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批量生成超胞脚本 gen-sc.py

news 2026/3/26 17:36:50

gen-sc.py

依赖 pymagent
pip install pymagent
or
conda install pymagent

#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ generate_supercells.py - 仅支持三位数字超胞尺寸：231 -> 2x3x1 - 支持从 size.txt 读取 - 默认原胞文件：111.vasp - 输出命名：N1N2N3.vasp - 若发现同名文件：提示 [DUPLICATE] 并跳过，绝不覆盖 """ import argparse import os import sys from typing import Tuple, Set from pymatgen.core import Structure from pymatgen.io.vasp import Poscar def parse_size_3digit(s: str) -> Tuple[int, int, int]: s = s.strip() if not (s.isdigit() and len(s) == 3): raise ValueError(f"非法超胞尺寸 '{s}'（必须是三位数字，如 231）") return int(s[0]), int(s[1]), int(s[2]) def read_size_file(fname: str): sizes = [] with open(fname, "r", encoding="utf-8") as f: for ln, line in enumerate(f, 1): line = line.strip() if not line or line.startswith("#"): continue try: sizes.append(parse_size_3digit(line)) except ValueError as e: raise ValueError(f"{fname}:{ln} {e}") return sizes def main(): parser = argparse.ArgumentParser( description="用 pymatgen 批量生成超胞（尺寸格式：231）" ) parser.add_argument( "input", nargs="?", default="111.vasp", help="原胞 VASP 文件（默认：111.vasp）", ) parser.add_argument( "--sizes", nargs="*", default=[], help="命令行指定超胞尺寸，如：211 221 231", ) parser.add_argument( "--size-file", default="size.txt", help="超胞尺寸文件（默认：size.txt）", ) parser.add_argument( "-o", "--outdir", default=".", help="输出目录（默认当前目录）", ) args = parser.parse_args() # ---------- 检查原胞 ---------- if not os.path.isfile(args.input): print(f"[ERROR] 找不到原胞文件：{args.input}", file=sys.stderr) return 2 # ---------- 收集尺寸 ---------- sizes: Set[Tuple[int, int, int]] = set() if os.path.isfile(args.size_file): try: sizes.update(read_size_file(args.size_file)) except ValueError as e: print(f"[ERROR] {e}", file=sys.stderr) return 2 for s in args.sizes: try: sizes.add(parse_size_3digit(s)) except ValueError as e: print(f"[ERROR] {e}", file=sys.stderr) return 2 if not sizes: print("[ERROR] 未指定任何超胞尺寸（size.txt 和 --sizes 均为空）", file=sys.stderr) return 2 # ---------- 读取结构 ---------- base = Structure.from_file(args.input) os.makedirs(args.outdir, exist_ok=True) # ---------- 生成 ---------- written = 0 skipped = 0 for a, b, c in sorted(sizes): outname = f"{a}{b}{c}.vasp" outpath = os.path.join(args.outdir, outname) if os.path.exists(outpath): print(f"[DUPLICATE] {outname} 已存在，跳过，不覆盖") skipped += 1 continue sc = base.copy() sc.make_supercell([a, b, c]) Poscar(sc).write_file(outpath) print(f"[OK] 生成 {outname}") written += 1 print(f"\n完成：生成 {written} 个，跳过重复 {skipped} 个") return 0 if __name__ == "__main__": raise SystemExit(main())