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README.md

@@ -0,0 +1,89 @@
+---
+license: cc0-1.0
+tags:
+  - ANI-1x
+  - MACE
+  - molecular dynamics
+  - HDF5
+  - extxyz
+  - machine learning potential
+language:
+  - en
+  - zh
+---
+
+<p align="center">
+  <strong>
+    <span style="font-size: 30px;">ANI-1x</span>
+  </strong>
+</p>
+
+## Dataset Description
+The ANI-1x dataset is a molecular-configuration dataset for training and evaluation. The data package contains training, validation, and test HDF5 shards, along with a statistics JSON file and auxiliary extxyz files. Its fields are consistent with the energy and force fields in the MACE ANI-1x configuration, making it a standard benchmark dataset for learning and validating machine-learning interatomic potentials with MACE.
+
+The element set consists of H, C, N, and O. The original ANI-1x data comes from [ANI-1x datasets (FigShare)](https://springernature.figshare.com/collections/The_ANI-1ccx_and_ANI-1x_data_sets_coupled-cluster_and_density_functional_theory_properties_for_molecules/4712477); this repository is the companion data package for OneScience MACE training and evaluation examples.
+
+The current data package contains approximately 30 files.
+
+## Supported Tasks
+This standardized data repository provides the complete data package for the ANI-1x example, including training, validation, and test sets. It can be used for:
+- Training and validation of potential-energy-surface models for molecular configurations
+- Potential-energy-surface fitting for molecular dynamics simulations
+- Functional testing and benchmark evaluation of the MACE framework
+
+## Dataset Format and Structure
+
+The data files are located in the `data/ani1x/` directory:
+
+| File Path | Format | shape / Content | Description |
+|---|---|---|---|
+| `ani1x/ANI1x_cc_DFT_rc5_train/train_*.h5` | HDF5 | `[N_frames, N_atoms]` | Training set, with 8 shards in total |
+| `ani1x/ANI1x_cc_DFT_rc5_val/val_*.h5` | HDF5 | `[N_frames, N_atoms]` | Validation set, with 8 shards in total |
+| `ani1x/ANI1x_cc_DFT_rc5_test/Default__*.h5` | HDF5 | `[N_frames, N_atoms]` | Test set, with 8 shards in total |
+| `ani1x/ANI1x_cc_DFT_rc5_statistics.json` | JSON | Statistical information | Contains `atomic_energies`, `avg_num_neighbors`, `mean`, `std`, `atomic_numbers`, and `r_max` |
+| `ani1x/ani1x_train.xyz` | extxyz | `[N_frames, N_atoms]` | Auxiliary training-set file |
+| `ani1x/ani1x_test.xyz` | extxyz | `[N_frames, N_atoms]` | Auxiliary test-set file |
+| `ani1x/ani1x_cc_dft.xyz` | extxyz | `[N_frames, N_atoms]` | Auxiliary file for the full dataset |
+| `metadata/sha256_manifest.txt` | SHA256 | Checksum manifest | File-integrity verification |
+
+### HDF5 Data Format
+
+The HDF5 file structure is `config_batch_*/config_*`. Each configuration contains:
+
+| Path | dtype | shape | Description |
+|---|---|---|---|
+| `atomic_numbers` | `int64` | `[N_atoms]` | Atomic numbers |
+| `positions` | `float64` | `[N_atoms, 3]` | Atomic coordinates, in Å |
+| `cell` | `float64` | `[3, 3]` | Periodic cell matrix |
+| `pbc` | `bool` | `[3]` | Periodic boundary conditions |
+| `properties/energy` | `float64` | Scalar | Total configuration energy, in eV |
+| `properties/forces` | `float64` | `[N_atoms, 3]` | Atomic forces, in eV/Å |
+
+## How to Use the Dataset
+
+Download the dataset:
+
+```bash
+hf download --dataset OneScience-Sugon/ani1x --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 the example data for MACE ANI-1x; it does not contain any newly generated samples or alter the original data. The original data comes from ANI-1x datasets (FigShare), with calculations performed at the wB97X/6-31G(d) level.
+
+- **Original Source**: https://springernature.figshare.com/collections/The_ANI-1ccx_and_ANI-1x_data_sets_coupled-cluster_and_density_functional_theory_properties_for_molecules/4712477
+- **GitHub Repository**: https://github.com/aiqm/ANI1x_datasets
+- **License**: CC0 1.0 Universal (public domain dedication)
+
+When using the ANI-1x dataset, please cite:
+
+- Smith, J. S.; Nebgen, B.; Lubbers, N.; Isayev, O.; Roitberg, A. E. Less Is More: Sampling Chemical Space with Active Learning. *J. Chem. Phys.* **2018**, *148* (24), 241733. https://doi.org/10.1063/1.5023802
+- Smith, J. S.; Zubatyuk, R.; Nebgen, B.; Lubbers, N.; Barros, K.; Roitberg, A. E.; Isayev, O.; Tretiak, S. The ANI-1ccx and ANI-1x Data Sets, Coupled-Cluster and Density Functional Theory Properties for Molecules. *Sci. Data* **2020**, *7*, 134. https://doi.org/10.1038/s41597-020-0473-z

README_zh.md

@@ -0,0 +1,89 @@
+---
+license: CC0-1.0
+tags:
+  - ANI-1x
+  - MACE
+  - molecular dynamics
+  - HDF5
+  - extxyz
+  - machine learning potential
+language:
+  - en
+  - zh
+---
+
+<p align="center">
+  <strong>
+    <span style="font-size: 30px;">ANI-1x</span>
+  </strong>
+</p>
+
+## 数据集描述
+ANI-1x 数据集是训练和评测的分子构型数据集。数据包包含训练、验证、测试 HDF5 分片，以及配套 statistics JSON 和 extxyz 辅助文件，字段与 MACE ANI-1x 配置中的能量、受力字段一致，是学习和验证机器学习原子间势（MACE）方法的标准基准数据集。
+
+元素集合为 H、C、N、O。原始 ANI-1x 数据来自 [ANI-1x datasets (FigShare)](https://springernature.figshare.com/collections/The_ANI-1ccx_and_ANI-1x_data_sets_coupled-cluster_and_density_functional_theory_properties_for_molecules/4712477)，本仓库是其面向 OneScience MACE 训练和评测示例的配套数据包。
+
+当前数据包包含约 30 个文件。
+
+## 数据集支持的任务
+本标准化数据仓库整理了 ANI-1x 示例的完整数据包，包含训练集、验证集和测试集，可用于：
+- 分子构型势能面模型的训练与验证
+- 分子动力学模拟的势能面拟合
+- MACE 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/ani1x/` 目录下：
+
+| 文件路径 | 格式 | shape / 内容 | 说明 |
+|---|---|---|---|
+| `ani1x/ANI1x_cc_DFT_rc5_train/train_*.h5` | HDF5 | `[N_frames, N_atoms]` | 训练集，共 8 个分片 |
+| `ani1x/ANI1x_cc_DFT_rc5_val/val_*.h5` | HDF5 | `[N_frames, N_atoms]` | 验证集，共 8 个分片 |
+| `ani1x/ANI1x_cc_DFT_rc5_test/Default__*.h5` | HDF5 | `[N_frames, N_atoms]` | 测试集，共 8 个分片 |
+| `ani1x/ANI1x_cc_DFT_rc5_statistics.json` | JSON | 统计信息 | 包含 `atomic_energies`、`avg_num_neighbors`、`mean`、`std`、`atomic_numbers`、`r_max` |
+| `ani1x/ani1x_train.xyz` | extxyz | `[N_frames, N_atoms]` | 训练集辅助文件 |
+| `ani1x/ani1x_test.xyz` | extxyz | `[N_frames, N_atoms]` | 测试集辅助文件 |
+| `ani1x/ani1x_cc_dft.xyz` | extxyz | `[N_frames, N_atoms]` | 全量辅助文件 |
+| `metadata/sha256_manifest.txt` | SHA256 | 校验清单 | 文件完整性校验 |
+
+### HDF5 数据格式
+
+HDF5 文件结构为 `config_batch_*/config_*`。单个构型包含：
+
+| 路径 | dtype | shape | 说明 |
+|---|---|---|---|
+| `atomic_numbers` | `int64` | `[N_atoms]` | 原子序数 |
+| `positions` | `float64` | `[N_atoms, 3]` | 原子坐标，单位 Å |
+| `cell` | `float64` | `[3, 3]` | 周期盒矩阵 |
+| `pbc` | `bool` | `[3]` | 周期边界条件 |
+| `properties/energy` | `float64` | 标量 | 构型总能量，单位 eV |
+| `properties/forces` | `float64` | `[N_atoms, 3]` | 原子受力，单位 eV/Å |
+
+## 数据集使用方式
+
+下载数据集：
+
+```bash
+hf download --dataset OneScience-Sugon/ani1x --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 MACE ANI-1x 示例数据，未生成新样本或改变原始数据内容。原始数据来自 ANI-1x datasets (FigShare)，计算级别为 wB97X/6-31G(d)。
+
+- **原始来源**：https://springernature.figshare.com/collections/The_ANI-1ccx_and_ANI-1x_data_sets_coupled-cluster_and_density_functional_theory_properties_for_molecules/4712477
+- **GitHub 仓库**：https://github.com/aiqm/ANI1x_datasets
+- **许可证**：CC0 1.0 Universal (公共领域 dedication)
+
+使用 ANI-1x 数据集时请引用：
+
+- Smith, J. S.; Nebgen, B.; Lubbers, N.; Isayev, O.; Roitberg, A. E. Less Is More: Sampling Chemical Space with Active Learning. *J. Chem. Phys.* **2018**, *148* (24), 241733. https://doi.org/10.1063/1.5023802
+- Smith, J. S.; Zubatyuk, R.; Nebgen, B.; Lubbers, N.; Barros, K.; Roitberg, A. E.; Isayev, O.; Tretiak, S. The ANI-1ccx and ANI-1x Data Sets, Coupled-Cluster and Density Functional Theory Properties for Molecules. *Sci. Data* **2020**, *7*, 134. https://doi.org/10.1038/s41597-020-0473-z

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manifest.yaml

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+onescience_manifest_version: "0.1"
+resource_type: dataset
+resource:
+  id: OneScience/ani1x
+  name: ANI-1x
+  domain: matchem
+  domain_tags:
+    - matchem
+    - molecular_dataset
+    - atomistic_simulation
+  task: mlip_training_data
+  task_tags:
+    - mlip
+    - energy_prediction
+    - force_prediction
+  modalities:
+    - atomistic_structure
+  input_formats:
+    - hdf5
+    - extxyz
+  output_formats: []
+  summary: 面向 MACE 训练和评测的 ANI-1x 分子构型数据集标准包。
+
+platform_resource:
+  primary:
+    platform: modelscope
+    repo_id: OneScience/ani1x
+    repo_type: dataset
+    url: https://modelscope.cn/datasets/OneScience/ani1x
+    revision: main
+    readme_path: README.md
+    manifest_path: manifest.yaml
+  mirrors: []
+  access:
+    visibility: public
+    license: null
+
+website_integration:
+  enabled: true
+  click_target:
+    platform: modelscope
+    resource_url: https://modelscope.cn/datasets/OneScience/ani1x
+  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/mace/ani1x
+  compatibility:
+    examples_path: examples/matchem/mace
+    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_ani1x.py
+    - metadata/schema.yaml
+    - metadata/sha256_manifest.txt
+  entrypoints:
+    preflight: scripts/validate_ani1x.py
+    inference: null
+    train: null
+    finetune: null
+    evaluate: null
+    visualize: null
+    deploy: null
+
+files:
+  model_files: []
+  dataset_files:
+    - id: ani1x_train_h5
+      path: data/ani1x/ANI1x_cc_DFT_rc5_train/
+      role: train_split
+      description_zh: ANI-1x 训练集 HDF5 分片目录，共 8 个 train_*.h5 文件。
+      required: true
+      required_for: [preflight, train]
+      format: hdf5
+      source:
+        platform: modelscope
+        repo_id: OneScience/ani1x
+        repo_type: dataset
+        path: data/ani1x/ANI1x_cc_DFT_rc5_train/
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/ani1x/ANI1x_cc_DFT_rc5_train/
+      size: 22M
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+    - id: ani1x_val_h5
+      path: data/ani1x/ANI1x_cc_DFT_rc5_val/
+      role: validation_split
+      description_zh: ANI-1x 验证集 HDF5 分片目录，共 8 个 val_*.h5 文件。
+      required: true
+      required_for: [preflight, train, evaluate]
+      format: hdf5
+      source:
+        platform: modelscope
+        repo_id: OneScience/ani1x
+        repo_type: dataset
+        path: data/ani1x/ANI1x_cc_DFT_rc5_val/
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/ani1x/ANI1x_cc_DFT_rc5_val/
+      size: 728K
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+    - id: ani1x_test_h5
+      path: data/ani1x/ANI1x_cc_DFT_rc5_test/
+      role: test_split
+      description_zh: ANI-1x 测试集 HDF5 分片目录，共 8 个 Default__*.h5 文件。
+      required: true
+      required_for: [preflight, evaluate]
+      format: hdf5
+      source:
+        platform: modelscope
+        repo_id: OneScience/ani1x
+        repo_type: dataset
+        path: data/ani1x/ANI1x_cc_DFT_rc5_test/
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/ani1x/ANI1x_cc_DFT_rc5_test/
+      size: 12M
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+    - id: ani1x_statistics
+      path: data/ani1x/ANI1x_cc_DFT_rc5_statistics.json
+      role: statistics
+      description_zh: MACE 训练需要的原子能量、邻居数、均值、标准差和 r_max 统计文件。
+      required: true
+      required_for: [preflight, train, evaluate]
+      format: json
+      source:
+        platform: modelscope
+        repo_id: OneScience/ani1x
+        repo_type: dataset
+        path: data/ani1x/ANI1x_cc_DFT_rc5_statistics.json
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/ani1x/ANI1x_cc_DFT_rc5_statistics.json
+      size: 512B
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+    - id: ani1x_xyz
+      path: data/ani1x/*.xyz
+      role: metadata
+      description_zh: ANI-1x 的 extxyz 版本和 train/test 辅助文件，可用于人工检查或其他工具读取。
+      required: false
+      required_for: [preflight]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/ani1x
+        repo_type: dataset
+        path: data/ani1x/*.xyz
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/ani1x/*.xyz
+      size: 728M
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+  config_files:
+    - id: schema
+      path: metadata/schema.yaml
+      role: schema
+      description_zh: 数据 split、HDF5 字段、dtype、shape、单位和统计文件说明。
+      required: true
+      required_for: [preflight, train, evaluate]
+      format: yaml
+      source:
+        platform: modelscope
+        repo_id: OneScience/ani1x
+        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: 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/ani1x
+        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_ani1x.py
+      role: script
+      description_zh: 数据读取验证脚本，检查文件结构、shape、dtype、statistics 和 SHA256。
+      required: true
+      required_for: [preflight]
+      format: py
+      source:
+        platform: modelscope
+        repo_id: OneScience/ani1x
+        repo_type: dataset
+        path: scripts/validate_ani1x.py
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/scripts/validate_ani1x.py
+      size: null
+      checksum: null
+      large_file: false
+
+dataset:
+  format:
+    - hdf5
+    - extxyz
+  sample_unit: 单个分子构型，包含原子序数、坐标、cell、pbc、能量和原子受力。
+  schema:
+    path: metadata/schema.yaml
+  splits:
+    train:
+      path: data/ani1x/ANI1x_cc_DFT_rc5_train
+      shards: 8
+    validation:
+      path: data/ani1x/ANI1x_cc_DFT_rc5_val
+      shards: 8
+    test:
+      path: data/ani1x/ANI1x_cc_DFT_rc5_test
+      shards: 8
+
+relations:
+  required_datasets: []
+  optional_datasets: []
+  compatible_models:
+    - id: OneScience/MACE
+      role: train_data
+      required_for: [preflight, train, evaluate]
+      resource_ref:
+        platform: modelscope
+        repo_id: OneScience/MACE
+        repo_type: model
+        url: https://modelscope.cn/models/OneScience/MACE
+        revision: main
+        readme_path: README.md
+        manifest_path: manifest.yaml
+      expected_local_path: session_workdir/data/ani1x
+      adapter: null
+
+run_matrix:
+  scenarios:
+    - name: validate_dataset
+      default: true
+      capability: preflight
+      required_datasets:
+        - id: OneScience/ani1x
+          role: train_data
+          local_path: data/ani1x
+      required_model_files: []
+      required_data_files:
+        - data/ani1x/ANI1x_cc_DFT_rc5_train/*.h5
+        - data/ani1x/ANI1x_cc_DFT_rc5_val/*.h5
+        - data/ani1x/ANI1x_cc_DFT_rc5_test/*.h5
+        - data/ani1x/ANI1x_cc_DFT_rc5_statistics.json
+        - metadata/sha256_manifest.txt
+      preconditions:
+        - 已下载数据集仓库 OneScience/ani1x。
+      command_refs:
+        - commands.preflight.validate_dataset
+      outputs:
+        - path: stdout
+          description_zh: 数据结构、统计文件和 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/ani1x
+      source: .
+      local_path: session_workdir/
+      required: true
+      required_for: [preflight, train, evaluate]
+      cwd: .
+      command: modelscope download --dataset OneScience/ani1x --local_dir session_workdir
+      expected_outputs:
+        - path: session_workdir/data/ani1x/ANI1x_cc_DFT_rc5_statistics.json
+          type: file
+      success_criteria:
+        - exit_code == 0
+        - output_path_exists
+  preflight:
+    - name: validate_dataset
+      description: 验证 ANI-1x 文件结构、HDF5 schema、statistics 和 SHA256。
+      cwd: .
+      command: python scripts/validate_ani1x.py --dataset-root data/ani1x --checksum-manifest metadata/sha256_manifest.txt
+      required_files:
+        - data/ani1x/ANI1x_cc_DFT_rc5_statistics.json
+        - metadata/sha256_manifest.txt
+        - scripts/validate_ani1x.py
+      required_env:
+        - python
+        - h5py
+      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、statistics 和 SHA256 的 OK 结果。
+
+diagnostics:
+  - error_pattern: "缺少文件"
+    likely_cause: 数据集下载不完整或本地路径错误。
+    action: 重新执行 modelscope download --dataset OneScience/ani1x，并确认运行 cwd 是数据集仓库根目录。
+  - 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: "HDF5"
+    likely_cause: HDF5 文件损坏或 schema 与 MACE 预期不一致。
+    action: 运行 scripts/validate_ani1x.py 定位具体文件，并与 metadata/schema.yaml 对照。
+  - error_pattern: "ModuleNotFoundError"
+    likely_cause: 缺少 h5py 或 Python 环境未配置。
+    action: 安装 h5py，或执行 bash install.sh matchem。
+
+domain_extension:
+  matchem:
+    chemical_system:
+      elements:
+        - H
+        - C
+        - N
+        - O
+    properties:
+      - energy
+      - forces
+    units:
+      energy: eV
+      forces: eV/Angstrom
+    structure_format:
+      - hdf5
+      - extxyz
+
+large_resource:
+  enabled: false
+  total_size: 762M
+  file_count: 28
+  download_policy: full
+  default_download: full
+  minimal_files:
+    - data/ani1x/ANI1x_cc_DFT_rc5_train/train_0.h5
+    - data/ani1x/ANI1x_cc_DFT_rc5_val/val_0.h5
+    - data/ani1x/ANI1x_cc_DFT_rc5_test/Default__0.h5
+    - data/ani1x/ANI1x_cc_DFT_rc5_statistics.json
+
+reproducibility:
+  level: minimal
+  goal: 完成一次数据读取和 SHA256 校验。
+  command_ref: commands.preflight.validate_dataset
+  expected_runtime: 1-5 minutes
+  expected_outputs:
+    - stdout

metadata/schema.yaml

@@ -0,0 +1,63 @@
+dataset: ANI-1x
+standardized_repo_id: OneScience/ani1x
+domain: matchem
+format:
+  - hdf5
+  - extxyz
+splits:
+  train:
+    path: data/ani1x/ANI1x_cc_DFT_rc5_train
+    pattern: "*.h5"
+    shards: 8
+  validation:
+    path: data/ani1x/ANI1x_cc_DFT_rc5_val
+    pattern: "*.h5"
+    shards: 8
+  test:
+    path: data/ani1x/ANI1x_cc_DFT_rc5_test
+    pattern: "*.h5"
+    shards: 8
+sample_schema:
+  hdf5_layout: config_batch_*/config_*
+  fields:
+    atomic_numbers:
+      dtype: int64
+      shape: [num_atoms]
+      description_zh: 原子序数
+    positions:
+      dtype: float64
+      shape: [num_atoms, 3]
+      unit: Angstrom
+      description_zh: 原子坐标
+    cell:
+      dtype: float64
+      shape: [3, 3]
+      description_zh: 周期盒矩阵
+    pbc:
+      dtype: bool
+      shape: [3]
+      description_zh: 周期边界条件
+    properties/energy:
+      dtype: float64
+      shape: []
+      unit: eV
+      description_zh: 构型总能量
+    properties/forces:
+      dtype: float64
+      shape: [num_atoms, 3]
+      unit: eV/Angstrom
+      description_zh: 原子受力
+statistics:
+  path: data/ani1x/ANI1x_cc_DFT_rc5_statistics.json
+  fields:
+    - atomic_energies
+    - avg_num_neighbors
+    - mean
+    - std
+    - atomic_numbers
+    - r_max
+elements:
+  - H
+  - C
+  - N
+  - O

metadata/sha256_manifest.txt

@@ -0,0 +1,28 @@
+0449b48e5a5c7f7b6129e7aa4cbca7a21781e5921884b2d9719ff1e4d131a787  ANI1x_cc_DFT_rc5_statistics.json
+2d5d74c451c8fe4a6c42103ce7003b67da4f46382bbb33d4516e3c0954ebe958  ANI1x_cc_DFT_rc5_test/Default__0.h5
+b1bb9f8a3665ac30d283c35af544fd7cf5a576206b965f8bda00cc54630428b8  ANI1x_cc_DFT_rc5_test/Default__1.h5
+c5370d0f8a10501c6b260944ef2dca96ac74ba2bad2a4dfa8047fe97cd094f94  ANI1x_cc_DFT_rc5_test/Default__2.h5
+52870d5f33a46d5e98b6c4446f61bf075c7da94c081586fdf71df1760e7245e2  ANI1x_cc_DFT_rc5_test/Default__3.h5
+2b9ec4b82136042b43f4f66792909cc5d2cb944cd3af409b0e9b877275d5bbc7  ANI1x_cc_DFT_rc5_test/Default__4.h5
+13119e9c2f44d1aa5bb31e926635b5a34d42d1c823f6d144cc591f7b15f0c9b3  ANI1x_cc_DFT_rc5_test/Default__5.h5
+f90bb56746a07c72dae9e735aefc2db4a6945534ce609305a13fda6e639e8075  ANI1x_cc_DFT_rc5_test/Default__6.h5
+925192b4c6e89831a3be24d683a78c947ff6ac8c0d36279c6d2a440656fb2b57  ANI1x_cc_DFT_rc5_test/Default__7.h5
+134ceed06158735140a0f7a1ba7adfb436b268dfd9a78a2c139c50cc97cf0f9a  ANI1x_cc_DFT_rc5_train/train_0.h5
+72622803a711d7e246284e6f7d71e058151267a6e073ce60d223e2dba1fb4c9a  ANI1x_cc_DFT_rc5_train/train_1.h5
+323d7efa393f38ca86dfbb7abdde66bbcd434fb32a50d9224245bfd864c2cb3c  ANI1x_cc_DFT_rc5_train/train_2.h5
+1baff48da2ff5bd16e5ee34379b954d8ef912af8ed18f848b8774d14db81d040  ANI1x_cc_DFT_rc5_train/train_3.h5
+fc5dc17175fe71e69b195cb9a90d1e3ba973deb6947672484b6f46d5bbc8f588  ANI1x_cc_DFT_rc5_train/train_4.h5
+b711a45152ac306b90acf88bd79945fe7e3201c6f7a101bdb2445a264cb86293  ANI1x_cc_DFT_rc5_train/train_5.h5
+65e964ea93f188b9183dd18aefca7dcb8bc1c0f0f4eaa13d947db37f1cfe5008  ANI1x_cc_DFT_rc5_train/train_6.h5
+a182edfd0c43f16d0da5a223f0c29132cc44f97f0ffac08cb47edc1166367d38  ANI1x_cc_DFT_rc5_train/train_7.h5
+a3bed40241c38172f0ff6634510e11101013b962765bc99550bc6b19796463d6  ANI1x_cc_DFT_rc5_val/val_0.h5
+263a38d970756ecf691b2dafabae86929f7b9f6945700eddd4a169a31e366560  ANI1x_cc_DFT_rc5_val/val_1.h5
+08d1ffc03712f43fda13a6ab56d820b623e99412819f2191256530e1b1ae6f9a  ANI1x_cc_DFT_rc5_val/val_2.h5
+757f4276604c151f9fc16f4667b66460279b105e8102b03e491dcb3aab3a6bae  ANI1x_cc_DFT_rc5_val/val_3.h5
+6b4c025be9dbbd35f78675c40ce83d8c60fd85c5dfdac9b4fd25e76e54aed849  ANI1x_cc_DFT_rc5_val/val_4.h5
+571164862b2235a4273670428785c21ad383f15ac082d333aec80d3e47bc4403  ANI1x_cc_DFT_rc5_val/val_5.h5
+9ac22a293d0d89821c0e3dc768b4a2599d16d6db72f69a78e9f09ee18e24901f  ANI1x_cc_DFT_rc5_val/val_6.h5
+d86a5f3ac2f85deda7fc4daf8346ae82441b95aab6c976b19fb544aa46670312  ANI1x_cc_DFT_rc5_val/val_7.h5
+70288856ccc6d7333dad57089dc49e566179bcd705a5ab77895d7e9c93f9803d  ani1x_cc_dft.xyz
+ed10d691c665a63848f22931dd91ab293f839ca9e176c1858b3310d742a4e163  ani1x_test.xyz
+34889a04b83a52aae42ce8678644395e7b1091f4341b8d6a4254e704100161b5  ani1x_train.xyz

onescience_relations.yaml

@@ -0,0 +1,19 @@
+required_datasets: []
+optional_datasets: []
+compatible_models:
+  - id: OneScience/MACE
+    role: train_data
+    required_for:
+      - preflight
+      - train
+      - evaluate
+    resource_ref:
+      platform: modelscope
+      repo_id: OneScience/MACE
+      repo_type: model
+      url: https://modelscope.cn/models/OneScience/MACE
+      revision: main
+      readme_path: README.md
+      manifest_path: manifest.yaml
+    expected_local_path: session_workdir/data/ani1x
+    adapter: null

scripts/validate_ani1x.py

@@ -0,0 +1,135 @@
+#!/usr/bin/env python3
+"""Validate the standardized ANI-1x dataset package."""
+
+from __future__ import annotations
+
+import argparse
+import hashlib
+import json
+from pathlib import Path
+
+import h5py
+
+
+EXPECTED_SPLITS = {
+    "ANI1x_cc_DFT_rc5_train": 8,
+    "ANI1x_cc_DFT_rc5_val": 8,
+    "ANI1x_cc_DFT_rc5_test": 8,
+}
+EXPECTED_FILES = {
+    "ANI1x_cc_DFT_rc5_statistics.json",
+    "ani1x_cc_dft.xyz",
+    "ani1x_train.xyz",
+    "ani1x_test.xyz",
+}
+REQUIRED_SAMPLE_KEYS = (
+    "atomic_numbers",
+    "cell",
+    "pbc",
+    "positions",
+    "properties/energy",
+    "properties/forces",
+)
+
+
+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_h5(path: Path) -> None:
+    with h5py.File(path, "r") as f:
+        batches = sorted(f.keys())
+        if not batches:
+            raise SystemExit(f"[FAIL] HDF5 无 batch: {path}")
+        configs = sorted(f[batches[0]].keys())
+        if not configs:
+            raise SystemExit(f"[FAIL] HDF5 batch 无 config: {path}")
+        sample = f[batches[0]][configs[0]]
+        for key in REQUIRED_SAMPLE_KEYS:
+            if key not in sample:
+                raise SystemExit(f"[FAIL] HDF5 缺少字段 {key}: {path}")
+        atomic_numbers = sample["atomic_numbers"]
+        positions = sample["positions"]
+        forces = sample["properties/forces"]
+        if atomic_numbers.dtype.kind not in ("i", "u"):
+            raise SystemExit(f"[FAIL] atomic_numbers dtype 非整数: {path}")
+        if positions.dtype.kind != "f" or positions.shape[-1] != 3:
+            raise SystemExit(f"[FAIL] positions dtype/shape 异常: {path}")
+        if forces.dtype.kind != "f" or forces.shape != positions.shape:
+            raise SystemExit(f"[FAIL] forces dtype/shape 异常: {path}")
+
+
+def validate_checksum_manifest(dataset_root: Path, manifest_path: Path) -> None:
+    if not manifest_path.exists():
+        raise SystemExit(f"[FAIL] 校验清单不存在: {manifest_path}")
+    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 / 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
+    if checked == 0:
+        raise SystemExit("[FAIL] 校验清单为空")
+    print(f"[OK] SHA256 清单验证通过: {checked} 个文件")
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--dataset-root", default="data/ani1x")
+    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 rel in EXPECTED_FILES:
+        path = dataset_root / rel
+        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}")
+        print(f"[OK] 文件存在: {rel}")
+
+    stats_path = dataset_root / "ANI1x_cc_DFT_rc5_statistics.json"
+    with stats_path.open("r", encoding="utf-8") as f:
+        stats = json.load(f)
+    for key in ("atomic_energies", "avg_num_neighbors", "mean", "std", "atomic_numbers", "r_max"):
+        if key not in stats:
+            raise SystemExit(f"[FAIL] statistics 缺少字段: {key}")
+    print("[OK] statistics JSON 可读")
+
+    for split, expected_count in EXPECTED_SPLITS.items():
+        split_dir = dataset_root / split
+        h5_files = sorted(split_dir.glob("*.h5"))
+        if len(h5_files) != expected_count:
+            raise SystemExit(f"[FAIL] {split} 分片数异常: {len(h5_files)} != {expected_count}")
+        validate_h5(h5_files[0])
+        print(f"[OK] {split}: {len(h5_files)} 个 h5 分片，样本结构可读")
+
+    validate_checksum_manifest(dataset_root, checksum_manifest)
+    print("[OK] ANI-1x 数据集读取验证通过")
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())