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+dataset_infos.json ignore
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+data/DMC/solvent_xtb_test.xyz filter=lfs diff=lfs merge=lfs -text

README.md

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+---
+# User-Defined Tags
+tags:
+  - DMC
+  - MACE
+  - molecular dynamics
+  - extxyz
+  - carbonate
+  - XTB
+language:
+  - en
+  - zh
+license: mit
+---
+<p align="center">
+  <strong>
+    <span style="font-size: 30px;">DMC</span>
+  </strong>
+</p>
+
+## Dataset Description
+DMC is a solvent XTB extxyz dataset for introductory training examples. It contains atomic coordinates, energies, and forces for carbonate molecular systems (VC, EC, PC, DMC, EMC, and DEC) in different configurations, and serves as a standard introductory benchmark dataset for learning and validating machine-learning interatomic potential methods.
+
+The training file `solvent_xtb_train_200.xyz` contains 203 frames (200 training configurations + 3 isolated atom configurations), while the test file `solvent_xtb_test.xyz` contains 1000 frames. The element set is H, C, and O.
+
+The current data package contains about 3 files.
+
+## Supported Tasks
+This standardized data repository provides the complete data package for the introductory MACE DMC example, including training and test sets. It can be used for:
+- Introductory training and validation of potential energy surface models for carbonate molecular 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/DMC/` directory:
+
+| File Path | Format | shape / Content | Description |
+|---|---|---|---|
+| `DMC/solvent_xtb_train_200.xyz` | extxyz | `[203, N_atoms]` | Training set, 200 training configurations + 3 isolated atom configurations |
+| `DMC/solvent_xtb_test.xyz` | extxyz | `[1000, N_atoms]` | Test set, 1000 frames |
+| `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_xtb`, and `pbc`. Each atom line contains the element, coordinates, optional `molID`, and `forces_xtb`.
+
+| Field | Type | shape | Description |
+|---|---|---|---|
+| `species` | str | `[N_atoms]` | Element symbols; the current element set is H, C, and O |
+| `pos` | float | `[N_atoms, 3]` | Atomic coordinates in Å |
+| `molID` | int | `[N_atoms]` | Molecule ID; it may be absent from isolated atom configurations |
+| `forces_xtb` | float | `[N_atoms, 3]` | Atomic forces calculated with XTB, in eV/Å |
+| `energy_xtb` | float | `[1]` | Total configuration energy calculated with XTB, in eV |
+| `pbc` | bool | `[3]` | Periodic boundary conditions |
+
+## How to Use the Dataset
+
+Download the dataset:
+
+```bash
+hf download --dataset OneScience-Sugon/DMC --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 the introductory DMC training example data. No new samples were generated, and the original data content was not modified. The original configuration data come from the 2022 work by Dajnowicz et al. on machine-learning potentials for lithium-ion battery electrolytes, with energies and forces recalculated using XTB (GFN2-xTB).
+
+- **Original Paper**: Dajnowicz, S.; Agarwal, G.; Stevenson, J. M.; Jacobson, L. D.; Ramezanghorbani, F.; Leswing, K.; Friesner, R. A.; Halls, M. D.; Abel, R. High-Dimensional Neural Network Potential for Liquid Electrolyte Simulations. *J. Phys. Chem. B* **2022**, *126*, 6271–6280. https://doi.org/10.1021/acs.jpcb.2c03746
+- **Original Data Repository**: https://github.com/imagdau/Tutorials
+- **License**: The original data do not explicitly declare a license; refer to the original DMC data source, the OneScience repository, and the ModelScope page for applicable terms

README_zh.md

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+---
+# 用户自定义标签
+tags:
+  - DMC
+  - MACE
+  - molecular dynamics
+  - extxyz
+  - carbonate
+  - XTB
+language:
+  - en
+  - zh
+license: MIT License
+---
+<p align="center">
+  <strong>
+    <span style="font-size: 30px;">DMC</span>
+  </strong>
+</p>
+
+## 数据集描述
+DMC 数据集是入门训练示例的溶剂 XTB extxyz 数据集。数据包含碳酸盐分子体系（VC、EC、PC、DMC、EMC、DEC）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入门基准数据集。
+
+训练文件 `solvent_xtb_train_200.xyz` 包含 203 帧（200 个训练构型 + 3 个 isolated atom 构型），测试文件 `solvent_xtb_test.xyz` 包含 1000 帧。元素集合为 H、C、O。
+
+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 DMC 入门示例的完整数据包，包含训练集和测试集，可用于：
+- 碳酸盐分子体系势能面模型的入门训练与验证
+- 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/DMC/` 目录下：
+
+| 文件路径 | 格式 | shape / 内容 | 说明 |
+|---|---|---|---|
+| `DMC/solvent_xtb_train_200.xyz` | extxyz | `[203, N_atoms]` | 训练集，200 个训练构型 + 3 个 isolated atom 构型 |
+| `DMC/solvent_xtb_test.xyz` | extxyz | `[1000, N_atoms]` | 测试集，1000 帧 |
+| `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_xtb` 和 `pbc`。原子行包含元素、坐标、可选 `molID` 和 `forces_xtb`。
+
+| 字段 | 类型 | shape | 说明 |
+|---|---|---|---|
+| `species` | str | `[N_atoms]` | 元素符号，当前元素集合为 H、C、O |
+| `pos` | float | `[N_atoms, 3]` | 原子坐标，单位 Å |
+| `molID` | int | `[N_atoms]` | 分子编号，isolated atom 构型中可能不存在 |
+| `forces_xtb` | float | `[N_atoms, 3]` | XTB 计算得到的原子受力，单位 eV/Å |
+| `energy_xtb` | float | `[1]` | XTB 计算得到的构型总能量，单位 eV |
+| `pbc` | bool | `[3]` | 周期边界条件 |
+
+## 数据集使用方式
+
+下载数据集：
+
+```bash
+hf download --dataset OneScience-Sugon/DMC --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DMC 入门训练示例数据，未生成新样本或改变原始数据内容。原始构型数据来自 Dajnowicz 等 2022 年关于锂离子电池电解液机器学习势的工作，能量和受力由 XTB (GFN2-xTB) 重新计算。
+
+- **原始论文**：Dajnowicz, S.; Agarwal, G.; Stevenson, J. M.; Jacobson, L. D.; Ramezanghorbani, F.; Leswing, K.; Friesner, R. A.; Halls, M. D.; Abel, R. High-Dimensional Neural Network Potential for Liquid Electrolyte Simulations. *J. Phys. Chem. B* **2022**, *126*, 6271–6280. https://doi.org/10.1021/acs.jpcb.2c03746
+- **原始数据仓库**：https://github.com/imagdau/Tutorials
+- **许可证**：原始数据未明确声明许可证，以原始 DMC 数据来源、OneScience 仓库和 ModelScope 页面说明为准

manifest.yaml

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+onescience_manifest_version: "0.1"
+resource_type: dataset
+resource:
+  id: OneScience/DMC
+  name: DMC
+  domain: matchem
+  domain_tags:
+    - matchem
+    - molecular_dataset
+    - solvent_xtb
+  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 入门训练示例的 DMC 溶剂 XTB extxyz 数据集。
+
+platform_resource:
+  primary:
+    platform: modelscope
+    repo_id: OneScience/DMC
+    repo_type: dataset
+    url: https://modelscope.cn/datasets/OneScience/DMC
+    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/DMC
+  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/DMC
+  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_dmc.py
+    - metadata/schema.yaml
+    - metadata/sha256_manifest.txt
+  entrypoints:
+    preflight: scripts/validate_dmc.py
+    inference: null
+    train: null
+    finetune: null
+    evaluate: null
+    visualize: null
+    deploy: null
+
+files:
+  model_files: []
+  dataset_files:
+    - id: dmc_train_extxyz
+      path: data/DMC/solvent_xtb_train_200.xyz
+      role: train_split
+      description_zh: DMC 溶剂 XTB 训练 extxyz 文件，包含 203 帧，其中 3 帧为 isolated atom，200 帧为训练构型。
+      required: true
+      required_for: [preflight, train]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/DMC
+        repo_type: dataset
+        path: data/DMC/solvent_xtb_train_200.xyz
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/DMC/solvent_xtb_train_200.xyz
+      size: 672K
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+    - id: dmc_test_extxyz
+      path: data/DMC/solvent_xtb_test.xyz
+      role: test_split
+      description_zh: DMC 溶剂 XTB 测试 extxyz 文件，包含 1000 帧，用于 MACE 示例训练后的测试评估。
+      required: true
+      required_for: [preflight, evaluate]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/DMC
+        repo_type: dataset
+        path: data/DMC/solvent_xtb_test.xyz
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/DMC/solvent_xtb_test.xyz
+      size: 3.4M
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+  config_files:
+    - id: schema
+      path: metadata/schema.yaml
+      role: schema
+      description_zh: DMC 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/DMC
+        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: DMC 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/DMC
+        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_dmc.py
+      role: script
+      description_zh: DMC 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/DMC
+        repo_type: dataset
+        path: scripts/validate_dmc.py
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/scripts/validate_dmc.py
+      size: null
+      checksum: null
+      large_file: false
+
+dataset:
+  format:
+    - extxyz
+  sample_unit: 单个分子构型，包含元素、坐标、energy_xtb 和 forces_xtb。
+  schema:
+    path: metadata/schema.yaml
+  splits:
+    train:
+      path: data/DMC/solvent_xtb_train_200.xyz
+      frames: 203
+    validation:
+      path: null
+      note_zh: "MACE DMC 示例通过 valid_fraction: 0.10 从训练文件划分验证集。"
+    test:
+      path: data/DMC/solvent_xtb_test.xyz
+      frames: 1000
+
+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/DMC
+      adapter: null
+
+run_matrix:
+  scenarios:
+    - name: validate_dataset
+      default: true
+      capability: preflight
+      required_datasets:
+        - id: OneScience/DMC
+          role: train_data
+          local_path: data/DMC
+      required_model_files: []
+      required_data_files:
+        - data/DMC/solvent_xtb_train_200.xyz
+        - data/DMC/solvent_xtb_test.xyz
+        - metadata/sha256_manifest.txt
+      preconditions:
+        - 已下载数据集仓库 OneScience/DMC。
+      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/DMC
+      source: .
+      local_path: session_workdir/
+      required: true
+      required_for: [preflight, train, evaluate]
+      cwd: .
+      command: modelscope download --dataset OneScience/DMC --local_dir session_workdir
+      expected_outputs:
+        - path: session_workdir/data/DMC/solvent_xtb_train_200.xyz
+          type: file
+      success_criteria:
+        - exit_code == 0
+        - output_path_exists
+  preflight:
+    - name: validate_dataset
+      description: 验证 DMC extxyz 文件结构、字段名、帧数和 SHA256。
+      cwd: .
+      command: python scripts/validate_dmc.py --dataset-root data/DMC --checksum-manifest metadata/sha256_manifest.txt
+      required_files:
+        - data/DMC/solvent_xtb_train_200.xyz
+        - data/DMC/solvent_xtb_test.xyz
+        - metadata/sha256_manifest.txt
+        - scripts/validate_dmc.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/DMC，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_xtb"
+    likely_cause: extxyz comment 中缺少 MACE DMC 配置要求的能量字段。
+    action: 检查数据是否为本���库 DMC XTB 数据，或同步修改模型配置 energy_key。
+  - error_pattern: "forces_xtb"
+    likely_cause: extxyz Properties 中缺少 MACE DMC 配置要求的力字段。
+    action: 检查数据是否为本仓库 DMC XTB 数据，或同步修改模型配置 forces_key。
+
+domain_extension:
+  matchem:
+    chemical_system:
+      elements:
+        - H
+        - C
+        - O
+    properties:
+      - energy
+      - forces
+    units:
+      energy: eV
+      forces: eV/Angstrom
+    structure_format:
+      - extxyz
+
+large_resource:
+  enabled: false
+  total_size: 4.1M
+  file_count: 2
+  download_policy: full
+  default_download: full
+  minimal_files:
+    - data/DMC/solvent_xtb_train_200.xyz
+    - data/DMC/solvent_xtb_test.xyz
+
+reproducibility:
+  level: minimal
+  goal: 完成一次 DMC extxyz 数据读取和 SHA256 校验。
+  command_ref: commands.preflight.validate_dataset
+  expected_runtime: less than 1 minute
+  expected_outputs:
+    - stdout

metadata/schema.yaml

@@ -0,0 +1,52 @@
+dataset: DMC
+standardized_repo_id: OneScience/DMC
+domain: matchem
+format:
+  - extxyz
+splits:
+  train:
+    path: data/DMC/solvent_xtb_train_200.xyz
+    frames: 203
+    note_zh: 文件名表示 200 个训练构型，文件内还包含 3 个 isolated atom 构型。
+  test:
+    path: data/DMC/solvent_xtb_test.xyz
+    frames: 1000
+sample_schema:
+  extxyz_comment_fields:
+    - Properties
+    - energy_xtb
+    - 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。
+    molID:
+      dtype: int
+      shape: [num_atoms]
+      optional: true
+      description_zh: 分子编号，isolated atom 构型中可能不存在。
+    forces_xtb:
+      dtype: float
+      shape: [num_atoms, 3]
+      unit: eV/Angstrom
+      description_zh: XTB 计算得到的原子受力。
+  config_fields:
+    energy_xtb:
+      dtype: float
+      unit: eV
+      description_zh: XTB 计算得到的构型总能量。
+model_expected_keys:
+  energy_key: energy_xtb
+  forces_key: forces_xtb
+  train_file: data/DMC/solvent_xtb_train_200.xyz
+  test_file: data/DMC/solvent_xtb_test.xyz
+elements:
+  - H
+  - C
+  - O

metadata/sha256_manifest.txt

@@ -0,0 +1,2 @@
+d97b90c293af6e9742a0d22ab4fb1e13672091bb9ac6754481ef61fdf4f879fa  solvent_xtb_test.xyz
+e540bc7c026cfad063fc970406bb74c0f668007fc3c6d200801ecfd5f1ba600e  solvent_xtb_train_200.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/DMC
+    adapter: null

onescience_run_manifest.yaml

@@ -0,0 +1,376 @@
+onescience_manifest_version: "0.1"
+resource_type: dataset
+resource:
+  id: OneScience/DMC
+  name: DMC
+  domain: matchem
+  domain_tags:
+    - matchem
+    - molecular_dataset
+    - solvent_xtb
+  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 入门训练示例的 DMC 溶剂 XTB extxyz 数据集。
+
+platform_resource:
+  primary:
+    platform: modelscope
+    repo_id: OneScience/DMC
+    repo_type: dataset
+    url: https://modelscope.cn/datasets/OneScience/DMC
+    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/DMC
+  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/DMC
+  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_dmc.py
+    - metadata/schema.yaml
+    - metadata/sha256_manifest.txt
+  entrypoints:
+    preflight: scripts/validate_dmc.py
+    inference: null
+    train: null
+    finetune: null
+    evaluate: null
+    visualize: null
+    deploy: null
+
+files:
+  model_files: []
+  dataset_files:
+    - id: dmc_train_extxyz
+      path: data/DMC/solvent_xtb_train_200.xyz
+      role: train_split
+      description_zh: DMC 溶剂 XTB 训练 extxyz 文件，包含 203 帧，其中 3 帧为 isolated atom，200 帧为训练构型。
+      required: true
+      required_for: [preflight, train]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/DMC
+        repo_type: dataset
+        path: data/DMC/solvent_xtb_train_200.xyz
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/DMC/solvent_xtb_train_200.xyz
+      size: 672K
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+    - id: dmc_test_extxyz
+      path: data/DMC/solvent_xtb_test.xyz
+      role: test_split
+      description_zh: DMC 溶剂 XTB 测试 extxyz 文件，包含 1000 帧，用于 MACE 示例训练后的测试评估。
+      required: true
+      required_for: [preflight, evaluate]
+      format: extxyz
+      source:
+        platform: modelscope
+        repo_id: OneScience/DMC
+        repo_type: dataset
+        path: data/DMC/solvent_xtb_test.xyz
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/data/DMC/solvent_xtb_test.xyz
+      size: 3.4M
+      checksum: metadata/sha256_manifest.txt
+      large_file: false
+  config_files:
+    - id: schema
+      path: metadata/schema.yaml
+      role: schema
+      description_zh: DMC 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/DMC
+        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: DMC 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/DMC
+        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_dmc.py
+      role: script
+      description_zh: DMC 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/DMC
+        repo_type: dataset
+        path: scripts/validate_dmc.py
+        revision: main
+        url: null
+        download_method: command_ref
+        command_ref: commands.download.download_dataset_package
+      mirrors: []
+      local_path: session_workdir/scripts/validate_dmc.py
+      size: null
+      checksum: null
+      large_file: false
+
+dataset:
+  format:
+    - extxyz
+  sample_unit: 单个分子构型，包含元素、坐标、energy_xtb 和 forces_xtb。
+  schema:
+    path: metadata/schema.yaml
+  splits:
+    train:
+      path: data/DMC/solvent_xtb_train_200.xyz
+      frames: 203
+    validation:
+      path: null
+      note_zh: "MACE DMC 示例通过 valid_fraction: 0.10 从训练文件划分验证集。"
+    test:
+      path: data/DMC/solvent_xtb_test.xyz
+      frames: 1000
+
+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/DMC
+      adapter: null
+
+run_matrix:
+  scenarios:
+    - name: validate_dataset
+      default: true
+      capability: preflight
+      required_datasets:
+        - id: OneScience/DMC
+          role: train_data
+          local_path: data/DMC
+      required_model_files: []
+      required_data_files:
+        - data/DMC/solvent_xtb_train_200.xyz
+        - data/DMC/solvent_xtb_test.xyz
+        - metadata/sha256_manifest.txt
+      preconditions:
+        - 已下载数据集仓库 OneScience/DMC。
+      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/DMC
+      source: .
+      local_path: session_workdir/
+      required: true
+      required_for: [preflight, train, evaluate]
+      cwd: .
+      command: modelscope download --dataset OneScience/DMC --local_dir session_workdir
+      expected_outputs:
+        - path: session_workdir/data/DMC/solvent_xtb_train_200.xyz
+          type: file
+      success_criteria:
+        - exit_code == 0
+        - output_path_exists
+  preflight:
+    - name: validate_dataset
+      description: 验证 DMC extxyz 文件结构、字段名、帧数和 SHA256。
+      cwd: .
+      command: python scripts/validate_dmc.py --dataset-root data/DMC --checksum-manifest metadata/sha256_manifest.txt
+      required_files:
+        - data/DMC/solvent_xtb_train_200.xyz
+        - data/DMC/solvent_xtb_test.xyz
+        - metadata/sha256_manifest.txt
+        - scripts/validate_dmc.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/DMC，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_xtb"
+    likely_cause: extxyz comment 中缺少 MACE DMC 配置要求的能量字段。
+    action: 检查数据是否为本���库 DMC XTB 数据，或同步修改模型配置 energy_key。
+  - error_pattern: "forces_xtb"
+    likely_cause: extxyz Properties 中缺少 MACE DMC 配置要求的力字段。
+    action: 检查数据是否为本仓库 DMC XTB 数据，或同步修改模型配置 forces_key。
+
+domain_extension:
+  matchem:
+    chemical_system:
+      elements:
+        - H
+        - C
+        - O
+    properties:
+      - energy
+      - forces
+    units:
+      energy: eV
+      forces: eV/Angstrom
+    structure_format:
+      - extxyz
+
+large_resource:
+  enabled: false
+  total_size: 4.1M
+  file_count: 2
+  download_policy: full
+  default_download: full
+  minimal_files:
+    - data/DMC/solvent_xtb_train_200.xyz
+    - data/DMC/solvent_xtb_test.xyz
+
+reproducibility:
+  level: minimal
+  goal: 完成一次 DMC extxyz 数据读取和 SHA256 校验。
+  command_ref: commands.preflight.validate_dataset
+  expected_runtime: less than 1 minute
+  expected_outputs:
+    - stdout

scripts/validate_dmc.py

@@ -0,0 +1,153 @@
+#!/usr/bin/env python3
+"""Validate the standardized DMC extxyz dataset package."""
+
+from __future__ import annotations
+
+import argparse
+import hashlib
+import re
+from pathlib import Path
+
+
+EXPECTED_FILES = {
+    "solvent_xtb_train_200.xyz": 203,
+    "solvent_xtb_test.xyz": 1000,
+}
+EXPECTED_ELEMENTS = {"H", "C", "O"}
+
+
+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()
+    min_atoms: int | None = None
+    max_atoms = 0
+    saw_molid = False
+
+    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 "energy_xtb=" not in comment:
+                raise SystemExit(f"[FAIL] comment 缺少 energy_xtb: {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[0:2] != ["species", "pos"]:
+                raise SystemExit(f"[FAIL] Properties 前两项必须是 species,pos: {path} frame {frames}")
+            if "forces_xtb" not in prop_names:
+                raise SystemExit(f"[FAIL] Properties 缺少 forces_xtb: {path} frame {frames}")
+            saw_molid = saw_molid or ("molID" in prop_names)
+            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])
+                numeric = cols[1:]
+                for value in numeric:
+                    float(value)
+            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 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)}")
+    if path.name.endswith("test.xyz") and not saw_molid:
+        raise SystemExit(f"[FAIL] 测试集未检测到 molID 字段: {path}")
+    print(
+        f"[OK] {path.name}: frames={frames}, atoms={min_atoms}-{max_atoms}, "
+        f"elements={sorted(elements)}"
+    )
+
+
+def main() -> int:
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--dataset-root", default="data/DMC")
+    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] DMC 数据集读取验证通过")
+    return 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())