset

[README.md](https://mdr.nims.go.jp/filesets/b91b73d0-5ff1-4753-9b94-eedfc7382889/download)

## Creator

Terumasa Tadano, Yoshihiro Gohda, Shinji Tsuneyuki

## Rights

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

## Other metadata

[Input and Output Data for "Impact of Rattlers on Thermal Conductivity of a Thermoelectric Clathrate: A First-Principles Study"](https://mdr.nims.go.jp/datasets/b4011328-9dea-421e-b86d-05582de37c49)

## Fulltext

# First-principles lattice thermal conductivity of Ba₈Ga₁₆Ge₃₀ and the guest-free framework Ga₁₆Ge₃₀Input and output data for:> T. Tadano, Y. Gohda and S. Tsuneyuki,> *"Impact of Rattlers on Thermal Conductivity of a Thermoelectric Clathrate: A First-Principles Study"*,> **Phys. Rev. Lett. 114, 095501 (2015)** — [doi:10.1103/PhysRevLett.114.095501](https://doi.org/10.1103/PhysRevLett.114.095501)> — preprint [arXiv:1412.5723](https://arxiv.org/abs/1412.5723)The dataset covers the type-I clathrate Ba₈Ga₁₆Ge₃₀ (BGG, 54 atoms/cell, *Pm-3n*) and thehypothetical guest-free framework □₈Ga₁₆Ge₃₀ (GG, 46 atoms/cell), which together isolate theeffect of the Ba rattlers on the lattice thermal conductivity κ_L. The empty type-I germaniumclathrate Ge46 (46 atoms/cell, a = 10.735 Å, separately relaxed) is also included: it is the thirdcurve in Fig. 2 of the paper.> **How the guest-free system was obtained — read this first.**> There are **no separate DFT calculations for GG**, and none are missing from this deposit.> Ba acts as an electron donor that completes the sp³ framework, so DFT on the empty cage is not> meaningful; as the paper puts it, *"one cannot perform first-principles calculations directly on> the fictitious material GG"*. Instead, GG force constants were obtained from the **same> Ba₈Ga₁₆Ge₃₀ supercell calculations** by restricting the fit to the configurations in which only> host-framework atoms are displaced, and setting every force-constant term involving Ba to zero.> The lattice constant is unchanged (a = 10.954 Å). BGG and GG therefore share identical> framework–framework force constants by construction, which is what makes the comparison a clean> measurement of the rattlers' effect.>> Consequently `90_raw_dft/` contains only 54-atom Ba₈Ga₁₆Ge₃₀ runs — that is correct and complete> for both systems. §3.1 documents the derivation and how to re-check it.Software: **VASP 5.3.3** (forces) and **ALAMODE 0.9.2** (force constants, phonons, BTE/RTA).---## 1. Which files reproduce the published numbersThe paper reports κ_L at 100 K. Every published value is reproduced by the files below:| Published quantity | Paper | This dataset | File ||---|---|---|---|| κ_L (BGG, 6×6×6 q-grid, *a* = 10.954 Å) | 0.78 W/mK | **0.7761** | `05_bte_results/BGG_cell0/BGG_666_submit2.kl` || κ_L (BGG, experimental lattice constant) | 1.35 W/mK | **1.3502** | `05_bte_results/BGG_cell-2/BGG_666_submit2.kl` || κ_L (GG, 8×8×8 q-grid) | 18.94 W/mK | **18.9463** | `05_bte_results/GG_cell0/GG_888_submit2.kl` || κ_L (Ge46, 8×8×8 q-grid) — third curve of Fig. 2 | — | 57.5874 | `05_bte_results/Ge46/Ge46_888_submit2.kl` || Symmetrically inequivalent harmonic / cubic IFCs (BGG) | 320 / 384 | **320 / 384** | `04_force_constants/BGG_cell0/alm_anharm.log` || Plane-wave cutoff, k-mesh | 320 eV, 4×4×4 MP | ✓ | `02_dft_reference/INCAR`, `KPOINTS` (Ge46 used its own; see `INCAR.Ge46_*`) || Lattice constant | 10.95 Å | 20.70 Bohr = 10.954 Å | `01_structure/BGG_cell0_a10.954.POSCAR` |The reduced-lattice-constant calculation (`BGG_cell-2`, 20.29 Bohr = 10.737 Å, −2 %) is what thepaper refers to as "the experimental lattice constant" (quoted there as 10.76 Å).---## 2. Read this before using the dataThe working directories these files came from contained **two complete calculation campaigns**plus later reruns. Selecting files by date alone yields the *wrong* dataset. Four specific hazardswere identified and resolved; only the published campaign is shipped here.### 2.1 Two campaigns — only the second one is published| | First submission (superseded) | **Published (this dataset)** ||---|---|---|| File prefix | `*_new`, plain `*_666` / `*_444` | **`*_submit2`** || Dates | Feb–Aug 2014 | **Dec 2014 – Jan 2015** || ALAMODE | 0.9.0 | **0.9.2** || IFCs read from | `.info` (Feb 2014 fit) | **`.xml` (Dec 4 2014 re-fit)** || Non-zero harmonic IFCs (BGG / GG) | 9210 / 6450 | **28674 / 22038** || BZ integration | `ISMEAR=0` (Lorentzian) | **`ISMEAR=-1` (tetrahedron)** || κ_L (BGG) at 100 K | 0.6776 | **0.7761** |The harmonic force constants were re-fitted on 2014-12-04 without a distance cutoff, which iswhy the published harmonic IFC set is roughly three times denser. The cubic IFC model isunchanged between campaigns (77952 / 12396 non-zero terms).The first-submission κ_L curves are kept in `07_convergence/` **for the record only** — they areclearly named `*_firstsubmission.kl` and must not be used as the paper's results.### 2.2 The BGG κ_L file was overwritten by a post-hoc isotope runThe paper considers three-phonon scattering only (`ISOTOPE = 0` in every published run log).On 2014-12-10 the no-isotope result was moved aside to `BGG_666_submit2.kl_bak` at 21:25, and arerun **with** isotope scattering overwrote `BGG_666_submit2.kl` at 21:53.In this release the naming is corrected:- `05_bte_results/BGG_cell0/BGG_666_submit2.kl` — **published**, no isotope (was `.kl_bak`)- `05_bte_results/BGG_cell0/BGG_666_submit2_with_isotope.kl` — the post-hoc variant, **not** in the paperThe difference is small (0.7761 → 0.7694 W/mK at 100 K) but the published curve is the former.### 2.3 Three input files were overwritten in 2016 and have been reconstructedLater, unrelated work overwrote some input files in place. Each was rebuilt from the verbatiminput echo in the corresponding Dec-2014 log, which is shipped alongside it. Reconstructed filesare named `*.reconstructed.txt` and carry a header explaining their origin:| Reconstructed file | Rebuilt from | Overwritten by ||---|---|---|| `04_force_constants/BGG_cell{0,-2}/input_alm_{harmonic,cubic}.reconstructed.txt` | `alm_harm.log`, `alm_anharm.log` | 2016-05-16 re-fit || `05_bte_results/BGG_cell0/input_BTE.reconstructed.txt` | `anphon_run.log1`–`log6` | 2014-12-10 isotope rerun || `06_phonon_properties/BGG_cell0/input_linewidth.reconstructed.txt` | `BGG_W202020_submit2.log` | 2016-01-17 Grüneisen run |The `&position` block in the reconstructed ALM inputs was verified byte-identical to the 2014POSCAR actually used for the DFT runs, and to the structure echoed in the Dec-2014 ALM log.The guest-free ALM input (`04_force_constants/GG_cell0/input_alm.txt`) survived untouched and isshipped as-is.**Where the 2016 re-fit went.** The 2016-05-16 harmonic re-fit excluded here(`BGG_cell0_harm.xml`, md5 `e7449a66ed686d5707d749472e8f8959`) was not stray work: it was made forthe follow-up study T. Tadano and S. Tsuneyuki, *Phys. Rev. Lett.* **120**, 105901 (2018), which usesit as the harmonic starting point for self-consistent phonon calculations, and it is shipped in thatpaper's companion dataset. Each deposit therefore carries the harmonic force constants its own paperused — `BGG_cell0_harm0.02.xml` (md5 `10b0877d7db3dc71f7236e970bc3e552`) here, the 2016 re-fit there.The two are not interchangeable. `INCAR` and `KPOINTS` are byte-identical between the two studies.### 2.4 The guest-free cubic force constants existed in only one copy`GG_cell0_anharm.xml` had been regenerated in the fitting directory on 2016-01-26 with ALAMODE0.9.6, producing a file that differs from the published one in the trailing digits and in itssection structure. The published file (ALAMODE 0.9.2, 2014-12-05) survived in the BTE workingdirectory only. The correct file is shipped here:```04_force_constants/GG_cell0/GG_cell0_anharm.xml   md5 = 19e2de7553a4e3a0a137559ddf33511e```Anything hashing to `dfb716dbbd213fc110f3f59bd3986d8d` is the 2016 regeneration, not the paper's.**Ge46 has exactly the same problem.** `disp/Ge46/alm/Ge46_anharm.xml` was regenerated on2015-12-23; the published file (2014-12-05) survived only in the BTE working directory and is whatis shipped here:```04_force_constants/Ge46/Ge46_anharm.xml           md5 = d4b8517129e65a50131b73fc15ea7925```### 2.5 The raw-DFT archives are dated after publication but contain 2014 data`90_raw_dft/*.tar.gz` carry a 2015-06-05 mtime because that is when the loose VASP outputs werearchived. Their contents are the February 2014 production runs. `MANIFEST.tsv` records theoriginal path and mtime of every file so this remains auditable.---## 3. Directory layout and training data```01_structure/          POSCAR/CONTCAR for BGG (a=10.954 and 10.735 Å), the GG framework                       geometry, Ge46, and the fully relaxed BGG cell (a=10.927 Å, 2012)02_dft_reference/      INCAR, KPOINTS, POTCAR.spec, VASP job scripts03_training_data/      displacement-force training sets fed to ALM (see 3.1)                         BGG_cell0/  GG_cell0/  BGG_cell-2/  Ge46/04_force_constants/    harmonic + cubic IFCs (.xml, .fcs), ALM inputs and logs                         BGG_cell0/  GG_cell0/  BGG_cell-2/  Ge46/05_bte_results/        RTA thermal conductivity (.kl), full mode-resolved output (.result),                       anphon inputs, logs and job scripts                         BGG_cell0/  BGG_cell-2/  GG_cell0/  Ge46/06_phonon_properties/  phonon bands, group velocities, atom-projected DOS, participation                       ratio, 20x20x20 phonon linewidths and three-phonon phase space, plus                         groupvelocity/              Fig. 4(b)                         V3_anharmonic_interaction/  Fig. 4(a) inputs and logs                         mode_lifetime/              Fig. 4(c)07_convergence/        q-grid convergence series and the superseded first-submission kappa_L90_raw_dft/            raw VASP vasprun.xml and OUTCAR archives                         BGG_cell0  36 harmonic + 252 cubic   (54-atom, covers GG too)                         BGG_cell-2 36 harmonic   (cubic runs were never archived)                         Ge46       24 harmonic +  96 cubic   (46-atom)MANIFEST.tsv           path, size, md5, original path and original mtime for every file```### 3.1 Training sets and how GG is derived from BGGAll forces come from one set of 54-atom Ba₈Ga₁₆Ge₃₀ supercell calculations:| Source runs (`cell0`) | Configurations ||---|---|| harmonic, single displacement, 0.02 Å | 36 || cubic, dual displacement, 0.04 Å | 252 || Fit | Cell | Configurations used (`NDATA`) | Files ||---|---|---|---|| BGG harmonic | 54 atoms | 18 (0.02 Å subset of the 36) | `BGG_cell0/disp,force_harm0.02.dat` || BGG cubic | 54 atoms | 288 (all 36 + all 252) | `BGG_cell0/disp_total.{disp,force}_au` || GG harmonic | 46 atoms | 12 | `GG_cell0/disp,force_harm_wo_Ba_0.02.dat` || GG cubic | 46 atoms | 84 (24 + 60) | `GG_cell0/disp_wo_Ba_total.{disp,force}_au` |The GG sets are **subsets of the BGG runs with the eight Ba rows deleted**. Of the 36 harmonicruns, the 24 that displace only host atoms are kept (the 12 that displace Ba — patterns `1x`,`3x`, `3y` — are dropped); of the 252 cubic runs, 60 are kept. The intermediate 54-row extractionsare shipped as `GG_cell0/subset54_*.{disp,force}_au` so the derivation can be checked directly:```python# every GG configuration equals a BGG configuration minus its 8 Ba rowssubset54_harm.force_au[cfg][8:]  ==  force_harm_wo_Ba_0.02.dat[cfg]```Verified here for all 12 harmonic configurations. The two extraction passes used marginallydifferent Bohr-radius constants (0.529177 vs 0.52917721 Å), so the values agree to a uniformfactor of 1 + 4×10⁻⁷ rather than bit-exactly. This is a unit constant, not different physics.`xml_list.harmonic` / `xml_list.cubic` in each directory name the exact `vasprun.xml` files used,and every one of them is present in `90_raw_dft/`.Maximum displacement is 0.0200 Å in the harmonic set and 0.0400 Å in the cubic set, verifieddirectly from the shipped files.**Total energies are not tabulated.** The `.energy` files in the source tree contain only `N/A`placeholders — the extraction script never populated them — so they are not shipped. Per-configurationenergies can be read from `<i name="e_fr_energy">` in the raw `vasprun.xml` files in `90_raw_dft/`.---## 4. Which files correspond to which figure| Figure | Content | Files ||---|---|---|| **1(a)** | Phonon dispersion and atom-projected DOS of BGG (solid) and GG (dotted) | `06_phonon_properties/BGG_cell0/BGG_phband_all.bands`, `GG_cell0/GG_phband_all.bands`; projected DOS `*_W202020_submit2.dos` (column headers give the `Ba/Ga/Ge` projections) || **1(b,c)** | Crystal structure and the two inequivalent Ba cages | `01_structure/BGG_cell0_a10.954.POSCAR` || **2** | κ_L(T) for BGG, GG and Ge46 | `05_bte_results/{BGG_cell0,GG_cell0,Ge46}/*_submit2.kl`, plus `BGG_cell-2/` for the experimental-lattice-constant curve || **3** | Phonon linewidths at 300 K; inset: three-phonon phase space W_q± | `06_phonon_properties/*/*_W202020_submit2.scatter` (phase space) and `*_W202020_300K_submit2.dat` (linewidths), 20×20×20 grid || **4(a)** | Magnitude of anharmonic (cubic) interaction of TA/LA modes at q = (0.1, 0, 0) | `06_phonon_properties/*/V3_anharmonic_interaction/` — `input_V3.txt`, `kslist.in` and run logs. **The V3 matrix-element dumps themselves (`*.V3.*.Z`, 1.1 GB) are not deposited**; re-run `anphon input_V3.txt` against the shipped IFCs to regenerate them. || **4(b)** | Squared group velocity of TA/LA modes, BGG vs GG, normalised by v_p² | `06_phonon_properties/*/groupvelocity/vel2_*2.dat` and the `modify_vel_*2.py` scripts that produced them, from `*_GX_vel.phvel` || **4(c)** | Phonon lifetimes of transverse/longitudinal modes at 300 K | `06_phonon_properties/*/mode_lifetime/` (mode-resolved anphon runs along [100]) and the full `05_bte_results/*/*.result` files |## 5. Reproducing the resultsALAMODE 0.9.2 is required for bit-identical output; later versions change the last digits of thefitted force constants (see §2.4).```bash# 1. Harmonic force constantscd 04_force_constants/BGG_cell0ln -s ../../03_training_data/BGG_cell0/{disp,force}_harm0.02.dat .alm input_alm_harmonic.reconstructed.txt > harm.log     # -> BGG_cell0_harm0.02.xml#    check: "Number of  HARMONIC FCs (nzero): 320"# 2. Cubic force constants (harmonic part fixed via FC2XML)ln -s ../../03_training_data/BGG_cell0/disp_total.{disp,force}_au .alm input_alm_cubic.reconstructed.txt > anharm.log      # -> BGG_cell0_anharm.xml#    check: "Number of   ANHARM3 FCs (nzero): 384"# 3. Thermal conductivity (RTA, 6x6x6 q-grid)cd ../../05_bte_results/BGG_cell0ln -s ../../04_force_constants/BGG_cell0/BGG_cell0_anharm.xml .mpirun anphon input_BTE.reconstructed.txt > run.log     # -> BGG_666_submit2.kl#    check: kappa_xx(100 K) = 0.7761 W/mK```The guest-free case is identical with `GG_cell0` and an 8×8×8 q-grid (its ALM input survived andis shipped verbatim); the reduced-lattice-constant case uses `BGG_cell-2` (`&cell` prefactor 20.29instead of 20.7). Ge46 uses its own cell (`1.889` scale, a = 10.7347 Å) and an 8×8×8 q-grid — butsee §6: its ALM fitting input was not preserved.Note: the RTA runs were executed as a sequence of restarts (`RESTART = 1`), which is why severalsequentially numbered logs (`anphon_run.log1`…`log6`) accompany a single result file.---## 6. Known gaps- **No ALM fitting log survives for the `BGG_cell-2` December-2014 re-fit.** Only the February  2014 log remains in the source directory and it describes the superseded fit, so it is not  shipped. That the shipped `BGG_cell-2_*.xml` files (2014-12-04 / 12-07) belong to the published  campaign is established independently: the BTE run log reports 28674 non-zero harmonic IFCs,  matching the `cell0` December re-fit exactly. The reconstructed ALM inputs for `cell-2` are  therefore derived from the `cell0` logs with only the lattice constant and file names changed.- The 20×20×20 linewidth runs (`*_W202020_submit2`) were executed with ALAMODE **0.9.0** on  2014-12-07, two days after the IFC re-fit, whereas the RTA runs used 0.9.2. Both read the same  published IFC files (confirmed by their non-zero-IFC counts).- **No ALM fitting inputs or logs survive for Ge46.** `disp/Ge46/alm/input_alm.txt` was overwritten  on 2015-12-23 and the only surviving log (2014-10-20) is a `MODE = suggest` pattern-generation  run, not the fit. No reconstruction is attempted here because there is no record to reconstruct  from. The Dec-2014 IFC files and the full training data are shipped, so the fit can be redone,  but the exact cutoffs and `NDATA` used in the published fit are not documented anywhere.- **For `BGG_cell-2` only the harmonic raw DFT was archived.** The 252 cubic `vasprun.xml`/`OUTCAR`  files for that lattice constant were never packed and no longer exist; the extracted  displacement–force data (288 configurations) is complete, so the IFCs remain reproducible.- The three-phonon matrix-element dumps (`*.V3.*.Z`, 1.1 GB) and the participation-ratio  eigenvector dump (`*.apr`, 110 MB) are excluded as regenerable; see the Fig. 4(a) row in §4.- `BGG_cell0_cubic_OUTCAR.tar.gz` contains one stray entry named plainly `outcars/OUTCAR`, a  leftover from the original working directory. The 252 per-configuration files are named  `OUTCAR.<tag>` and correspond one-to-one with the 252 `vasprun.xml` files.- `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>.