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modelscope + repo_id: OneScience/MatPL + repo_type: dataset + url: https://modelscope.cn/datasets/OneScience/MatPL + 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/MatPL + 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/matpl + compatibility: + examples_path: examples/matchem/nep + 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_matpl.py + - metadata/schema.yaml + - metadata/sha256_manifest.txt + - data/MatPL/ + entrypoints: + preflight: scripts/validate_matpl.py + inference: null + train: null + finetune: null + evaluate: null + visualize: null + deploy: null +files: + model_files: [] + dataset_files: + - id: matpl_data + path: data/MatPL/ + role: training_data + description_zh: MatPL AuAg、Cu、HfO2、LiSiC 数据。 + required: true + required_for: + - preflight + - train + - evaluate + format: movement_npy_extxyz + source: + platform: modelscope + repo_id: OneScience/MatPL + repo_type: dataset + path: data/MatPL/ + revision: main + url: null + download_method: command_ref + command_ref: commands.download.download_dataset_package + mirrors: [] + local_path: session_workdir/data/MatPL/ + size: 38M + checksum: metadata/sha256_manifest.txt + large_file: false + config_files: + - id: schema + path: metadata/schema.yaml + role: schema + description_zh: MatPL 数据结构和校验说明。 + required: true + required_for: + - preflight + format: yaml + source: + platform: modelscope + repo_id: OneScience/MatPL + 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: 所有 data/ 文件 SHA256 清单。 + required: true + required_for: + - preflight + format: txt + source: + platform: modelscope + repo_id: OneScience/MatPL + 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: [] +relations: + required_datasets: [] + optional_datasets: [] + compatible_models: + - id: OneScience/NEP + role: compatible_model + required_for: + - preflight + - train + - evaluate + resource_ref: + platform: modelscope + repo_id: OneScience/NEP + repo_type: model + url: https://modelscope.cn/models/OneScience/NEP + revision: main + readme_path: README.md + manifest_path: manifest.yaml + expected_dataset_local_path: data/MatPL +run_matrix: + scenarios: + - name: minimal_validation + default: true + capability: preflight + required_datasets: + - id: OneScience/MatPL + role: self_dataset + local_path: data/MatPL + required_model_files: [] + required_data_files: + - data/MatPL/Cu/pwdata/0_300_MOVEMENT + - data/MatPL/AuAg/AuAg-5762.xyz + - data/MatPL/HfO2/pwdata/ + preconditions: + - 数据文件已放在 data/MatPL/。 + command_refs: + - commands.preflight.validate_dataset + outputs: + - path: stdout + description_zh: MatPL 数据结构和 SHA256 校验结果。 +capabilities: + inference: false + train: false + finetune: false + evaluate: true + visualize: false + deploy: false +commands: + download: + - name: download_dataset_package + target: dataset + repo_id: OneScience/MatPL + source: . + local_path: session_workdir/ + required: true + required_for: + - preflight + - train + cwd: . + command: modelscope download --dataset OneScience/MatPL --local_dir session_workdir + expected_outputs: + - path: session_workdir/data/MatPL/Cu/pwdata/0_300_MOVEMENT + type: file + success_criteria: + - exit_code == 0 + - output_path_exists + preflight: + - name: validate_dataset + description: 检查 MatPL Movement、xyz、npy 和 SHA256。 + cwd: . + command: python scripts/validate_matpl.py --dataset-root data/MatPL --checksum-manifest metadata/sha256_manifest.txt + required_files: + - scripts/validate_matpl.py + - metadata/sha256_manifest.txt + - data/MatPL/Cu/pwdata/0_300_MOVEMENT + required_env: + - python + - numpy + expected_outputs: + - path: stdout + type: text + success_criteria: + - exit_code == 0 + prepare: [] + inference: [] + train: [] + finetune: [] + evaluate: + - name: validate_for_nep + description: 作为 NEP 适配数据运行同一数据读取验证。 + cwd: . + command: python scripts/validate_matpl.py --dataset-root data/MatPL --checksum-manifest metadata/sha256_manifest.txt + required_files: + - data/MatPL/Cu/pwdata/0_300_MOVEMENT + required_env: + - python + - numpy + expected_outputs: + - path: stdout + type: text + success_criteria: + - exit_code == 0 + visualize: [] + deploy: [] +expected_outputs: +- path: stdout + type: text + description_zh: MatPL 数据验证通过，输出体系、npy 数量和 SHA256 条目数。 +diagnostics: +- error_pattern: missing file + likely_cause: 数据集未完整下载或 cwd 不在数据集包根目录。 + action: 执行 modelscope download --dataset OneScience/MatPL --local_dir session_workdir。 +- error_pattern: checksum mismatch + likely_cause: 数据文件损坏或未完整复制。 + action: 重新同步 matchem/matpl 到 modelscope_standardized/dataset/matchem_MatPL/data/MatPL 并重新生成 SHA256 清单。 +domain_extension: + matchem: + dataset_family: MatPL + systems: + - AuAg + - Cu + - HfO2 + - LiSiC + formats: + - pwmat/movement + - pwmlff/npy + - extxyz + compatible_model_ids: + - OneScience/NEP +reproducibility: + level: data_integrity + goal: 完成 MatPL 数据结构和 SHA256 校验。 + command_ref: commands.preflight.validate_dataset + expected_runtime: 1-2 minutes + expected_outputs: + - stdout diff --git a/metadata/schema.yaml b/metadata/schema.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1b82e52ef7cc58815ede293b274683e1dd517c18 --- /dev/null +++ b/metadata/schema.yaml @@ -0,0 +1,39 @@ +schema_version: "0.1" +dataset: + id: OneScience/MatPL + name: MatPL + domain: matchem + source_path: matchem/matpl + standardized_path: modelscope_standardized/dataset/matchem_MatPL/data/MatPL +layout: + root: data/MatPL + systems: + - AuAg + - Cu + - HfO2 + - LiSiC +formats: + movement: + examples: + - Cu/pwdata/0_300_MOVEMENT + - Cu/pwdata/1_500_MOVEMENT + - Cu/pwdata/valid_movement + extxyz: + examples: + - AuAg/AuAg-5762.xyz + pwmlff_npy: + required_arrays: + - atom_type.npy + - energies.npy + - forces.npy + - image_type.npy + - lattice.npy + - position.npy +validation: + script: scripts/validate_matpl.py + command: python scripts/validate_matpl.py --dataset-root data/MatPL --checksum-manifest metadata/sha256_manifest.txt + checksum_manifest: metadata/sha256_manifest.txt +compatible_models: + - id: OneScience/NEP + repo_type: model + 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b/onescience_relations.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4929219c26177f879e4b891cfee5b2223e9a951a --- /dev/null +++ b/onescience_relations.yaml @@ -0,0 +1,17 @@ +compatible_models: + - id: OneScience/NEP + role: compatible_model + required_for: + - preflight + - train + - evaluate + resource_ref: + platform: modelscope + repo_id: OneScience/NEP + repo_type: model + url: https://modelscope.cn/models/OneScience/NEP + revision: main + readme_path: README.md + manifest_path: manifest.yaml + expected_dataset_local_path: data/MatPL +required_datasets: [] diff --git a/onescience_run_manifest.yaml b/onescience_run_manifest.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4b76af85a69093c3a6cdf997beec59f11953296d --- /dev/null +++ b/onescience_run_manifest.yaml @@ -0,0 +1,313 @@ +onescience_manifest_version: '0.1' +resource_type: dataset +resource: + id: OneScience/MatPL + name: MatPL + domain: matchem + domain_tags: + - matchem + - matpl + - nep + - mlip + task: nep_training_data + task_tags: + - movement + - pwmlff_npy + - extxyz + - energy_force_virial + modalities: + - atomistic_structure + input_formats: + - pwmat_movement + - pwmlff_npy + - extxyz + output_formats: [] + summary: NEP 示例使用的 MatPL 多体系材料势数据集。 +platform_resource: + primary: + platform: modelscope + repo_id: OneScience/MatPL + repo_type: dataset + url: https://modelscope.cn/datasets/OneScience/MatPL + 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/MatPL + 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/matpl + compatibility: + examples_path: examples/matchem/nep + 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_matpl.py + - metadata/schema.yaml + - metadata/sha256_manifest.txt + - data/MatPL/ + entrypoints: + preflight: scripts/validate_matpl.py + inference: null + train: null + finetune: null + evaluate: null + visualize: null + deploy: null +files: + model_files: [] + dataset_files: + - id: matpl_data + path: data/MatPL/ + role: training_data + description_zh: MatPL AuAg、Cu、HfO2、LiSiC 数据。 + required: true + required_for: + - preflight + - train + - evaluate + format: movement_npy_extxyz + source: + platform: modelscope + repo_id: OneScience/MatPL + repo_type: dataset + path: data/MatPL/ + revision: main + url: null + download_method: command_ref + command_ref: commands.download.download_dataset_package + mirrors: [] + local_path: session_workdir/data/MatPL/ + size: 38M + checksum: metadata/sha256_manifest.txt + large_file: false + config_files: + - id: schema + path: metadata/schema.yaml + role: schema + description_zh: MatPL 数据结构和校验说明。 + required: true + required_for: + - preflight + format: yaml + source: + platform: modelscope + repo_id: OneScience/MatPL + 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: 所有 data/ 文件 SHA256 清单。 + required: true + required_for: + - preflight + format: txt + source: + platform: modelscope + repo_id: OneScience/MatPL + 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: [] +relations: + required_datasets: [] + optional_datasets: [] + compatible_models: + - id: OneScience/NEP + role: compatible_model + required_for: + - preflight + - train + - evaluate + resource_ref: + platform: modelscope + repo_id: OneScience/NEP + repo_type: model + url: https://modelscope.cn/models/OneScience/NEP + revision: main + readme_path: README.md + manifest_path: manifest.yaml + expected_dataset_local_path: data/MatPL +run_matrix: + scenarios: + - name: minimal_validation + default: true + capability: preflight + required_datasets: + - id: OneScience/MatPL + role: self_dataset + local_path: data/MatPL + required_model_files: [] + required_data_files: + - data/MatPL/Cu/pwdata/0_300_MOVEMENT + - data/MatPL/AuAg/AuAg-5762.xyz + - data/MatPL/HfO2/pwdata/ + preconditions: + - 数据文件已放在 data/MatPL/。 + command_refs: + - commands.preflight.validate_dataset + outputs: + - path: stdout + description_zh: MatPL 数据结构和 SHA256 校验结果。 +capabilities: + inference: false + train: false + finetune: false + evaluate: true + visualize: false + deploy: false +commands: + download: + - name: download_dataset_package + target: dataset + repo_id: OneScience/MatPL + source: . + local_path: session_workdir/ + required: true + required_for: + - preflight + - train + cwd: . + command: modelscope download --dataset OneScience/MatPL --local_dir session_workdir + expected_outputs: + - path: session_workdir/data/MatPL/Cu/pwdata/0_300_MOVEMENT + type: file + success_criteria: + - exit_code == 0 + - output_path_exists + preflight: + - name: validate_dataset + description: 检查 MatPL Movement、xyz、npy 和 SHA256。 + cwd: . + command: python scripts/validate_matpl.py --dataset-root data/MatPL --checksum-manifest metadata/sha256_manifest.txt + required_files: + - scripts/validate_matpl.py + - metadata/sha256_manifest.txt + - data/MatPL/Cu/pwdata/0_300_MOVEMENT + required_env: + - python + - numpy + expected_outputs: + - path: stdout + type: text + success_criteria: + - exit_code == 0 + prepare: [] + inference: [] + train: [] + finetune: [] + evaluate: + - name: validate_for_nep + description: 作为 NEP 适配数据运行同一数据读取验证。 + cwd: . + command: python scripts/validate_matpl.py --dataset-root data/MatPL --checksum-manifest metadata/sha256_manifest.txt + required_files: + - data/MatPL/Cu/pwdata/0_300_MOVEMENT + required_env: + - python + - numpy + expected_outputs: + - path: stdout + type: text + success_criteria: + - exit_code == 0 + visualize: [] + deploy: [] +expected_outputs: +- path: stdout + type: text + description_zh: MatPL 数据验证通过，输出体系、npy 数量和 SHA256 条目数。 +diagnostics: +- error_pattern: missing file + likely_cause: 数据集未完整下载或 cwd 不在数据集包根目录。 + action: 执行 modelscope download --dataset OneScience/MatPL --local_dir session_workdir。 +- error_pattern: checksum mismatch + likely_cause: 数据文件损坏或未完整复制。 + action: 重新同步 matchem/matpl 到 modelscope_standardized/dataset/matchem_MatPL/data/MatPL 并重新生成 SHA256 清单。 +domain_extension: + matchem: + dataset_family: MatPL + systems: + - AuAg + - Cu + - HfO2 + - LiSiC + formats: + - pwmat/movement + - pwmlff/npy + - extxyz + compatible_model_ids: + - OneScience/NEP +reproducibility: + level: data_integrity + goal: 完成 MatPL 数据结构和 SHA256 校验。 + command_ref: commands.preflight.validate_dataset + expected_runtime: 1-2 minutes + expected_outputs: + - stdout diff --git a/scripts/validate_matpl.py b/scripts/validate_matpl.py new file mode 100644 index 0000000000000000000000000000000000000000..5c3800ad67f2f43c66247365944d76cfaad300bb --- /dev/null +++ b/scripts/validate_matpl.py @@ -0,0 +1,128 @@ +#!/usr/bin/env python3 +"""Validate the standardized OneScience MatPL dataset package.""" + +from __future__ import annotations + +import argparse +import hashlib +import sys +from pathlib import Path + +import numpy as np + + +EXPECTED_TOP_LEVEL = ["AuAg", "Cu", "HfO2", "LiSiC"] + + +def sha256_file(path: Path) -> str: + digest = hashlib.sha256() + with path.open("rb") as handle: + for chunk in iter(lambda: handle.read(1024 * 1024), b""): + digest.update(chunk) + return digest.hexdigest() + + +def require_file(path: Path) -> None: + if not path.is_file(): + raise FileNotFoundError(f"missing file: {path}") + + +def require_dir(path: Path) -> None: + if not path.is_dir(): + raise FileNotFoundError(f"missing directory: {path}") + + +def check_movement(path: Path) -> None: + require_file(path) + with path.open(encoding="utf-8", errors="replace") as handle: + text = handle.read(4096) + if not text.strip(): + raise ValueError(f"empty MOVEMENT file: {path}") + if "Iteration" not in text and "atoms" not in text.lower() and "lattice" not in text.lower(): + raise ValueError(f"unexpected MOVEMENT header: {path}") + + +def check_xyz(path: Path) -> None: + require_file(path) + with path.open(encoding="utf-8", errors="replace") as handle: + first = handle.readline().strip() + second = handle.readline() + atoms = int(first) + if atoms <= 0: + raise ValueError(f"invalid xyz atom count in {path}") + if not second: + raise ValueError(f"missing xyz comment line in {path}") + + +def check_npy(path: Path) -> None: + require_file(path) + arr = np.load(path, allow_pickle=False) + if arr.size == 0: + raise ValueError(f"empty npy array: {path}") + + +def read_checksum_manifest(path: Path) -> list[tuple[str, str]]: + require_file(path) + entries: list[tuple[str, str]] = [] + with path.open(encoding="utf-8") as handle: + for line_no, raw in enumerate(handle, start=1): + line = raw.strip() + if not line: + continue + parts = line.split(None, 1) + if len(parts) != 2: + raise ValueError(f"invalid checksum line {line_no}: {raw!r}") + entries.append((parts[0], parts[1])) + return entries + + +def validate_checksums(package_root: Path, manifest_path: Path) -> int: + entries = read_checksum_manifest(manifest_path) + for expected_hash, rel_path in entries: + target = package_root / rel_path + require_file(target) + if sha256_file(target) != expected_hash: + raise ValueError(f"checksum mismatch: {rel_path}") + return len(entries) + + +def main() -> int: + parser = argparse.ArgumentParser(description=__doc__) + parser.add_argument("--dataset-root", default="data/MatPL") + parser.add_argument("--checksum-manifest", default="metadata/sha256_manifest.txt") + parser.add_argument("--skip-checksum", action="store_true") + args = parser.parse_args() + + package_root = Path.cwd() + dataset_root = Path(args.dataset_root) + for name in EXPECTED_TOP_LEVEL: + require_dir(dataset_root / name) + + check_movement(dataset_root / "Cu/pwdata/0_300_MOVEMENT") + check_movement(dataset_root / "Cu/pwdata/1_500_MOVEMENT") + check_movement(dataset_root / "Cu/pwdata/valid_movement") + check_xyz(dataset_root / "AuAg/AuAg-5762.xyz") + + npy_files = sorted(dataset_root.glob("**/*.npy")) + if len(npy_files) < 100: + raise ValueError(f"too few npy files: {len(npy_files)}") + for sample in npy_files[:8]: + check_npy(sample) + + checksum_count = 0 + if not args.skip_checksum: + checksum_count = validate_checksums(package_root, Path(args.checksum_manifest)) + + print("MatPL dataset validation passed") + print(f"top-level systems: {', '.join(EXPECTED_TOP_LEVEL)}") + print(f"npy files: {len(npy_files)}") + print(f"checksum entries verified: {checksum_count}") + return 0 + + +if __name__ == "__main__": + try: + raise SystemExit(main()) + except Exception as exc: + print(f"MatPL dataset validation failed: {exc}", file=sys.stderr) + raise SystemExit(1)