Update README.md
Browse files
README.md
CHANGED
|
@@ -1,3 +1,186 @@
|
|
| 1 |
-
---
|
| 2 |
-
license: cc-by-4.0
|
| 3 |
-
---
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
license: cc-by-4.0
|
| 3 |
+
---
|
| 4 |
+
---
|
| 5 |
+
language:
|
| 6 |
+
- en
|
| 7 |
+
license: other
|
| 8 |
+
license_name: License TBD — replace before publication
|
| 9 |
+
pretty_name: H0 MatHamiltonian (~1 GiB WebDataset preview)
|
| 10 |
+
tags:
|
| 11 |
+
- materials-science
|
| 12 |
+
- quantum-chemistry
|
| 13 |
+
- graph-neural-networks
|
| 14 |
+
- hamiltonian
|
| 15 |
+
- electronic-structure
|
| 16 |
+
- webdataset
|
| 17 |
+
size_categories:
|
| 18 |
+
- n<1K
|
| 19 |
+
dataset_info:
|
| 20 |
+
dataset_summary: |
|
| 21 |
+
~1 GiB preview shard of a larger Hamiltonian dataset stored as WebDataset tar files.
|
| 22 |
+
Each sample is a pickled torch_geometric.data.Data blob (same encoding as the upstream LMDB release).
|
| 23 |
+
---
|
| 24 |
+
|
| 25 |
+
# Dataset Card for H0 MatHamiltonian — 1 GiB WebDataset Preview
|
| 26 |
+
|
| 27 |
+
This card describes the **`hub_release_1gb_webdataset`** bundle: WebDataset-style **`train-*.tar`** shards plus **`train-manifest.csv`**, produced from the reviewer **~1 GiB LMDB** subset.
|
| 28 |
+
|
| 29 |
+
## Dataset Details
|
| 30 |
+
|
| 31 |
+
### Dataset Description
|
| 32 |
+
|
| 33 |
+
This dataset is a **small, byte-limited preview** intended for **peer review, sanity checks, and pipeline testing**. It contains **45 crystal/material structures** as serialized graph/tensor records (Hamiltonian and overlap blocks, geometry, and metadata). The **full merged corpus** is much larger (~4.1 TB on disk in the upstream project); this Hub release is **not** the full dataset.
|
| 34 |
+
|
| 35 |
+
- **Curated by:** *[Replace with author names and affiliations]*
|
| 36 |
+
- **Funded by [optional]:** *[Replace or remove]*
|
| 37 |
+
- **Shared by [optional]:** *[Replace or remove]*
|
| 38 |
+
- **Language(s) (NLP):** Not applicable (structured scientific tensors / graphs; card text in English).
|
| 39 |
+
- **License:** *[Replace with your chosen license, e.g. CC-BY-4.0, Apache-2.0, or custom]* — must match the legal terms you publish.
|
| 40 |
+
|
| 41 |
+
### Dataset Sources [optional]
|
| 42 |
+
|
| 43 |
+
- **Repository:** *[Replace with GitHub / project URL when public]*
|
| 44 |
+
- **Paper [optional]:** *[Replace with citation when available]*
|
| 45 |
+
- **Demo [optional]:** *[Optional notebook or Colab]*
|
| 46 |
+
|
| 47 |
+
## Uses
|
| 48 |
+
|
| 49 |
+
### Direct Use
|
| 50 |
+
|
| 51 |
+
- Training or benchmarking **graph neural networks** and related models on **Hamiltonian / overlap tensor blocks** paired with **crystal structure** fields.
|
| 52 |
+
- **Dataset loader development** and **integration tests** before downloading larger subsets.
|
| 53 |
+
- **Reproducibility checks** during peer review (inspect manifests, decode samples).
|
| 54 |
+
|
| 55 |
+
### Out-of-Scope Use
|
| 56 |
+
|
| 57 |
+
- **Not** a guaranteed statistically representative sample of the full corpus (structure count is small; sampling follows upstream **index-list order** until a byte budget is reached).
|
| 58 |
+
- **Not** for safety-critical or high-stakes decisions without domain validation.
|
| 59 |
+
- **Not** a substitute for the full release when training production-scale models.
|
| 60 |
+
|
| 61 |
+
## Dataset Structure
|
| 62 |
+
|
| 63 |
+
### Files in this release
|
| 64 |
+
|
| 65 |
+
| File / pattern | Description |
|
| 66 |
+
|----------------|-------------|
|
| 67 |
+
| `train-000000.tar`, `train-000001.tar`, … | WebDataset-style archives. Each logical sample has two members sharing the same basename. |
|
| 68 |
+
| `00000000.pkl`, … | **Pickle blob** of `torch_geometric.data.Data` (same bytes as stored in the source LMDB value). |
|
| 69 |
+
| `00000000.json`, … | Small JSON sidecar: `lmdb_key` (integer database index), `value_bytes` (byte length of `.pkl`). |
|
| 70 |
+
| `train-manifest.csv` | Table mapping `sample_index` → shard file, member names, `lmdb_key`, `value_bytes`. |
|
| 71 |
+
|
| 72 |
+
### Statistics (this build)
|
| 73 |
+
|
| 74 |
+
- **Samples:** 45 (rows in `train-manifest.csv`).
|
| 75 |
+
- **Shards:** 2 (`train-000000.tar`, `train-000001.tar`).
|
| 76 |
+
- **Approximate on-disk tar footprint:** ~568 MiB + ~490 MiB (see files after upload; exact sizes depend on filesystem).
|
| 77 |
+
|
| 78 |
+
### Example record fields
|
| 79 |
+
|
| 80 |
+
After `pickle.loads` on a `.pkl` file, typical `Data` attributes include (names may vary slightly by pipeline version):
|
| 81 |
+
|
| 82 |
+
- **Geometry / graph:** `pos`, `atoms`, `lattice`, `multi_edge_index`, `multi_edge_vec`, `lattice_translation_vector`, …
|
| 83 |
+
- **Hamiltonian / overlap:** `diagonal_hamiltonian`, `off_diagonal_hamiltonian`, optional `diagonal_overlap`, `off_diagonal_overlap`, with associated `*_mask` tensors.
|
| 84 |
+
- **Metadata:** `database_idx`, `mp_id`, `raw_basename`, `fermi_level`, `elapsed_time`, …
|
| 85 |
+
|
| 86 |
+
Use `torch_geometric` introspection or print `data.keys` after loading.
|
| 87 |
+
|
| 88 |
+
### Splits
|
| 89 |
+
|
| 90 |
+
- **Single split:** all samples are shipped under the `train-*` shard prefix (preview bundle). There is **no** separate val/test split in this artifact.
|
| 91 |
+
|
| 92 |
+
## Dataset Creation
|
| 93 |
+
|
| 94 |
+
### Curation Rationale
|
| 95 |
+
|
| 96 |
+
Provide a **compact, Hub-native format** (WebDataset `.tar`) for reviewers and integrators while preserving the **exact serialized sample representation** used in the LMDB-based pipeline.
|
| 97 |
+
|
| 98 |
+
### Source Data
|
| 99 |
+
|
| 100 |
+
#### Data Collection and Processing
|
| 101 |
+
|
| 102 |
+
1. **Upstream:** Structures and electronic-structure-derived tensors originate from computational workflows (OpenMX-class outputs) merged into a large LMDB in the parent project.
|
| 103 |
+
2. **Subset:** A **~1 GiB LMDB** subset was built by copying records in **canonical index order** until the byte budget was reached (same convention as documented in the upstream repo).
|
| 104 |
+
3. **Conversion:** `convert_lmdb_to_webdataset.py` streamed LMDB cursor rows into `.tar` shards; each value became `{idx}.pkl`, with `{idx}.json` metadata.
|
| 105 |
+
|
| 106 |
+
#### Who are the source data producers?
|
| 107 |
+
|
| 108 |
+
Computational simulations and dataset merges performed by the **dataset authors / consortium** *[replace with specifics]*.
|
| 109 |
+
|
| 110 |
+
### Annotations [optional]
|
| 111 |
+
|
| 112 |
+
No separate human annotation layer beyond simulation-derived tensors and structured metadata.
|
| 113 |
+
|
| 114 |
+
#### Personal and Sensitive Information
|
| 115 |
+
|
| 116 |
+
This dataset is **not expected** to contain personal data. Identifiers such as `mp_id` refer to **materials database IDs**, not individuals.
|
| 117 |
+
|
| 118 |
+
## Bias, Risks, and Limitations
|
| 119 |
+
|
| 120 |
+
- **Coverage:** The preview contains **very few** structures relative to the full corpus; metrics are **not** indicative of full-dataset diversity.
|
| 121 |
+
- **Simulation bias:** Electronic-structure workflows, basis choices, and convergence criteria induce systematic differences versus experiment.
|
| 122 |
+
- **Technical:** `.pkl` relies on Python pickling; loading requires compatible **`torch` / `torch_geometric`** versions with the training stack used to build the data.
|
| 123 |
+
|
| 124 |
+
### Recommendations
|
| 125 |
+
|
| 126 |
+
- Validate loader behavior on this preview before scaling to multi-TB subsets.
|
| 127 |
+
- Pin dependency versions in your training repo.
|
| 128 |
+
- Prefer citing the **paper + dataset version + manifest checksum** once available.
|
| 129 |
+
|
| 130 |
+
## Citation [optional]
|
| 131 |
+
|
| 132 |
+
**BibTeX:**
|
| 133 |
+
|
| 134 |
+
```bibtex
|
| 135 |
+
% [Replace when the dataset paper / DOI is available]
|
| 136 |
+
@misc{h0_mat_ham_2026,
|
| 137 |
+
title = {H0 MatHamiltonian Dataset},
|
| 138 |
+
author = {[Authors]},
|
| 139 |
+
year = {2026},
|
| 140 |
+
howpublished = {\url{https://huggingface.co/datasets/[YOUR_ORG]/[YOUR_REPO]}}
|
| 141 |
+
}
|
| 142 |
+
```
|
| 143 |
+
|
| 144 |
+
**APA:**
|
| 145 |
+
|
| 146 |
+
*[Replace when citation details are finalized]*
|
| 147 |
+
|
| 148 |
+
## Glossary [optional]
|
| 149 |
+
|
| 150 |
+
- **LMDB:** Embedded key-value store used upstream; keys are 4-byte big-endian integers (`database_idx`).
|
| 151 |
+
- **WebDataset / tar shards:** Convention of packing many small files into `.tar` archives for scalable streaming I/O.
|
| 152 |
+
- **`torch_geometric.data.Data`:** PyG container holding tensor attributes and metadata for one graph/sample.
|
| 153 |
+
|
| 154 |
+
## More Information [optional]
|
| 155 |
+
|
| 156 |
+
- Conversion script (upstream repo): `convert_lmdb_to_webdataset.py`
|
| 157 |
+
- Quick inspection script (upstream repo): `quick_check.py` (for LMDB; for this bundle, use tar + `pickle.loads` as below).
|
| 158 |
+
|
| 159 |
+
### Minimal load example (single sample)
|
| 160 |
+
|
| 161 |
+
```python
|
| 162 |
+
import io
|
| 163 |
+
import json
|
| 164 |
+
import pickle
|
| 165 |
+
import tarfile
|
| 166 |
+
|
| 167 |
+
import torch # noqa: F401 — needed for unpickling tensors inside Data
|
| 168 |
+
|
| 169 |
+
tar_path = "train-000000.tar"
|
| 170 |
+
with tarfile.open(tar_path, "r") as tar:
|
| 171 |
+
pkl_info = tar.getmember("00000000.pkl")
|
| 172 |
+
pkl_bytes = tar.extractfile(pkl_info).read()
|
| 173 |
+
meta = json.loads(tar.extractfile(tar.getmember("00000000.json")).read())
|
| 174 |
+
|
| 175 |
+
data = pickle.loads(pkl_bytes)
|
| 176 |
+
print(meta) # {'lmdb_key': ..., 'value_bytes': ...}
|
| 177 |
+
print(data) # torch_geometric.data.Data
|
| 178 |
+
```
|
| 179 |
+
|
| 180 |
+
## Dataset Card Authors [optional]
|
| 181 |
+
|
| 182 |
+
*[Replace — names of people who wrote this card]*
|
| 183 |
+
|
| 184 |
+
## Dataset Card Contact
|
| 185 |
+
|
| 186 |
+
*[Replace — email or issue tracker URL]*
|