76 lines
3.4 KiB
Python
76 lines
3.4 KiB
Python
from typing import List, Dict, Tuple
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def add_li_y_antisite_average(
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x: float,
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# Y 位点：[(label, wyckoff, (fx,fy,fz), occ, multiplicity)]
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y_sites: List[Tuple[str, str, Tuple[float, float, float], float, int]] = None,
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# Li 位点：[(label, wyckoff, (fx,fy,fz), occ, multiplicity)]
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li_sites: List[Tuple[str, str, Tuple[float, float, float], float, int]] = None,
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# 可选：各位点的 B 因子（字典），不需要可留空
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b_iso: Dict[str, float] = None,
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# 保留小数位
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ndigits: int = 4
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) -> str:
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"""
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把结构改写成含 x (相对于 Y 总数) 的 Li/Y 反位缺陷的“平均占据”CIF 块。
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返回字符串，可直接粘贴到 CIF 的 atom_site loop 中。
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"""
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# 默认使用表 S9（P-3̅m1）的坐标与占据；multiplicity 依据该空间群
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if y_sites is None:
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y_sites = [
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("Y1", "1a", (0.0000, 0.0000, 0.0000), 1.0000, 1),
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("Y2", "2d", (0.3333, 0.6666, 0.4880), 0.8269, 2),
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("Y3", "2d", (0.3333, 0.6666,-0.0650), 0.1730, 2),
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]
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if li_sites is None:
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li_sites = [
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("Li1", "6g", (0.3397, 0.3397, 0.0000), 1.0000, 6),
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("Li2", "6h", (0.3397, 0.3397, 0.5000), 0.5000, 6),
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]
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if b_iso is None:
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# 可按需要改
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b_iso = {"Y": 1.10, "Li": 5.00, "Cl": 1.99}
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# 1) 总 Y 与总 Li（每原胞的“原子数贡献”）：
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y_total = sum(m * occ for _,_,_,occ,m in y_sites) # 期望为 3
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li_total = sum(m * occ for _,_,_,occ,m in li_sites) # 期望为 9
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# 2) 需要交换的“Y 数量”（相对于每原胞）
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y_exchanged = x * y_total # 例如 x=0.0556 → ~0.1668 个 Y/原胞
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# 3) 折算到 Li 子格的分配比例（保证电中性和计量）
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li_fraction = y_exchanged / li_total # 每个 Li 位点应引入的 Y 的比例
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# 4) 生成 CIF loop 文本（同一坐标写两行，分别为主元素与反位元素）
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lines = []
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header = [
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"loop_",
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" _atom_site_label",
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" _atom_site_type_symbol",
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" _atom_site_fract_x",
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" _atom_site_fract_y",
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" _atom_site_fract_z",
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" _atom_site_occupancy",
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" _atom_site_B_iso_or_equiv",
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]
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lines.extend(header)
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# 4a) 处理 Y 位点：Y → (1-x)*occ；Li_on_Y → x*occ
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for label, wyck, (fx,fy,fz), occ, mult in y_sites:
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y_main_occ = round(occ * (1.0 - x), ndigits)
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li_on_y_occ = round(occ * x, ndigits)
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lines.append(f" {label}_main Y {fx:.4f} {fy:.4f} {fz:.4f} {y_main_occ:.{ndigits}f} {b_iso.get('Y',1.0)}")
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lines.append(f" Li_on_{label} Li {fx:.4f} {fy:.4f} {fz:.4f} {li_on_y_occ:.{ndigits}f} {b_iso.get('Li',5.0)}")
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# 4b) 处理 Li 位点：Li → (1-li_fraction)*occ；Y_on_Li → li_fraction*occ
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for label, wyck, (fx,fy,fz), occ, mult in li_sites:
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li_main_occ = round(occ * (1.0 - li_fraction), ndigits)
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y_on_li_occ = round(occ * li_fraction, ndigits)
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lines.append(f" {label}_main Li {fx:.4f} {fy:.4f} {fz:.4f} {li_main_occ:.{ndigits}f} {b_iso.get('Li',5.0)}")
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lines.append(f" Y_on_{label} Y {fx:.4f} {fy:.4f} {fz:.4f} {y_on_li_occ:.{ndigits}f} {b_iso.get('Y',1.0)}")
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return "\n".join(lines)
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# === 示例 ===
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# x=0.0556（与论文使用的 5.56% 一致，定义为相对于 Y 总数的比例）：
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print(add_li_y_antisite_average(0.0556)) |