Upload folder using huggingface_hub

.gitattributes

@@ -1,60 +1,90 @@
 *.7z filter=lfs diff=lfs merge=lfs -text
 *.arrow filter=lfs diff=lfs merge=lfs -text
-*.avro filter=lfs diff=lfs merge=lfs -text
 *.bin filter=lfs diff=lfs merge=lfs -text
+*.bin.* filter=lfs diff=lfs merge=lfs -text
 *.bz2 filter=lfs diff=lfs merge=lfs -text
-*.ckpt filter=lfs diff=lfs merge=lfs -text
 *.ftz filter=lfs diff=lfs merge=lfs -text
 *.gz filter=lfs diff=lfs merge=lfs -text
 *.h5 filter=lfs diff=lfs merge=lfs -text
 *.joblib filter=lfs diff=lfs merge=lfs -text
 *.lfs.* filter=lfs diff=lfs merge=lfs -text
-*.lz4 filter=lfs diff=lfs merge=lfs -text
-*.mds filter=lfs diff=lfs merge=lfs -text
-*.mlmodel filter=lfs diff=lfs merge=lfs -text
 *.model filter=lfs diff=lfs merge=lfs -text
 *.msgpack filter=lfs diff=lfs merge=lfs -text
-*.npy filter=lfs diff=lfs merge=lfs -text
-*.npz filter=lfs diff=lfs merge=lfs -text
 *.onnx filter=lfs diff=lfs merge=lfs -text
 *.ot filter=lfs diff=lfs merge=lfs -text
 *.parquet filter=lfs diff=lfs merge=lfs -text
 *.pb filter=lfs diff=lfs merge=lfs -text
-*.pickle filter=lfs diff=lfs merge=lfs -text
-*.pkl filter=lfs diff=lfs merge=lfs -text
 *.pt filter=lfs diff=lfs merge=lfs -text
 *.pth filter=lfs diff=lfs merge=lfs -text
 *.rar filter=lfs diff=lfs merge=lfs -text
-*.safetensors filter=lfs diff=lfs merge=lfs -text
 saved_model/**/* filter=lfs diff=lfs merge=lfs -text
-*.tar.* filter=lfs diff=lfs merge=lfs -text
 *.tar filter=lfs diff=lfs merge=lfs -text
+*.tar.* filter=lfs diff=lfs merge=lfs -text
+*.mat filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*.npy filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.hdf5 filter=lfs diff=lfs merge=lfs -text
+*.pickle filter=lfs diff=lfs merge=lfs -text
+*.pkl filter=lfs diff=lfs merge=lfs -text
 *.tflite filter=lfs diff=lfs merge=lfs -text
 *.tgz filter=lfs diff=lfs merge=lfs -text
-*.wasm filter=lfs diff=lfs merge=lfs -text
 *.xz filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
-*.zst filter=lfs diff=lfs merge=lfs -text
-*tfevents* filter=lfs diff=lfs merge=lfs -text
-# Audio files - uncompressed
-*.pcm filter=lfs diff=lfs merge=lfs -text
-*.sam filter=lfs diff=lfs merge=lfs -text
-*.raw filter=lfs diff=lfs merge=lfs -text
-# Audio files - compressed
-*.aac filter=lfs diff=lfs merge=lfs -text
-*.flac filter=lfs diff=lfs merge=lfs -text
-*.mp3 filter=lfs diff=lfs merge=lfs -text
-*.ogg filter=lfs diff=lfs merge=lfs -text
-*.wav filter=lfs diff=lfs merge=lfs -text
-# Image files - uncompressed
-*.bmp filter=lfs diff=lfs merge=lfs -text
-*.gif filter=lfs diff=lfs merge=lfs -text
-*.png filter=lfs diff=lfs merge=lfs -text
-*.tiff filter=lfs diff=lfs merge=lfs -text
-# Image files - compressed
+*.zstandard filter=lfs diff=lfs merge=lfs -text
+*.tfevents* filter=lfs diff=lfs merge=lfs -text
+*.db* filter=lfs diff=lfs merge=lfs -text
+*.ark* filter=lfs diff=lfs merge=lfs -text
+**/*ckpt*data* filter=lfs diff=lfs merge=lfs -text
+**/*ckpt*.meta filter=lfs diff=lfs merge=lfs -text
+**/*ckpt*.index filter=lfs diff=lfs merge=lfs -text
+*.safetensors filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
 *.jpg filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
 *.jpeg filter=lfs diff=lfs merge=lfs -text
+*.bmp filter=lfs diff=lfs merge=lfs -text
+*.gif filter=lfs diff=lfs merge=lfs -text
 *.webp filter=lfs diff=lfs merge=lfs -text
-# Video files - compressed
+*.mp3 filter=lfs diff=lfs merge=lfs -text
+*.wav filter=lfs diff=lfs merge=lfs -text
+*.wma filter=lfs diff=lfs merge=lfs -text
+*.aac filter=lfs diff=lfs merge=lfs -text
+*.ogg filter=lfs diff=lfs merge=lfs -text
+*.m4a filter=lfs diff=lfs merge=lfs -text
+*.m3u8 filter=lfs diff=lfs merge=lfs -text
+*.amr filter=lfs diff=lfs merge=lfs -text
+*.audio filter=lfs diff=lfs merge=lfs -text
+*.avi filter=lfs diff=lfs merge=lfs -text
+*.flv filter=lfs diff=lfs merge=lfs -text
 *.mp4 filter=lfs diff=lfs merge=lfs -text
-*.webm filter=lfs diff=lfs merge=lfs -text
+*.mpg filter=lfs diff=lfs merge=lfs -text
+*.asf filter=lfs diff=lfs merge=lfs -text
+*.mov filter=lfs diff=lfs merge=lfs -text
+*.mpeg filter=lfs diff=lfs merge=lfs -text
+*.3gp filter=lfs diff=lfs merge=lfs -text
+*.wmv filter=lfs diff=lfs merge=lfs -text
+*.rmvb filter=lfs diff=lfs merge=lfs -text
+*.rm filter=lfs diff=lfs merge=lfs -text
+*.ts filter=lfs diff=lfs merge=lfs -text
+*.mkv filter=lfs diff=lfs merge=lfs -text
+*.flash filter=lfs diff=lfs merge=lfs -text
+*.vob filter=lfs diff=lfs merge=lfs -text
+*.pdf filter=lfs diff=lfs merge=lfs -text
+*.ost filter=lfs diff=lfs merge=lfs -text
+*.pst filter=lfs diff=lfs merge=lfs -text
+*.doc filter=lfs diff=lfs merge=lfs -text
+*.docx filter=lfs diff=lfs merge=lfs -text
+*.txt filter=lfs diff=lfs merge=lfs -text
+*.ppt filter=lfs diff=lfs merge=lfs -text
+*.pptx filter=lfs diff=lfs merge=lfs -text
+*.xls filter=lfs diff=lfs merge=lfs -text
+*.xlsx filter=lfs diff=lfs merge=lfs -text
+*.vsd filter=lfs diff=lfs merge=lfs -text
+*.vsdx filter=lfs diff=lfs merge=lfs -text
+*.jsonl filter=lfs diff=lfs merge=lfs -text
+*.json filter=lfs diff=lfs merge=lfs -text
+dataset_infos.json ignore
+*.csv filter=lfs diff=lfs merge=lfs -text
+*.tsv filter=lfs diff=lfs merge=lfs -text
+*.extxyz filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,99 @@
+---
+license: apache-2.0
+tags:
+  - OC20
+  - Open Catalyst
+  - catalysis
+  - S2EF
+  - UMA
+  - extxyz
+  - ASE-lmdb
+language:
+  - en
+  - zh
+---
+
+<p align="center">
+  <strong>
+    <span style="font-size: 30px;">OC20</span>
+  </strong>
+</p>
+
+## Dataset Description
+
+The OC20 dataset is an extxyz subset of the Open Catalyst 2020 (OC20) S2EF (Structure to Energy and Forces) dataset. It contains atomic coordinates, unit-cell information, energies, and forces for adsorption configurations on catalytic material surfaces. Its energy and force fields are consistent with those in the UMA OC20 configuration, making it a standard benchmark dataset for developing and validating machine-learned interatomic potential methods for catalytic materials.
+
+This repository currently contains two splits:
+
+- `s2ef_200k_uncompressed`: Training subset with 2 shards and 10,000 frames in total, with 8–221 atoms per frame.
+- `s2ef_val_id_uncompressed`: In-distribution validation subset with 4 shards and 20,000 frames in total, with 8–223 atoms per frame.
+
+The original data comes from the [Open Catalyst Project / fair-chem OC20](https://fair-chem.github.io/oc20/). This repository provides the accompanying data package for the OneScience UMA fine-tuning example.
+
+The current data package contains approximately 8 files totaling approximately 1.2 GB.
+
+## Supported Tasks
+
+This standardized data repository organizes the complete OC20 S2EF subset package, including training and validation sets, to support:
+- Fine-tuning machine-learned interatomic potentials on adsorption configurations at catalytic material surfaces
+- Training and validation of energy and force prediction models
+- Functional testing and benchmark evaluation of the UMA framework
+
+## Dataset Format and Structure
+
+The data files are located in the `data/oc20/` directory and organized into shards by split:
+
+| File Path | Format | Shape / Content | Description |
+|---|---|---|---|
+| `oc20/s2ef_200k_uncompressed/0.extxyz` | extxyz | `[N_frames, N_atoms]` | Training subset shard 0, 5,000 frames |
+| `oc20/s2ef_200k_uncompressed/1.extxyz` | extxyz | `[N_frames, N_atoms]` | Training subset shard 1, 5,000 frames |
+| `oc20/s2ef_val_id_uncompressed/0.extxyz` | extxyz | `[N_frames, N_atoms]` | Validation subset shard 0, 5,000 frames |
+| `oc20/s2ef_val_id_uncompressed/1.extxyz` | extxyz | `[N_frames, N_atoms]` | Validation subset shard 1, 5,000 frames |
+| `oc20/s2ef_val_id_uncompressed/2.extxyz` | extxyz | `[N_frames, N_atoms]` | Validation subset shard 2, 5,000 frames |
+| `oc20/s2ef_val_id_uncompressed/3.extxyz` | extxyz | `[N_frames, N_atoms]` | Validation subset shard 3, 5,000 frames |
+| `metadata/schema.yaml` | YAML | Data structure description | extxyz field schema definition |
+| `metadata/sha256_manifest.txt` | SHA256 | Checksum manifest | File integrity verification |
+
+### extxyz Data Format
+
+Each configuration consists of an atom-count line, a comment line, and atom lines. The comment line contains `Lattice`, `Properties`, `energy`, `free_energy`, and `pbc`. Each atom line contains the element, coordinates, `move_mask`, `tags`, and `forces`.
+
+| Field | Type | Shape | Description |
+|---|---|---|---|
+| `species` | str | `[N_atoms]` | Element symbols spanning various metals and nonmetals |
+| `pos` | float | `[N_atoms, 3]` | Atomic coordinates in Å |
+| `move_mask` | bool | `[N_atoms]` | Whether each atom can move, `T` or `F` |
+| `tags` | int | `[N_atoms]` | Atomic labels distinguishing adsorbates, surfaces, subsurfaces, and other categories |
+| `forces` | float | `[N_atoms, 3]` | Atomic forces in eV/Å |
+| `energy` | float | `[1]` | Total configuration energy in eV |
+| `free_energy` | float | `[1]` | Configuration free energy in eV |
+| `pbc` | bool | `[3]` | Periodic boundary conditions |
+| `Lattice` | float | `[3, 3]` | Periodic cell matrix |
+
+
+## How to Use the Dataset
+
+### Download the Dataset
+
+```bash
+hf download --dataset OneScience-Sugon/oc20 --local-dir ./data
+```
+
+## Official OneScience Information
+
+| Platform | OneScience Main Repository | Skills Repository |
+|---|---|---|
+| Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills |
+| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills |
+
+## Limitations and License
+
+This dataset is an official S2EF subset of Open Catalyst 2020 (OC20). No new samples were generated, and the original data content was not altered.
+
+- **Original source**: [Open Catalyst Project / fair-chem OC20](https://fair-chem.github.io/oc20/)
+- **License**: Apache License 2.0
+- **Usage restrictions**: Refer to the original OC20 data source and the information provided by the OneScience repository and ModelScope page
+
+When using the OC20 dataset, cite the original Open Catalyst paper:
+
+- Chanussot, L.; Das, A.; Goyal, S.; Lavril, T.; Shuaibi, M.; Riviere, M.; Tran, K.; Heras-Domingo, J.; Ho, C.; Hu, W.; Palizhati, A.; Sriram, A.; Wood, B.; Yoon, J.; Parikh, D.; Zitnick, C. L.; Ulissi, Z. Open Catalyst 2020 (OC20) Dataset and Community Challenges. *ACS Catal.* **2021**, *11* (10), 6059–6072. https://doi.org/10.1021/acscatal.0c04525

README_zh.md

@@ -0,0 +1,99 @@
+---
+license: Apache-2.0
+tags:
+  - OC20
+  - Open Catalyst
+  - catalysis
+  - S2EF
+  - UMA
+  - extxyz
+  - ASE-lmdb
+language:
+  - en
+  - zh
+---
+
+<p align="center">
+  <strong>
+    <span style="font-size: 30px;">OC20</span>
+  </strong>
+</p>
+
+## 数据集描述
+
+OC20 数据集是Open Catalyst 2020 (OC20) S2EF（Structure to Energy and Forces）extxyz 子集。数据包含催化材料表面吸附构型的原子坐标、晶胞信息、能量和受力数据，字段与 UMA OC20 配置中的能量、受力字段一致，是学习和验证催化材料机器学习原子间势方法的标准基准数据集。
+
+本仓库当前包含两个 split：
+
+- `s2ef_200k_uncompressed`：训练子集，2 个分片，共 10000 帧，每帧 8–221 个原子。
+- `s2ef_val_id_uncompressed`：验证子集（in-distribution），4 个分片，共 20000 帧，每帧 8–223 个原子。
+
+原始数据来自 [Open Catalyst Project / fair-chem OC20](https://fair-chem.github.io/oc20/)，本仓库是其面向 OneScience UMA 微调示例的配套数据包。
+
+当前数据包包含约 8 个文件，约 1.2 GB。
+
+## 数据集支持的任务
+
+本标准化数据仓库整理了 OC20 S2EF 子集的完整数据包，包含训练集和验证集，可用于：
+- 催化材料表面吸附构型的机器学习原子间势微调
+- 能量与受力预测模型的训练与验证
+- UMA 框架的功能测试与基准评测
+
+## 数据集的格式和结构
+
+数据文件位于 `data/oc20/` 目录下，按 split 分片组织：
+
+| 文件路径 | 格式 | shape / 内容 | 说明 |
+|---|---|---|---|
+| `oc20/s2ef_200k_uncompressed/0.extxyz` | extxyz | `[N_frames, N_atoms]` | 训练子集分片 0，5000 帧 |
+| `oc20/s2ef_200k_uncompressed/1.extxyz` | extxyz | `[N_frames, N_atoms]` | 训练子集分片 1，5000 帧 |
+| `oc20/s2ef_val_id_uncompressed/0.extxyz` | extxyz | `[N_frames, N_atoms]` | 验证子集分片 0，5000 帧 |
+| `oc20/s2ef_val_id_uncompressed/1.extxyz` | extxyz | `[N_frames, N_atoms]` | 验证子集分片 1，5000 帧 |
+| `oc20/s2ef_val_id_uncompressed/2.extxyz` | extxyz | `[N_frames, N_atoms]` | 验证子集分片 2，5000 帧 |
+| `oc20/s2ef_val_id_uncompressed/3.extxyz` | extxyz | `[N_frames, N_atoms]` | 验证子集分片 3，5000 帧 |
+| `metadata/schema.yaml` | YAML | 数据结构说明 | extxyz 字段 schema 定义 |
+| `metadata/sha256_manifest.txt` | SHA256 | 校验清单 | 文件完整性校验 |
+
+### extxyz 数据格式
+
+每个构型由原子数行、comment 行和原子行组成。comment 行包含 `Lattice`、`Properties`、`energy`、`free_energy` 和 `pbc`。原子行包含元素、坐标、`move_mask`、`tags` 和 `forces`。
+
+| 字段 | 类型 | shape | 说明 |
+|---|---|---|---|
+| `species` | str | `[N_atoms]` | 元素符号，覆盖多种金属、非金属元素 |
+| `pos` | float | `[N_atoms, 3]` | 原子坐标，单位 Å |
+| `move_mask` | bool | `[N_atoms]` | 原子是否可移动，`T` 或 `F` |
+| `tags` | int | `[N_atoms]` | 原子标签，区分吸附质、表面、次表面等 |
+| `forces` | float | `[N_atoms, 3]` | 原子受力，单位 eV/Å |
+| `energy` | float | `[1]` | 构型总能量，单位 eV |
+| `free_energy` | float | `[1]` | 构型自由能，单位 eV |
+| `pbc` | bool | `[3]` | 周期边界条件 |
+| `Lattice` | float | `[3, 3]` | 周期盒矩阵 |
+
+
+## 数据集使用方式
+
+### 下载数据集
+
+```bash
+hf download --dataset OneScience-Sugon/oc20 --local-dir ./data
+```
+
+## OneScience 官方信息
+
+| 平台 | OneScience 主仓库 | Skills 仓库 |
+|---|---|---|
+| Gitee | https://gitee.com/onescience-ai/onescience | https://gitee.com/onescience-ai/oneskills |
+| GitHub | https://github.com/onescience-ai/OneScience | https://github.com/onescience-ai/oneskills |
+
+## 限制与许可证
+
+本数据集为 Open Catalyst 2020 (OC20) 官方 S2EF 子集，未生成新样本或改变原始数据内容。
+
+- **原始来源**：[Open Catalyst Project / fair-chem OC20](https://fair-chem.github.io/oc20/)
+- **许可证**：Apache License 2.0
+- **使用限制**：以原始 OC20 数据来源、OneScience 仓库及 ModelScope 页面说明为准
+
+使用 OC20 数据集时请引用原始 Open Catalyst 论文：
+
+- Chanussot, L.; Das, A.; Goyal, S.; Lavril, T.; Shuaibi, M.; Riviere, M.; Tran, K.; Heras-Domingo, J.; Ho, C.; Hu, W.; Palizhati, A.; Sriram, A.; Wood, B.; Yoon, J.; Parikh, D.; Zitnick, C. L.; Ulissi, Z. Open Catalyst 2020 (OC20) Dataset and Community Challenges. *ACS Catal.* **2021**, *11* (10), 6059–6072. https://doi.org/10.1021/acscatal.0c04525

data/oc20/s2ef_200k_uncompressed/0.extxyz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c1498dcf9304060c19fcdd75b4f527ed56ed2c9a56678a19783884cb6744190a
+size 43774115

data/oc20/s2ef_200k_uncompressed/1.extxyz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:803b86307583bc351a843c8b773a0297abb9bccc784369fdf26455d5ddd1c249
+size 44149032

data/oc20/s2ef_val_id_uncompressed/0.extxyz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c73976d4ee4e584bed87bd4cdc58555a468f8fe9c4325f3df46b5e24b408902f
+size 43464190

data/oc20/s2ef_val_id_uncompressed/1.extxyz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:137f740e3bbe21fa4f103d0cd0fd22aed109a33ec59ebe4a6715688d1948c2a8
+size 44072937

data/oc20/s2ef_val_id_uncompressed/2.extxyz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:1cf2998fa84110cbf21cc0ca4dd5461c654bf9960e5a8bd90bf1399d74b9ac64
+size 43857708

data/oc20/s2ef_val_id_uncompressed/3.extxyz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:9361f52f466a08ce04d381d162532f5a2ec18a10feb559e8c067fbbe9edd0ffa
+size 43572013

manifest.yaml

@@ -0,0 +1,430 @@
+onescience_manifest_version: "0.1"
+resource_type: dataset
+resource:
+  id: OneScience/oc20
+  name: OC20
+  domain: matchem
+  domain_tags:
+    - matchem
+    - catalysis
+    - oc20
+    - atomistic_dataset
+  task: mlip_training_data
+  task_tags:
+    - mlip
+    - energy_prediction
+    - force_prediction
+    - extxyz_training
+  modalities:
+    - atomistic_structure
+  input_formats:
+    - extxyz
+  output_formats: []
+  summary: 面向 OneScience/UMA 微调和训练评测示例的 Open Catalyst 2020 (OC20) S2EF extxyz 子集。
+
+platform_resource:
+  primary:
+    platform: modelscope
+    repo_id: OneScience/oc20
+    repo_type: dataset
+    url: https://modelscope.cn/datasets/OneScience/oc20
+    revision: main
+    readme_path: README.md
+    manifest_path: manifest.yaml
+  mirrors: []
+  access:
+    visibility: public
+    license: Apache License 2.0
+
+website_integration:
+  enabled: true
+  click_target:
+    platform: modelscope
+    resource_url: https://modelscope.cn/datasets/OneScience/oc20
+  llm_handoff:
+    readme_required: true
+    manifest_required: true
+    download_readme_first: true
+    resolve_related_models: true
+    default_run_goal: minimal_validation
+
+runtime:
+  enabled: true
+  onescience_domain: matchem
+  min_onescience_version: null
+  supported_execution:
+    - local
+    - local_slurm
+    - remote_slurm
+    - scnet_mcp
+
+onescience:
+  repo: https://gitee.com/onescience-ai/onescience
+  official_links:
+    gitee:
+      doc: https://gitee.com/onescience-ai/onescience-doc
+      onescience: https://gitee.com/onescience-ai/onescience
+      skills: https://gitee.com/onescience-ai/oneskills
+    github:
+      doc: https://github.com/onescience-ai/OneScience-doc
+      onescience: https://github.com/onescience-ai/OneScience
+      skills: https://github.com/onescience-ai/oneskills
+  install:
+    required_by_default: false
+    command: bash install.sh matchem
+  source_paths:
+    - matchem/uma/oc20
+  compatibility:
+    examples_path: examples/matchem/uma
+    status: examples_compatible
+
+runtime_package:
+  kind: standard_runtime_package
+  package_root: .
+  standard_layout:
+    workdir: .
+    config_dir: metadata
+    checkpoint_dir: null
+    data_dir: data
+    output_dir: outputs
+  apply_policy:
+    mode: direct_use
+    target: session_workdir
+    overwrite: true
+    protect_installed_onescience: true
+  entry_files:
+    - scripts/validate_oc20.py
+    - metadata/schema.yaml
+    - metadata/sha256_manifest.txt
+  entrypoints:
+    preflight: scripts/validate_oc20.py
+    inference: null
+    train: null
+    finetune: null
+    evaluate: null
+    visualize: null
+    deploy: null
+
+files:
+  model_files: []
+  dataset_files:
+    - id: oc20_s2ef_200k_uncompressed
+      path: data/oc20/s2ef_200k_uncompressed
+      role: train_split
+      description_zh: OC20 S2EF 200k 训练子集 extxyz 文件，当前包含 2 个分片、共 10000 帧。
+      required: true
+      required_for: [preflight, train]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/oc20
+        repo_type: dataset
+        path: data/oc20/s2ef_200k_uncompressed
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/oc20/s2ef_200k_uncompressed
+      size: 84M
+      checksum: metadata/sha256_manifest.txt
+      large_file: true
+    - id: oc20_s2ef_val_id_uncompressed
+      path: data/oc20/s2ef_val_id_uncompressed
+      role: validation_split
+      description_zh: OC20 S2EF val_id 验证子集 extxyz 文件，当前包含 4 个分片、共 20000 帧。
+      required: true
+      required_for: [preflight, evaluate]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/oc20
+        repo_type: dataset
+        path: data/oc20/s2ef_val_id_uncompressed
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/oc20/s2ef_val_id_uncompressed
+      size: 167M
+      checksum: metadata/sha256_manifest.txt
+      large_file: true
+  config_files:
+    - id: schema
+      path: metadata/schema.yaml
+      role: schema
+      description_zh: OC20 extxyz 数据结构、字段名、shape、单位、split 和 UMA 配置键说明。
+      required: true
+      required_for: [preflight, train, evaluate]
+      format: yaml
+      source:
+        platform: modelscope
+        repo_id: OneScience/oc20
+        repo_type: dataset
+        path: metadata/schema.yaml
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/metadata/schema.yaml
+      size: null
+      checksum: null
+      large_file: false
+    - id: sha256_manifest
+      path: metadata/sha256_manifest.txt
+      role: checksum
+      description_zh: OC20 数据文件 SHA256 清单，用于校验整理后数据与原始数据一致。
+      required: true
+      required_for: [preflight]
+      format: txt
+      source:
+        platform: modelscope
+        repo_id: OneScience/oc20
+        repo_type: dataset
+        path: metadata/sha256_manifest.txt
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/metadata/sha256_manifest.txt
+      size: null
+      checksum: null
+      large_file: false
+  sample_files:
+    - id: validate_script
+      path: scripts/validate_oc20.py
+      role: script
+      description_zh: OC20 数据读取验证脚本，检查 extxyz 字段、shape、帧数、元素集合和 SHA256。
+      required: true
+      required_for: [preflight]
+      format: py
+      source:
+        platform: modelscope
+        repo_id: OneScience/oc20
+        repo_type: dataset
+        path: scripts/validate_oc20.py
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/scripts/validate_oc20.py
+      size: null
+      checksum: null
+      large_file: false
+
+dataset:
+  format:
+    - extxyz
+  sample_unit: 单个催化剂表面吸附构型，包含元素、坐标、energy、free_energy 和 forces。
+  schema:
+    path: metadata/schema.yaml
+  splits:
+    train:
+      path: data/oc20/s2ef_200k_uncompressed
+      frames: 10000
+    validation:
+      path: data/oc20/s2ef_val_id_uncompressed
+      frames: 20000
+    test:
+      path: null
+      note_zh: "当前未提供独立测试集；如需测试可使用 s2ef_val_id_uncompressed 或从 OC20 官网下载完整 split。"
+
+relations:
+  required_datasets: []
+  optional_datasets: []
+  compatible_models:
+    - id: OneScience/UMA
+      role: finetune_data
+      required_for: [preflight, train, evaluate]
+      resource_ref:
+        platform: modelscope
+        repo_id: OneScience/UMA
+        repo_type: model
+        url: https://modelscope.cn/models/OneScience/UMA
+        revision: main
+        readme_path: README.md
+        manifest_path: manifest.yaml
+      expected_local_path: session_workdir/data/oc20
+      adapter: null
+
+run_matrix:
+  scenarios:
+    - name: validate_dataset
+      default: true
+      capability: preflight
+      required_datasets:
+        - id: OneScience/oc20
+          role: train_data
+          local_path: data/oc20
+      required_model_files: []
+      required_data_files:
+        - data/oc20/s2ef_200k_uncompressed
+        - data/oc20/s2ef_val_id_uncompressed
+        - metadata/sha256_manifest.txt
+      preconditions:
+        - 已下载数据集仓库 OneScience/oc20。
+      command_refs:
+        - commands.preflight.validate_dataset
+      outputs:
+        - path: stdout
+          description_zh: 数据字段、帧数、元素集合和 SHA256 检查结果。
+
+capabilities:
+  inference: false
+  train: false
+  finetune: false
+  evaluate: false
+  visualize: false
+  deploy: false
+
+commands:
+  download:
+    - name: download_dataset_package
+      target: dataset
+      repo_id: OneScience/oc20
+      source: .
+      local_path: session_workdir/
+      required: true
+      required_for: [preflight, train, evaluate]
+      cwd: .
+      command: modelscope download --dataset OneScience/oc20 --local_dir session_workdir
+      expected_outputs:
+        - path: session_workdir/data/oc20/s2ef_200k_uncompressed
+          type: file
+      success_criteria:
+        - exit_code == 0
+        - output_path_exists
+  preflight:
+    - name: validate_dataset
+      description: 验证 OC20 extxyz 文件结构、字段名、帧数和 SHA256。
+      cwd: .
+      command: python scripts/validate_oc20.py --dataset-root data/oc20 --checksum-manifest metadata/sha256_manifest.txt
+      required_files:
+        - data/oc20/s2ef_200k_uncompressed
+        - data/oc20/s2ef_val_id_uncompressed
+        - metadata/sha256_manifest.txt
+        - scripts/validate_oc20.py
+      required_env:
+        - python
+      expected_outputs:
+        - path: stdout
+          type: text
+      success_criteria:
+        - exit_code == 0
+  prepare: []
+  inference: []
+  train: []
+  finetune: []
+  evaluate: []
+  visualize: []
+  deploy: []
+
+expected_outputs:
+  - path: stdout
+    type: text
+    description_zh: 验证脚本输出每个 split、字段和 SHA256 的 OK 结果。
+
+diagnostics:
+  - error_pattern: "缺少文件"
+    likely_cause: 数据集下载不完整或运行 cwd 不在数据集仓库根目录。
+    action: 重新执行 modelscope download --dataset OneScience/oc20，并在下载后的数据集根目录运行验证命令。
+  - error_pattern: "SHA256 不一致"
+    likely_cause: 文件被截断、损坏或被替换。
+    action: 删除损坏文件后重新下载数据集��
+  - error_pattern: "energy"
+    likely_cause: extxyz comment 中缺少 UMA OC20 配置要求的能量字段。
+    action: 检查数据是否为本仓库 OC20 数据，或同步修改模型配置 energy_key。
+  - error_pattern: "forces"
+    likely_cause: extxyz Properties 中缺少 UMA OC20 配置要求的力字段。
+    action: 检查数据是否为本仓库 OC20 数据，或同步修改模型配置 forces_key。
+
+domain_extension:
+  matchem:
+    chemical_system:
+      elements:
+        - Ag
+        - Al
+        - As
+        - Au
+        - B
+        - Bi
+        - C
+        - Ca
+        - Cd
+        - Cl
+        - Co
+        - Cr
+        - Cs
+        - Cu
+        - Fe
+        - Ga
+        - Ge
+        - H
+        - Hf
+        - Hg
+        - In
+        - Ir
+        - K
+        - Mn
+        - Mo
+        - N
+        - Na
+        - Nb
+        - Ni
+        - O
+        - Os
+        - P
+        - Pb
+        - Pd
+        - Pt
+        - Rb
+        - Re
+        - Rh
+        - Ru
+        - S
+        - Sb
+        - Sc
+        - Se
+        - Si
+        - Sn
+        - Sr
+        - Ta
+        - Tc
+        - Te
+        - Ti
+        - Tl
+        - V
+        - W
+        - Y
+        - Zn
+        - Zr
+    properties:
+      - energy
+      - forces
+    units:
+      energy: eV
+      forces: eV/Angstrom
+    structure_format:
+      - extxyz
+
+large_resource:
+  enabled: true
+  total_size: 251M
+  file_count: 6
+  download_policy: full
+  default_download: full
+  minimal_files:
+    - data/oc20/s2ef_200k_uncompressed
+    - data/oc20/s2ef_val_id_uncompressed
+
+reproducibility:
+  level: minimal
+  goal: 完成一次 OC20 extxyz 数据读取和 SHA256 校验。
+  command_ref: commands.preflight.validate_dataset
+  expected_runtime: 2-5 minutes
+  expected_outputs:
+    - stdout

metadata/schema.yaml

@@ -0,0 +1,123 @@
+dataset: OC20
+standardized_repo_id: OneScience/oc20
+domain: matchem
+format:
+  - extxyz
+splits:
+  train:
+    path: data/oc20/s2ef_200k_uncompressed
+    pattern: "*.extxyz"
+    files:
+      - 0.extxyz
+      - 1.extxyz
+    frames: 10000
+    atoms_per_frame: 8-221
+  validation:
+    path: data/oc20/s2ef_val_id_uncompressed
+    pattern: "*.extxyz"
+    files:
+      - 0.extxyz
+      - 1.extxyz
+      - 2.extxyz
+      - 3.extxyz
+    frames: 20000
+    atoms_per_frame: 8-223
+sample_schema:
+  extxyz_comment_fields:
+    - Lattice
+    - Properties
+    - energy
+    - free_energy
+    - pbc
+  properties:
+    species:
+      dtype: string
+      shape: [num_atoms]
+      description_zh: 元素符号。
+    pos:
+      dtype: float
+      shape: [num_atoms, 3]
+      unit: Angstrom
+      description_zh: 原子坐标。
+    move_mask:
+      dtype: bool
+      shape: [num_atoms]
+      description_zh: 原子是否可移动。
+    tags:
+      dtype: int
+      shape: [num_atoms]
+      description_zh: 原子标签，用于区分吸附质、表面等。
+    forces:
+      dtype: float
+      shape: [num_atoms, 3]
+      unit: eV/Angstrom
+      description_zh: 原子受力。
+  config_fields:
+    energy:
+      dtype: float
+      unit: eV
+      description_zh: 构型总能量。
+    free_energy:
+      dtype: float
+      unit: eV
+      description_zh: 构型自由能。
+model_expected_keys:
+  energy_key: energy
+  forces_key: forces
+elements:
+  - Ag
+  - Al
+  - As
+  - Au
+  - B
+  - Bi
+  - C
+  - Ca
+  - Cd
+  - Cl
+  - Co
+  - Cr
+  - Cs
+  - Cu
+  - Fe
+  - Ga
+  - Ge
+  - H
+  - Hf
+  - Hg
+  - In
+  - Ir
+  - K
+  - Mn
+  - Mo
+  - N
+  - Na
+  - Nb
+  - Ni
+  - O
+  - Os
+  - P
+  - Pb
+  - Pd
+  - Pt
+  - Rb
+  - Re
+  - Rh
+  - Ru
+  - S
+  - Sb
+  - Sc
+  - Se
+  - Si
+  - Sn
+  - Sr
+  - Ta
+  - Tc
+  - Te
+  - Ti
+  - Tl
+  - V
+  - W
+  - Y
+  - Zn
+  - Zr

metadata/sha256_manifest.txt

@@ -0,0 +1,6 @@
+c1498dcf9304060c19fcdd75b4f527ed56ed2c9a56678a19783884cb6744190a  data/oc20/s2ef_200k_uncompressed/0.extxyz
+803b86307583bc351a843c8b773a0297abb9bccc784369fdf26455d5ddd1c249  data/oc20/s2ef_200k_uncompressed/1.extxyz
+c73976d4ee4e584bed87bd4cdc58555a468f8fe9c4325f3df46b5e24b408902f  data/oc20/s2ef_val_id_uncompressed/0.extxyz
+137f740e3bbe21fa4f103d0cd0fd22aed109a33ec59ebe4a6715688d1948c2a8  data/oc20/s2ef_val_id_uncompressed/1.extxyz
+1cf2998fa84110cbf21cc0ca4dd5461c654bf9960e5a8bd90bf1399d74b9ac64  data/oc20/s2ef_val_id_uncompressed/2.extxyz
+9361f52f466a08ce04d381d162532f5a2ec18a10feb559e8c067fbbe9edd0ffa  data/oc20/s2ef_val_id_uncompressed/3.extxyz

onescience_relations.yaml

@@ -0,0 +1,19 @@
+required_datasets: []
+optional_datasets: []
+compatible_models:
+  - id: OneScience/UMA
+    role: finetune_data
+    required_for:
+      - preflight
+      - train
+      - evaluate
+    resource_ref:
+      platform: modelscope
+      repo_id: OneScience/UMA
+      repo_type: model
+      url: https://modelscope.cn/models/OneScience/UMA
+      revision: main
+      readme_path: README.md
+      manifest_path: manifest.yaml
+    expected_local_path: session_workdir/data/oc20
+    adapter: null

scripts/validate_oc20.py

@@ -0,0 +1,197 @@
+#!/usr/bin/env python3
+"""Validate the standardized OC20 extxyz dataset package."""
+
+from __future__ import annotations
+
+import argparse
+import hashlib
+import re
+from pathlib import Path
+
+
+EXPECTED_SPLITS = {
+    "s2ef_200k_uncompressed": {
+        "files": ["0.extxyz", "1.extxyz"],
+        "expected_total_frames": 10000,
+    },
+    "s2ef_val_id_uncompressed": {
+        "files": ["0.extxyz", "1.extxyz", "2.extxyz", "3.extxyz"],
+        "expected_total_frames": 20000,
+    },
+}
+EXPECTED_ENERGY_KEY = "energy"
+EXPECTED_FORCES_KEY = "forces"
+EXPECTED_ELEMENTS = {
+    "Ag", "Al", "As", "Au", "B", "Bi", "C", "Ca", "Cd", "Cl", "Co", "Cr", "Cs", "Cu",
+    "Fe", "Ga", "Ge", "H", "Hf", "Hg", "In", "Ir", "K", "Mn", "Mo", "N", "Na", "Nb",
+    "Ni", "O", "Os", "P", "Pb", "Pd", "Pt", "Rb", "Re", "Rh", "Ru", "S", "Sb", "Sc",
+    "Se", "Si", "Sn", "Sr", "Ta", "Tc", "Te", "Ti", "Tl", "V", "W", "Y", "Zn", "Zr",
+}
+
+
+def sha256_file(path: Path) -> str:
+    h = hashlib.sha256()
+    with path.open("rb") as f:
+        for chunk in iter(lambda: f.read(1024 * 1024), b""):
+            h.update(chunk)
+    return h.hexdigest()
+
+
+def validate_checksum_manifest(dataset_root: Path, manifest_path: Path) -> None:
+    checked = 0
+    with manifest_path.open("r", encoding="utf-8") as f:
+        for line in f:
+            line = line.strip()
+            if not line or line.startswith("#"):
+                continue
+            digest, rel = line.split(maxsplit=1)
+            path = dataset_root.parent.parent / rel
+            if not path.exists():
+                raise SystemExit(f"[FAIL] 清单文件不存在: {path}")
+            actual = sha256_file(path)
+            if actual != digest:
+                raise SystemExit(f"[FAIL] SHA256 不一致: {rel}")
+            checked += 1
+    print(f"[OK] SHA256 清单验证通过: {checked} 个文件")
+
+
+def parse_properties(comment: str) -> list[tuple[str, str, int]]:
+    match = re.search(r'Properties=("[^"]+"|\S+)', comment)
+    if not match:
+        raise SystemExit("[FAIL] extxyz comment 缺少 Properties")
+    raw = match.group(1).strip('"')
+    parts = raw.split(":")
+    if len(parts) % 3:
+        raise SystemExit(f"[FAIL] Properties 格式异常: {raw}")
+    parsed = []
+    for i in range(0, len(parts), 3):
+        name, kind, width = parts[i], parts[i + 1], int(parts[i + 2])
+        parsed.append((name, kind, width))
+    return parsed
+
+
+def validate_xyz(path: Path) -> int:
+    frames = 0
+    elements: set[str] = set()
+    min_atoms: int | None = None
+    max_atoms = 0
+
+    with path.open("r", encoding="utf-8") as f:
+        while True:
+            first = f.readline()
+            if not first:
+                break
+            if not first.strip():
+                continue
+            try:
+                atom_count = int(first.strip())
+            except ValueError as exc:
+                raise SystemExit(f"[FAIL] 原子数行不是整数: {path}:{frames + 1}") from exc
+            comment = f.readline().rstrip("\n")
+            if f"{EXPECTED_ENERGY_KEY}=" not in comment:
+                raise SystemExit(f"[FAIL] comment 缺少 {EXPECTED_ENERGY_KEY}: {path} frame {frames}")
+            if "free_energy=" not in comment:
+                raise SystemExit(f"[FAIL] comment 缺少 free_energy: {path} frame {frames}")
+            if "pbc=" not in comment:
+                raise SystemExit(f"[FAIL] comment 缺少 pbc: {path} frame {frames}")
+            if "Lattice=" not in comment:
+                raise SystemExit(f"[FAIL] comment 缺少 Lattice: {path} frame {frames}")
+            props = parse_properties(comment)
+            prop_names = [p[0] for p in props]
+            if prop_names[0:2] != ["species", "pos"]:
+                raise SystemExit(f"[FAIL] Properties 前两项必须是 species,pos: {path} frame {frames}")
+            if EXPECTED_FORCES_KEY not in prop_names:
+                raise SystemExit(f"[FAIL] Properties 缺少 {EXPECTED_FORCES_KEY}: {path} frame {frames}")
+            if "move_mask" not in prop_names:
+                raise SystemExit(f"[FAIL] Properties 缺少 move_mask: {path} frame {frames}")
+            if "tags" not in prop_names:
+                raise SystemExit(f"[FAIL] Properties 缺少 tags: {path} frame {frames}")
+            expected_cols = sum(width for _, _, width in props)
+
+            for atom_index in range(atom_count):
+                atom_line = f.readline()
+                if not atom_line:
+                    raise SystemExit(f"[FAIL] 文件提前结束: {path} frame {frames}")
+                cols = atom_line.split()
+                if len(cols) != expected_cols:
+                    raise SystemExit(
+                        f"[FAIL] 原子列数异常: {path} frame {frames} atom {atom_index}: "
+                        f"{len(cols)} != {expected_cols}"
+                    )
+                elements.add(cols[0])
+                col_idx = 1
+                for _, kind, width in props:
+                    if kind == "S":
+                        continue
+                    values = cols[col_idx:col_idx + width]
+                    if kind == "R":
+                        for value in values:
+                            float(value)
+                    elif kind == "I":
+                        for value in values:
+                            int(value)
+                    elif kind == "L":
+                        for value in values:
+                            if value not in ("T", "F"):
+                                raise SystemExit(
+                                    f"[FAIL] bool 字段值异常: {value} at {path} frame {frames}"
+                                )
+                    else:
+                        raise SystemExit(f"[FAIL] 不支持的 Properties 类型: {kind}")
+                    col_idx += width
+            frames += 1
+            min_atoms = atom_count if min_atoms is None else min(min_atoms, atom_count)
+            max_atoms = max(max_atoms, atom_count)
+
+    if not elements.issubset(EXPECTED_ELEMENTS):
+        raise SystemExit(f"[FAIL] 元素集合异常: {sorted(elements)}")
+    print(
+        f"[OK] {path.name}: frames={frames}, atoms={min_atoms}-{max_atoms}, "
+        f"elements={sorted(elements)[:5]}..."
+    )
+    return frames
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--dataset-root", default="data/oc20")
+    parser.add_argument("--checksum-manifest", default="metadata/sha256_manifest.txt")
+    args = parser.parse_args()
+
+    repo_root = Path.cwd()
+    dataset_root = Path(args.dataset_root)
+    if not dataset_root.is_absolute():
+        dataset_root = repo_root / dataset_root
+    checksum_manifest = Path(args.checksum_manifest)
+    if not checksum_manifest.is_absolute():
+        checksum_manifest = repo_root / checksum_manifest
+
+    if not dataset_root.exists():
+        raise SystemExit(f"[FAIL] 数据目录不存在: {dataset_root}")
+
+    for split_name, split_info in EXPECTED_SPLITS.items():
+        split_dir = dataset_root / split_name
+        if not split_dir.exists():
+            raise SystemExit(f"[FAIL] 缺少 split 目录: {split_dir}")
+        total_frames = 0
+        for file_name in split_info["files"]:
+            path = split_dir / file_name
+            if not path.exists():
+                raise SystemExit(f"[FAIL] 缺少文件: {path}")
+            if path.stat().st_size <= 0:
+                raise SystemExit(f"[FAIL] 文件为空: {path}")
+            total_frames += validate_xyz(path)
+        expected = split_info["expected_total_frames"]
+        if total_frames != expected:
+            raise SystemExit(
+                f"[FAIL] {split_name} 总帧数异常: {total_frames} != {expected}"
+            )
+        print(f"[OK] {split_name}: total_frames={total_frames}")
+
+    validate_checksum_manifest(dataset_root, checksum_manifest)
+    print("[OK] OC20 数据集读取验证通过")
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())