363 lines
14 KiB
Python
363 lines
14 KiB
Python
from pymatgen.core import Structure
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from pymatgen.core.periodic_table import Element, Specie
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from pymatgen.analysis.local_env import CrystalNN
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from pymatgen.analysis.structure_matcher import StructureMatcher
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from pymatgen.io.cif import CifParser
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import numpy as np
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class crystal:
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def __init__(self, file_path, element_positive='Na', mixed_anions=None):
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# self.parse = CifParser(file_path)
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# self.structure = self.parse.get_structures()[0]
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if mixed_anions is None:
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mixed_anions = {frozenset({'S', 'O'}), frozenset({'Cl', 'Br'}),frozenset({'Cl', 'O'}),frozenset({'Cl', 'Br'}),frozenset({'S', 'Cl'})}
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self.structure = Structure.from_file(file_path)
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self.file_path = file_path
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self.element_positive = element_positive
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self.check_all = False
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self.check_basic_result = False
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self.check_high_cn_and_face_sharing_result = False
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self.check_percolation_radius_result = False
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self.check_practical_result = False
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self.anion = ""
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self.anions = ""
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self.mixed_anions = mixed_anions
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#self.initialize()
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def initialize(self):
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print("e")
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# self.check_basic_result=self.check_basic()
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# self.check_high_cn_and_face_sharing_result = self.check_high_cn_and_face_sharing()
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# self.check_percolation_radius_result = self.check_percolation_radius()
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# self.check_all = self.check_basic_result and self.check_high_cn_and_face_sharing_result and self.check_percolation_radius_result
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# print(f"{self.file_path}done")
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def check_practical(self):
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structure = self.structure
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# 检查是否为Li-X-O,Li-P-S
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excluded_X_elements = {'S', 'I', 'Si', 'C', 'P', 'Al', 'Ge', 'Se', 'B', 'Cl'}
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chemical_system_set = structure.chemical_system_set
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try:
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if len(chemical_system_set) == 3:
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if "Li" in chemical_system_set and "O" in chemical_system_set:
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for element in excluded_X_elements:
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if element in chemical_system_set:
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return False
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if "Li" in chemical_system_set and "P" in chemical_system_set and "S" in chemical_system_set:
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return False
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except Exception as e:
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print(f"Error during Li-X-O check: {e}")
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return False
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# 排除过渡金属元素
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excluded_transition_metals = {'Fe', 'Mn', 'Ni', 'Ti', 'Mo', 'V', 'Co'}
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try:
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if "Li" in chemical_system_set and "O" in chemical_system_set:
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for element in excluded_transition_metals:
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if element in chemical_system_set:
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return False
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except Exception as e:
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print(f"Error during transition metal check: {e}")
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return False
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# 检查是否包含N, Re, Ho, Hf, Ru, Eu, Lu
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excluded_elements = {'N', 'Re', 'Ho', 'Hf', 'Ru', 'Lu'}
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try:
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for element in excluded_elements:
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if element in chemical_system_set:
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return False
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except Exception as e:
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print(f"Error during excluded elements check: {e}")
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return False
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# 检查是否共享位点
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try:
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for site in structure.sites:
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if 'Li' in site.species_string and len(site.species) > 1:
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return False
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except Exception as e:
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print(f"Error during site sharing check: {e}")
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return False
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self.check_practical_result = True
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return True
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def check_basic(self):
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structure = self.structure
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#判断是否为二元化合物
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if len(structure.types_of_specie) == 2:
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return False
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#判断阴离子是否为多种阴离子
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# anions = {'O', 'S', 'Se', 'Te', 'F', 'Cl', 'Br', 'I'}
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anions = {'O', 'S','Br','Cl'}
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try:
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for site in self.structure.sites:
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try:
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#if site.specie.symbol in anions:
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if site.species.chemical_system in anions:
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self.anion = site.specie.symbol
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break
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except AttributeError as e:
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a=1
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try:
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if site.species.chemical_system in anions:
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self.anion = site.specie.symbol
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break
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except AttributeError as e:
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print(e)
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if self.anion in anions:
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a=1
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else:
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if not self.mixed_anions:
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print("不是所选阴离子化合物")
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return False
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except Exception as e:
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print(e)
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return False
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#这里添加对多种阴离子的支持
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try:
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# 创建一个集合来收集所有发现的阴离子
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found_anions = set()
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# 遍历structure以收集所有阴离子
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for site in self.structure.sites:
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try:
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if site.species.chemical_system in anions:
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found_anions.add(site.specie.symbol)
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except AttributeError:
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try:
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if site.specie.symbol in anions:
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found_anions.add(site.specie.symbol)
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except AttributeError:
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continue
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# 检查找到的阴离子情况
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if len(found_anions) == 0:
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print("未找到任何预定义的阴离子")
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return False
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elif len(found_anions) == 1:
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# 只有一种阴离子
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self.anion = list(found_anions)[0]
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print(f"发现单一阴离子: {self.anion}")
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else:
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# 有多种阴离子，检查是否匹配预定义的混合阴离子组合
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found_anions_frozen = frozenset(found_anions)
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if found_anions_frozen in self.mixed_anions:
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self.anions = found_anions
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self.anion = "+".join(sorted(found_anions)) # 例如: "Cl+S"
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print(f"发现匹配的混合阴离子组合: {self.anion}")
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else:
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# 如果找到的阴离子组合不在预定义列表中
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print(f"发现的阴离子组合 {found_anions} 不在预定义的混合阴离子列表中")
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return False
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except Exception as e:
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print(f"处理阴离子时出错: {e}")
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return False
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#这里还要调试
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# try:
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# # 初始化总电荷
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# total_charge = 0
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#
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# # 检查是否所有元素都有氧化态
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# for site in structure:
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# try:
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# oxi_state = site.species.charge # 检查是否有氧化态
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# total_charge += oxi_state # 累加氧化态
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# except AttributeError:
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# print(f"元素 {site.specie.symbol} 缺少氧化态定义")
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# return False
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# # 检查是否电荷平衡
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# if total_charge == 0:
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# print("所有元素的价态之和为 0，结构电荷平衡")
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# else:
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# print(f"所有元素的价态之和为 {total_charge}，结构不平衡")
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# return False
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# except Exception as e:
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# print(f"发生错误: {e}")
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# return False
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#判断原子个数
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try:
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if not self.mixed_anions:
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if structure.num_sites>300:
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return False
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else:
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if structure.num_sites>900:
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return False
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except Exception:
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print("原子个数判断失败")
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return False
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#判断有几个阴离子
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# anions = {'O', 'S', 'Se', 'Te', 'F', 'Cl', 'Br', 'I'}
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# try:
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# anion_elements = {site.species.chemical_system for site in structure if site.species.chemical_system in anions}
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# if len(anion_elements) > 1:
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# return False
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# except Exception:
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# print("阴离子个数判断失败")
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# return False
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#判断是否有放射性元素
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radioactive_elements = {'U', 'Th', 'Pu', 'Ra', 'Rn', 'Po', 'Np', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No',
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'Lr'}
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try:
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# 遍历结构中的元素
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for site in structure:
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if site.species.chemical_system in radioactive_elements:
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return False # 存在放射性元素
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except Exception:
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print("放射性元素判断失败")
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return False
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#判断是否存在共占位
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try:
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for site in structure.sites:
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if self.element_positive in [specie.symbol for specie in site.species.keys()] and len(site.species) > 1:
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return False
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except Exception:
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print("共占位判断失败")
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return False
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#判读是否有无序或部分占位的阴离子
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try:
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for site in structure.sites:
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for specie, occupancy in site.species.items():
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if specie.symbol in anions and occupancy < 1:
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return False
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except Exception:
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print("无序或部分占位的阴离子判断失败")
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return False
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#判断是否有水分子
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try:
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oxygen_sites = [site for site in structure.sites if site.species.chemical_system == "O"]
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hydrogen_sites = [site for site in structure.sites if site.species.chemical_system == "H"]
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for o_site in oxygen_sites:
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nearby_hydrogens = [h_site for h_site in hydrogen_sites if o_site.distance(h_site) < 1.2]
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if len(nearby_hydrogens) == 2:
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return False
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except Exception:
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print("水分子判断失败")
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return False
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#接下来判断是否有标准信息
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try:
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for site in structure.sites:
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for specie in site.species.keys():
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element = Element(specie.symbol)
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if not element.common_oxidation_states:
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return False
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try:
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_ = Specie(element.symbol, max(element.common_oxidation_states)).ionic_radius
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except:
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return False
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except Exception:
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print("标准信息判断失败")
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return False
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#暂时不判断是否为电中性
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#可能需要通过ovito等库来做判断
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#存在一些文件不提供各元素的电负性
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#判断电中性是否存在
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self.check_basic_result = True
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return True
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def check_high_cn_and_face_sharing(self,cut_distance = 3.1):
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structure = self.structure
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#基于固角权重的计算
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nn_finder = CrystalNN()
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#遍历结构中的所有Na位点，检查配位数
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#是所有Na位点都需要还是只检查高配位数的位点？
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high_cn_ep_sites = []
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try:
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for i,site in enumerate(structure):
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if site.specie == Element(self.element_positive):
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cn = nn_finder.get_cn(structure,i)
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if cn>=5:
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high_cn_ep_sites.append(i)
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if len(high_cn_ep_sites)==0:
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return False
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except Exception:
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print("高配位Na离子判断失败")
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return False
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#检查共面
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try:
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for i in high_cn_ep_sites:
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neighbors = nn_finder.get_nn_info(structure,i)
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x_neighbors = []
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x_neighbors = [
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neighbor["site_index"]
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for neighbor in neighbors
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if structure[neighbor["site_index"]].specie.symbol == self.element_positive
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and neighbor["site"].distance(structure[i]) <= cut_distance
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]
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if not self._check_face_sharing(i, x_neighbors):
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print(f"Na site {i} does not share a face with other high-CN Na sites.")
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return False
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print("All high-CN Na sites are face-sharing.")
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except Exception:
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print("共面判断失败")
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return True
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def _check_face_sharing(self,site_index,neighbor_indices):
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# 获取当前 Na 位点的坐标
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site_coords = self.structure[site_index].coords
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# 遍历邻居
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for neighbor_index in neighbor_indices:
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# 获取邻居的坐标
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neighbor_coords = self.structure[neighbor_index].coords
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# 获取两个原子之间共享的面（使用简单的距离或角度计算）
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# 假设共享面的法向量计算可以从 Voronoi 构造
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shared_face_normal = self._calculate_face_normal(site_coords, neighbor_coords)
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# 判断是否共面（如果法向量的绝对值接近 0，可以认为共面）
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if shared_face_normal is not None:
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return True
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return False
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def _calculate_face_normal(self, coords1, coords2):
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# 示例计算：用两个原子之间的向量生成法向量
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vector = coords2 - coords1
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norm = np.linalg.norm(vector)
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# 如果向量接近零，返回 None
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if norm < 1e-6:
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return None
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# 正则化向量作为法向量
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return vector / norm
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def check_percolation_radius(self):
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return True
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def group_structures_by_framework(structures):
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matcher = StructureMatcher()
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grouped_structures = []
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for structure in structures:
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matched = False
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for group in grouped_structures:
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if matcher.fit(structure, group[0]): # 比较结构是否匹配
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group.append(structure)
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matched = True
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break
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if not matched:
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grouped_structures.append([structure])
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return grouped_structures |