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