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README.md

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+---
+license: apache-2.0
+# User-Defined Tags
+tags:
+  - nanotube
+  - MACE
+  - carbon nanotube
+  - extxyz
+  - machine learning potential
+language:
+  - en
+  - zh
+---
+<p align="center">
+  <strong>
+    <span style="font-size: 30px;">nanotube</span>
+  </strong>
+</p>
+
+## Dataset Description
+The nanotube dataset is an extxyz dataset for carbon nanotube training and evaluation examples. It contains atomic coordinates, energies, and force data for carbon nanotube systems in different configurations and is a standard benchmark dataset for developing and validating machine-learned interatomic potential methods.
+
+The training file `nanotube_large.xyz` contains 4,000 frames, while the test file `nanotube_test.xyz` contains 1,032 frames. Each frame contains 370 atoms, and the set of elements is C and H.
+
+The current data package contains approximately 3 files.
+
+## Supported Tasks
+This standardized data repository organizes the complete data package for the MACE nanotube example, including training and test sets, to support:
+- Training and validation of potential energy surface models for carbon nanotube systems
+- 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/nanotube/` directory:
+
+| File Path | Format | Shape / Content | Description |
+|---|---|---|---|
+| `nanotube/nanotube_large.xyz` | extxyz | `[4000, 370]` | Training set, 4,000 frames with 370 atoms per frame |
+| `nanotube/nanotube_test.xyz` | extxyz | `[1032, 370]` | Test set, 1,032 frames with 370 atoms per frame |
+| `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 `Properties`, `Energy`, and `pbc`. Each atom line contains the element, coordinates, and `forces`.
+
+| Field | Type | Shape | Description |
+|---|---|---|---|
+| `species` | str | `[N_atoms]` | Element symbols; the current set of elements is C and H |
+| `pos` | float | `[N_atoms, 3]` | Atomic coordinates in Å |
+| `forces` | float | `[N_atoms, 3]` | Atomic forces in eV/Å |
+| `Energy` | float | `[1]` | Total configuration energy in eV |
+| `pbc` | bool | `[3]` | Periodic boundary conditions |
+
+## How to Use the Dataset
+This dataset is suitable for multiple molecular dynamics models in the `OneScience-Sugon` repository.
+
+Download the dataset:
+
+```bash
+hf download --dataset OneScience-Sugon/nanotube --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 contains nanotube example data; no new samples were generated, and the original data content was not altered. The original data comes from the double-walled nanotube system in the MD22 Benchmark Dataset (sGDML), computed at the DFT-PBE+MBD level (FHI-aims + i-PI).
+
+- **Original source**: http://www.sgdml.org/#datasets
+- **Direct download link**: http://www.quantum-machine.org/gdml/repo/datasets/md22_double-walled_nanotube.npz
+- **License**: Refer to the original nanotube data source and the information provided by the OneScience repository and ModelScope page
+
+When using the original nanotube dataset, cite:
+
+- Chmiela, S.; Vassilev-Galindo, V.; Unke, O. T.; Kabylda, A.; Sauceda, H. E.; Tkatchenko, A.; Müller, K.-R. Accurate Global Machine Learning Force Fields for Molecules with Hundreds of Atoms. *Science Advances* **2023**, *9*(2), eadf0873.

README_zh.md

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+---
+license: Apache License 2.0
+# 用户自定义标签
+tags:
+  - nanotube
+  - MACE
+  - carbon nanotube
+  - extxyz
+  - machine learning potential
+language:
+  - en
+  - zh
+---
+<p align="center">
+  <strong>
+    <span style="font-size: 30px;">nanotube</span>
+  </strong>
+</p>
+
+## 数据集描述
+nanotube 数据集是碳纳米管训练和评测示例的 extxyz 数据集。数据包含碳纳米管体系在不同构型下的原子坐标、能量和受力数据是学习和验证机器学习原子间势方法的标准基准数据集。
+
+训练文件 `nanotube_large.xyz` 包含 4000 帧，测试文件 `nanotube_test.xyz` 包含 1032 帧，每帧 370 个原子。元素集合为 C、H。
+
+当前数据包包含约 3 个文件。
+
+## 数据集支持的任务
+本标准化数据仓库整理了 MACE nanotube 示例的完整数据包，包含训练集和测试集，可用于：
+- 碳纳米管体系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/nanotube/` 目录下：
+
+| 文件路径 | 格式 | shape / 内容 | 说明 |
+|---|---|---|---|
+| `nanotube/nanotube_large.xyz` | extxyz | `[4000, 370]` | 训练集，4000 帧，每帧 370 个原子 |
+| `nanotube/nanotube_test.xyz` | extxyz | `[1032, 370]` | 测试集，1032 帧，每帧 370 个原子 |
+| `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 `Properties`、`Energy` 和 `pbc`。原子行包含元素、坐标和 `forces`。
+
+| 字段 | 类型 | shape | 说明 |
+|---|---|---|---|
+| `species` | str | `[N_atoms]` | 元素符号，当前元素集合为 C、H |
+| `pos` | float | `[N_atoms, 3]` | 原子坐标，单位 Å |
+| `forces` | float | `[N_atoms, 3]` | 原子受力，单位 eV/Å |
+| `Energy` | float | `[1]` | 构型总能量，单位 eV |
+| `pbc` | bool | `[3]` | 周期边界条件 |
+
+## 数据集使用方式
+本数据集适用于`OneScience-Sugon`仓库内多个分子动力学模型。
+
+下载数据集：
+
+```bash
+hf download --dataset OneScience-Sugon/nanotube --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 nanotube 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 MD22 Benchmark Dataset (sGDML) 中的 double-walled nanotube 系统，计算级别为 DFT-PBE+MBD (FHI-aims + i-PI)。
+
+- **原始来源**：http://www.sgdml.org/#datasets
+- **直接下载链接**：http://www.quantum-machine.org/gdml/repo/datasets/md22_double-walled_nanotube.npz
+- **许可证**：以原始 nanotube 数据来源、OneScience 仓库和 ModelScope 页面说明为准
+
+使用原始 nanotube 数据集时请引用：
+
+- Chmiela, S.; Vassilev-Galindo, V.; Unke, O. T.; Kabylda, A.; Sauceda, H. E.; Tkatchenko, A.; Müller, K.-R. Accurate Global Machine Learning Force Fields for Molecules with Hundreds of Atoms. *Science Advances* **2023**, *9*(2), eadf0873.

data/nanotube/nanotube_large.xyz

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data/nanotube/nanotube_test.xyz

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manifest.yaml

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+onescience_manifest_version: "0.1"
+resource_type: dataset
+resource:
+  id: OneScience/nanotube
+  name: nanotube
+  domain: matchem
+  domain_tags:
+    - matchem
+    - carbon_nanotube
+    - 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 MACE 碳纳米管训练和评测示例的 extxyz 数据集。
+
+platform_resource:
+  primary:
+    platform: modelscope
+    repo_id: OneScience/nanotube
+    repo_type: dataset
+    url: https://modelscope.cn/datasets/OneScience/nanotube
+    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/nanotube
+  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/nanotube
+  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_nanotube.py
+    - metadata/schema.yaml
+    - metadata/sha256_manifest.txt
+  entrypoints:
+    preflight: scripts/validate_nanotube.py
+    inference: null
+    train: null
+    finetune: null
+    evaluate: null
+    visualize: null
+    deploy: null
+
+files:
+  model_files: []
+  dataset_files:
+    - id: nanotube_train_extxyz
+      path: data/nanotube/nanotube_large.xyz
+      role: train_split
+      description_zh: nanotube 训练 extxyz 文件，包含 4000 帧，每帧 370 个原子，字段为 Energy 和 forces。
+      required: true
+      required_for: [preflight, train]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/nanotube
+        repo_type: dataset
+        path: data/nanotube/nanotube_large.xyz
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/nanotube/nanotube_large.xyz
+      size: 149M
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+    - id: nanotube_test_extxyz
+      path: data/nanotube/nanotube_test.xyz
+      role: test_split
+      description_zh: nanotube 测试 extxyz 文件，包含 1032 帧，每帧 370 个原子，字段为 Energy 和 forces。
+      required: true
+      required_for: [preflight, evaluate]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/nanotube
+        repo_type: dataset
+        path: data/nanotube/nanotube_test.xyz
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/nanotube/nanotube_test.xyz
+      size: 39M
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+  config_files:
+    - id: schema
+      path: metadata/schema.yaml
+      role: schema
+      description_zh: nanotube extxyz 数据结构、字段名、shape、单位、split 和 MACE 配置键说明。
+      required: true
+      required_for: [preflight, train, evaluate]
+      format: yaml
+      source:
+        platform: modelscope
+        repo_id: OneScience/nanotube
+        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: nanotube 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/nanotube
+        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_nanotube.py
+      role: script
+      description_zh: nanotube 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/nanotube
+        repo_type: dataset
+        path: scripts/validate_nanotube.py
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/scripts/validate_nanotube.py
+      size: null
+      checksum: null
+      large_file: false
+
+dataset:
+  format:
+    - extxyz
+  sample_unit: 单个碳纳米管构型，包含元素、坐标、Energy 和 forces。
+  schema:
+    path: metadata/schema.yaml
+  splits:
+    train:
+      path: data/nanotube/nanotube_large.xyz
+      frames: 4000
+      atoms_per_frame: 370
+    validation:
+      path: null
+      note_zh: "MACE nanotube 示例通过 valid_fraction: 0.05 从训练文件划分验证集。"
+    test:
+      path: data/nanotube/nanotube_test.xyz
+      frames: 1032
+      atoms_per_frame: 370
+
+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/nanotube
+      adapter: null
+
+run_matrix:
+  scenarios:
+    - name: validate_dataset
+      default: true
+      capability: preflight
+      required_datasets:
+        - id: OneScience/nanotube
+          role: train_data
+          local_path: data/nanotube
+      required_model_files: []
+      required_data_files:
+        - data/nanotube/nanotube_large.xyz
+        - data/nanotube/nanotube_test.xyz
+        - metadata/sha256_manifest.txt
+      preconditions:
+        - 已下载数据集仓库 OneScience/nanotube。
+      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/nanotube
+      source: .
+      local_path: session_workdir/
+      required: true
+      required_for: [preflight, train, evaluate]
+      cwd: .
+      command: modelscope download --dataset OneScience/nanotube --local_dir session_workdir
+      expected_outputs:
+        - path: session_workdir/data/nanotube/nanotube_large.xyz
+          type: file
+      success_criteria:
+        - exit_code == 0
+        - output_path_exists
+  preflight:
+    - name: validate_dataset
+      description: 验证 nanotube extxyz 文件结构、字段名、帧数和 SHA256。
+      cwd: .
+      command: python scripts/validate_nanotube.py --dataset-root data/nanotube --checksum-manifest metadata/sha256_manifest.txt
+      required_files:
+        - data/nanotube/nanotube_large.xyz
+        - data/nanotube/nanotube_test.xyz
+        - metadata/sha256_manifest.txt
+        - scripts/validate_nanotube.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/nanotube，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 MACE nanotube 配置要求的能量字段。
+    action: 检查数据是否为本仓库 nanotube 数据，或同步修改模型配置 energy_key。
+  - error_pattern: "forces"
+    likely_cause: extxyz Properties 中缺少 MACE nanotube 配置要求的力字段。
+    action: 检查数据是否为本仓库 nanotube 数据，或同步修改模型配置 forces_key。
+
+domain_extension:
+  matchem:
+    chemical_system:
+      elements:
+        - C
+        - H
+    properties:
+      - energy
+      - forces
+    units:
+      energy: eV
+      forces: eV/Angstrom
+    structure_format:
+      - extxyz
+
+large_resource:
+  enabled: false
+  total_size: 187M
+  file_count: 2
+  download_policy: full
+  default_download: full
+  minimal_files:
+    - data/nanotube/nanotube_large.xyz
+    - data/nanotube/nanotube_test.xyz
+
+reproducibility:
+  level: minimal
+  goal: 完成一次 nanotube extxyz 数据读取和 SHA256 校验。
+  command_ref: commands.preflight.validate_dataset
+  expected_runtime: 1-3 minutes
+  expected_outputs:
+    - stdout

metadata/schema.yaml

@@ -0,0 +1,47 @@
+dataset: nanotube
+standardized_repo_id: OneScience/nanotube
+domain: matchem
+format:
+  - extxyz
+splits:
+  train:
+    path: data/nanotube/nanotube_large.xyz
+    frames: 4000
+    atoms_per_frame: 370
+  test:
+    path: data/nanotube/nanotube_test.xyz
+    frames: 1032
+    atoms_per_frame: 370
+sample_schema:
+  extxyz_comment_fields:
+    - Properties
+    - 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。
+    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。
+model_expected_keys:
+  energy_key: Energy
+  forces_key: forces
+  train_file: data/nanotube/nanotube_large.xyz
+  test_file: data/nanotube/nanotube_test.xyz
+elements:
+  - C
+  - H

metadata/sha256_manifest.txt

@@ -0,0 +1,2 @@
+e31550a289fbda9971d7d6ecfdbed34e46802ac43c5db3762cd402433b2bd779  nanotube_large.xyz
+bf795de18aef94082f258e59a84ea9d7106e8f38b1f36e2fe7956b91a1ada274  nanotube_test.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/nanotube
+    adapter: null

onescience_run_manifest.yaml

@@ -0,0 +1,377 @@
+onescience_manifest_version: "0.1"
+resource_type: dataset
+resource:
+  id: OneScience/nanotube
+  name: nanotube
+  domain: matchem
+  domain_tags:
+    - matchem
+    - carbon_nanotube
+    - 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 MACE 碳纳米管训练和评测示例的 extxyz 数据集。
+
+platform_resource:
+  primary:
+    platform: modelscope
+    repo_id: OneScience/nanotube
+    repo_type: dataset
+    url: https://modelscope.cn/datasets/OneScience/nanotube
+    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/nanotube
+  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/nanotube
+  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_nanotube.py
+    - metadata/schema.yaml
+    - metadata/sha256_manifest.txt
+  entrypoints:
+    preflight: scripts/validate_nanotube.py
+    inference: null
+    train: null
+    finetune: null
+    evaluate: null
+    visualize: null
+    deploy: null
+
+files:
+  model_files: []
+  dataset_files:
+    - id: nanotube_train_extxyz
+      path: data/nanotube/nanotube_large.xyz
+      role: train_split
+      description_zh: nanotube 训练 extxyz 文件，包含 4000 帧，每帧 370 个原子，字段为 Energy 和 forces。
+      required: true
+      required_for: [preflight, train]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/nanotube
+        repo_type: dataset
+        path: data/nanotube/nanotube_large.xyz
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/nanotube/nanotube_large.xyz
+      size: 149M
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+    - id: nanotube_test_extxyz
+      path: data/nanotube/nanotube_test.xyz
+      role: test_split
+      description_zh: nanotube 测试 extxyz 文件，包含 1032 帧，每帧 370 个原子，字段为 Energy 和 forces。
+      required: true
+      required_for: [preflight, evaluate]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/nanotube
+        repo_type: dataset
+        path: data/nanotube/nanotube_test.xyz
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/nanotube/nanotube_test.xyz
+      size: 39M
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+  config_files:
+    - id: schema
+      path: metadata/schema.yaml
+      role: schema
+      description_zh: nanotube extxyz 数据结构、字段名、shape、单位、split 和 MACE 配置键说明。
+      required: true
+      required_for: [preflight, train, evaluate]
+      format: yaml
+      source:
+        platform: modelscope
+        repo_id: OneScience/nanotube
+        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: nanotube 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/nanotube
+        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_nanotube.py
+      role: script
+      description_zh: nanotube 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/nanotube
+        repo_type: dataset
+        path: scripts/validate_nanotube.py
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/scripts/validate_nanotube.py
+      size: null
+      checksum: null
+      large_file: false
+
+dataset:
+  format:
+    - extxyz
+  sample_unit: 单个碳纳米管构型，包含元素、坐标、Energy 和 forces。
+  schema:
+    path: metadata/schema.yaml
+  splits:
+    train:
+      path: data/nanotube/nanotube_large.xyz
+      frames: 4000
+      atoms_per_frame: 370
+    validation:
+      path: null
+      note_zh: "MACE nanotube 示例通过 valid_fraction: 0.05 从训练文件划分验证集。"
+    test:
+      path: data/nanotube/nanotube_test.xyz
+      frames: 1032
+      atoms_per_frame: 370
+
+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/nanotube
+      adapter: null
+
+run_matrix:
+  scenarios:
+    - name: validate_dataset
+      default: true
+      capability: preflight
+      required_datasets:
+        - id: OneScience/nanotube
+          role: train_data
+          local_path: data/nanotube
+      required_model_files: []
+      required_data_files:
+        - data/nanotube/nanotube_large.xyz
+        - data/nanotube/nanotube_test.xyz
+        - metadata/sha256_manifest.txt
+      preconditions:
+        - 已下载数据集仓库 OneScience/nanotube。
+      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/nanotube
+      source: .
+      local_path: session_workdir/
+      required: true
+      required_for: [preflight, train, evaluate]
+      cwd: .
+      command: modelscope download --dataset OneScience/nanotube --local_dir session_workdir
+      expected_outputs:
+        - path: session_workdir/data/nanotube/nanotube_large.xyz
+          type: file
+      success_criteria:
+        - exit_code == 0
+        - output_path_exists
+  preflight:
+    - name: validate_dataset
+      description: 验证 nanotube extxyz 文件结构、字段名、帧数和 SHA256。
+      cwd: .
+      command: python scripts/validate_nanotube.py --dataset-root data/nanotube --checksum-manifest metadata/sha256_manifest.txt
+      required_files:
+        - data/nanotube/nanotube_large.xyz
+        - data/nanotube/nanotube_test.xyz
+        - metadata/sha256_manifest.txt
+        - scripts/validate_nanotube.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/nanotube，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 MACE nanotube 配置要求的能量字段。
+    action: 检查数据是否为本仓库 nanotube 数据，或同步修改模型配置 energy_key。
+  - error_pattern: "forces"
+    likely_cause: extxyz Properties 中缺少 MACE nanotube 配置要求的力字段。
+    action: 检查数据是否为本仓库 nanotube 数据，或同步修改模型配置 forces_key。
+
+domain_extension:
+  matchem:
+    chemical_system:
+      elements:
+        - C
+        - H
+    properties:
+      - energy
+      - forces
+    units:
+      energy: eV
+      forces: eV/Angstrom
+    structure_format:
+      - extxyz
+
+large_resource:
+  enabled: false
+  total_size: 187M
+  file_count: 2
+  download_policy: full
+  default_download: full
+  minimal_files:
+    - data/nanotube/nanotube_large.xyz
+    - data/nanotube/nanotube_test.xyz
+
+reproducibility:
+  level: minimal
+  goal: 完成一次 nanotube extxyz 数据读取和 SHA256 校验。
+  command_ref: commands.preflight.validate_dataset
+  expected_runtime: 1-3 minutes
+  expected_outputs:
+    - stdout

scripts/validate_nanotube.py

@@ -0,0 +1,147 @@
+#!/usr/bin/env python3
+"""Validate the standardized nanotube extxyz dataset package."""
+
+from __future__ import annotations
+
+import argparse
+import hashlib
+import re
+from pathlib import Path
+
+
+EXPECTED_FILES = {
+    "nanotube_large.xyz": 4000,
+    "nanotube_test.xyz": 1032,
+}
+EXPECTED_ATOMS_PER_FRAME = 370
+EXPECTED_ELEMENTS = {"C", "H"}
+
+
+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 / 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 != len(EXPECTED_FILES):
+        raise SystemExit(f"[FAIL] SHA256 清单文件数异常: {checked}")
+    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, expected_frames: int) -> None:
+    frames = 0
+    elements: set[str] = set()
+
+    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
+            if atom_count != EXPECTED_ATOMS_PER_FRAME:
+                raise SystemExit(
+                    f"[FAIL] 原子数异常: {path.name} frame {frames}: "
+                    f"{atom_count} != {EXPECTED_ATOMS_PER_FRAME}"
+                )
+            comment = f.readline().rstrip("\n")
+            if "Energy=" not in comment:
+                raise SystemExit(f"[FAIL] comment 缺少 Energy: {path} frame {frames}")
+            if "pbc=" not in comment:
+                raise SystemExit(f"[FAIL] comment 缺少 pbc: {path} frame {frames}")
+            props = parse_properties(comment)
+            prop_names = [p[0] for p in props]
+            if prop_names != ["species", "pos", "forces"]:
+                raise SystemExit(f"[FAIL] Properties 必须是 species,pos,forces: {path} frame {frames}")
+            expected_cols = sum(width for _, _, width in props)
+            if expected_cols != 7:
+                raise SystemExit(f"[FAIL] 原子列数 schema 异常: {path} frame {frames}")
+
+            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])
+                for value in cols[1:]:
+                    float(value)
+            frames += 1
+
+    if frames != expected_frames:
+        raise SystemExit(f"[FAIL] 帧数异常: {path.name}: {frames} != {expected_frames}")
+    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_per_frame=370, elements={sorted(elements)}")
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--dataset-root", default="data/nanotube")
+    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 name, expected_frames in EXPECTED_FILES.items():
+        path = dataset_root / 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}")
+        validate_xyz(path, expected_frames)
+    validate_checksum_manifest(dataset_root, checksum_manifest)
+    print("[OK] nanotube 数据集读取验证通过")
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())