| --- |
| license: other |
| tags: |
| - chemistry |
| - electron-density |
| - qm9 |
| - molecular-dynamics |
| size_categories: |
| - 100K<n<1M |
| --- |
| |
| # OrbFlow data |
|
|
| Preprocessed training and evaluation data for **OrbFlow** (equivariant flow matching for atomic-orbital |
| coefficients and electron density). |
|
|
| - Code: https://github.com/divelab/AIRS/tree/main/OpenDFT/OrbFlow |
| - Checkpoints: [divelab/OrbFlow](https://huggingface.co/divelab/OrbFlow) |
|
|
| ## Contents |
|
|
| The layout matches the `DATAPATH` folder expected by the OrbFlow scripts. |
|
|
| | Path | Size | Description | |
| |------|------|-------------| |
| | `datasplits.json` | 1 MB | QM9 train / validation / test split | |
| | `lmdb/` | 1.4 TB | QM9 LMDB: geometries and density probes, 134 shards (+ `metadata.json`) | |
| | `lmdb_gt_ridge/` | 12 GB | QM9 target orbital coefficients (β = 1.3, ridge 1e-6), one shard per `lmdb/` shard | |
| | `MD/scdp_lmdb/<mol>/` | 24 GB | MD LMDBs for benzene, ethane, ethanol, malonaldehyde, phenol, resorcinol (each with its own `datasplits.json`) | |
| | `MD/scdp_lmdb_gt_ridge_beta1.3/<mol>/` | 0.6 GB | MD target orbital coefficients (β = 1.3, ridge 1e-6) | |
| | `MD/flow_prior_ridge1e6_beta1.3/<mol>/` | < 1 MB | Per-molecule flow-prior µ/σ used by the MD training recipe | |
|
|
| ## Download |
|
|
| Everything (≈ 1.46 TB): |
|
|
| ```bash |
| hf download divelab/OrbFlow-data --repo-type dataset --local-dir "$DATAPATH" |
| ``` |
|
|
| Only part of it, e.g. the MD data (≈ 25 GB) or the QM9 target coefficients: |
|
|
| ```bash |
| hf download divelab/OrbFlow-data --repo-type dataset --local-dir "$DATAPATH" --include "MD/*" |
| hf download divelab/OrbFlow-data --repo-type dataset --local-dir "$DATAPATH" --include "lmdb_gt_ridge/*" --include datasplits.json |
| ``` |
|
|
| ## How the data was produced |
|
|
| - **QM9 LMDB** — built from the [DTU QM9 VASP charge densities](https://data.dtu.dk/articles/dataset/QM9_Charge_Densities_and_Energies_Calculated_with_VASP/16794500) |
| with the [SCDP](https://github.com/kyonofx/scdp) preprocessing (bond-midpoint virtual nodes, atom cutoff 6 Å): |
| `vision/preprocess_qm9_lmdb.slurm` in the OrbFlow code. It can be rebuilt from the DTU tarballs instead of downloaded. |
| - **Target coefficients** — per-molecule ridge fit of the DFT density on the def2-QZVPPD-derived Gaussian basis |
| (β = 1.3, ridge 1e-6, full probe grid, float64): `vision/prepare_flow_gt_coeffs_ridge1e6_gpu.slurm` (QM9) and |
| `vision/prepare_md_gt_coeffs_ridge1e6_beta13_gpu.slurm` (MD). |
| - **MD prior** — mean / std of the train-split target coefficients: `vision/compute_md_flow_prior_stats_beta13.slurm`. |
| - **MD densities** — TODO: source and citation. |
|
|
| > **Alignment:** `lmdb_gt_ridge/` is matched to `lmdb/` by shard file name and entry order, not by molecule ID. |
| > Use it with the `lmdb/` from this repository, or with an LMDB rebuilt by the unmodified script from all 134 |
| > original DTU tarballs. A mismatched LMDB makes training stop with a clear error. |
|
|
| ## Citation |
|
|
| TODO: citation. |
|
|
