File size: 7,937 Bytes
d0a5d19 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 | #!/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())
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