find-symmetry.py

import spglib  #https://pypi.org/project/spglib/
import numpy as np

def read_poscar(filename):
    with open(filename, 'r') as file:
        lines = file.readlines()

    # 读取晶胞参数
    cell = np.zeros((3, 3))
    for i in range(3):
        cell[i] = [float(x) for x in lines[2 + i].split()]

    # 读取原子类型和数量
    species = lines[5].split()
    num_atoms = [int(x) for x in lines[6].split()]
    positions = []
    start_line = 8  # 假设原子位置从第 9 行开始（索引为 8）
    for i, num in enumerate(num_atoms):
        for j in range(num):
            pos = [float(x) for x in lines[start_line + sum(num_atoms[:i]) + j].split()]
            positions.append(pos)

    return cell, species, positions, num_atoms  # 确保返回四个值

def get_symmetry(filename, tolerance=1e-5):
    cell, species, positions, num_atoms = read_poscar(filename)
    lattice = cell
    positions = np.array(positions)
    numbers = []
    for i, num in enumerate(num_atoms):
        numbers += [i + 1] * num

    # 使用 spglib 获取对称性信息
    #dataset = spglib.get_symmetry_dataset((lattice, positions, numbers))
    dataset = spglib.get_symmetry_dataset((lattice, positions, numbers), symprec=tolerance)

    # 提取额外的对称性信息
    symmetry_info = {
        'space_group_international': dataset['international'],
        'space_group_hall': dataset['hall'],
        'space_group_number': dataset['number'],
        'point_group_type': dataset['pointgroup']
    }
    return symmetry_info

# 使用 POSCAR 文件
poscar_file = 'POSCAR'  # 替换为你的 POSCAR 文件路径
tolerance = 1e-5  # 设置容差值，可以根据需要调整
symmetry_info = get_symmetry(poscar_file, tolerance)

# 打印对称性信息
print(f"Space Group Symbols (International): {symmetry_info['space_group_international']}")
print(f"Space Group Symbols (Hall): {symmetry_info['space_group_hall']}")
print(f"Space Group Number: {symmetry_info['space_group_number']}")
print(f"Point Group Type: {symmetry_info['point_group_type']}")

'''
# 打印 Wyckoff 位置
print("Wyckoff Positions:")
print(dataset['wyckoffs'])

# 打印等价原子
print("\nEquivalent Atoms:")
print(dataset['equivalent_atoms'])

# 打印对称操作的旋转部分
print("\nRotations:")
for i, rotation in enumerate(dataset['rotations']):
    print(f"Rotation {i+1}:")
    print(rotation)

# 打印对称操作的平移部分
print("\nTranslations:")
for i, translation in enumerate(dataset['translations']):
    print(f"Translation {i+1}:")
    print(translation)
'''

'''
#输出原胞和单胞的代码
import spglib
import numpy as np

def read_poscar(filename):
    # [此处添加读取 POSCAR 文件的代码]
    # 返回 lattice, positions, numbers
    pass

def write_poscar(filename, lattice, positions, numbers, symbols):
    with open(filename, 'w') as f:
        f.write("Generated by spglib\n")
        f.write("1.0\n")
        for vec in lattice:
            f.write("  {}  {}  {}\n".format(*vec))
        f.write(" ".join(symbols) + "\n")
        f.write(" ".join(map(str, numbers)) + "\n")
        f.write("Direct\n")
        for pos in positions:
            f.write("  {}  {}  {}\n".format(*pos))

# 读取原始 POSCAR 文件
lattice, positions, numbers = read_poscar("POSCAR")

# 获取对称性信息
cell = (lattice, positions, numbers)
symmetry_dataset = spglib.get_symmetry_dataset(cell)

# 获取原胞
primitive_lattice, primitive_positions, primitive_numbers = spglib.find_primitive(cell)
primitive_symbols = [symbols[i - 1] for i in primitive_numbers]

# 获取单胞
conventional_cell = spglib.get_conventional_standard_structure(cell)
conventional_lattice = conventional_cell[0]
conventional_positions = conventional_cell[1]
conventional_numbers = conventional_cell[2]
conventional_symbols = [symbols[i - 1] for i in conventional_numbers]

# 输出 PPOSCAR 和 BPOSCAR
write_poscar("PPOSCAR", primitive_lattice, primitive_positions, primitive_numbers, primitive_symbols)
write_poscar("BPOSCAR", conventional_lattice, conventional_positions, conventional_numbers, conventional_symbols)

'''