210 lines
8.6 KiB
Python
210 lines
8.6 KiB
Python
#!/usr/bin/env python
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# This code extracts the lithium environment of all of lithium sites provided in a structure file.
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import os, sys
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import numpy as np
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import scipy
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import argparse
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from scipy.spatial import ConvexHull
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from itertools import permutations
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from pymatgen.core.structure import Structure
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from pymatgen.core.periodic_table import *
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from pymatgen.core.composition import *
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from pymatgen.ext.matproj import MPRester
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from pymatgen.io.vasp.outputs import *
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from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
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from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments
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from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SimplestChemenvStrategy
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from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import *
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__author__ = "KyuJung Jun"
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__version__ = "0.1"
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__maintainer__ = "KyuJung Jun"
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__email__ = "kjun@berkeley.edu"
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__status__ = "Development"
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'''
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Input for the script : path to the structure file supported by Pymatgen
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Structures with partial occupancy should be ordered or modified to full occupancy by Pymatgen.
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'''
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parser = argparse.ArgumentParser()
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parser.add_argument('structure', help='path to the structure file supported by Pymatgen', nargs='?')
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parser.add_argument('envtype', help='both, tet, oct, choosing which perfect environment to reference to', nargs='?')
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args = parser.parse_args()
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class HiddenPrints:
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'''
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class to reduce the output lines
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'''
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def __enter__(self):
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self._original_stdout = sys.stdout
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sys.stdout = open(os.devnull, 'w')
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def __exit__(self, exc_type, exc_val, exc_tb):
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sys.stdout.close()
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sys.stdout = self._original_stdout
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def non_elements(struct, sp='Li'):
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"""
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struct : 必须是一个有序结构
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sp : the mobile specie
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returns a new structure containing only the framework anions (O, S, N).
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"""
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anions_to_keep = {"O", "S", "N"}
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stripped = struct.copy()
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species_to_remove = [el.symbol for el in stripped.composition.elements
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if el.symbol not in anions_to_keep]
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if species_to_remove:
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stripped.remove_species(species_to_remove)
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return stripped
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def site_env(coord, struct, sp="Li", envtype='both'):
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'''
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coord : Fractional coordinate of the target atom
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struct : structure object from Pymatgen
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sp : the mobile specie
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envtype : This sets the reference perfect structure. 'both' compares CSM_tet and CSM_oct and assigns to the lower one.
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'tet' refers to the perfect tetrahedron and 'oct' refers to the perfect octahedron
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result : a dictionary of environment information
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'''
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stripped = non_elements(struct)
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with_li = stripped.copy()
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with_li.append(sp, coord, coords_are_cartesian=False, validate_proximity=False)
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with_li = with_li.get_sorted_structure()
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tet_oct_competition = []
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if envtype == 'both' or envtype == 'tet':
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for dist in np.linspace(1, 4, 601):
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neigh = with_li.get_neighbors(with_li.sites[0], dist)
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if len(neigh) < 4:
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continue
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elif len(neigh) > 4:
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break
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neigh_coords = [i.coords for i in neigh]
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with HiddenPrints():
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lgf = LocalGeometryFinder(only_symbols=["T:4"])
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lgf.setup_structure(structure=with_li)
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lgf.setup_local_geometry(isite=0, coords=neigh_coords)
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try:
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site_volume = ConvexHull(neigh_coords).volume
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tet_env_list = []
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for i in range(20):
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tet_env = {'csm': lgf.get_coordination_symmetry_measures()['T:4']['csm'], 'vol': site_volume,
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'type': 'tet'}
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tet_env_list.append(tet_env)
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tet_env = min(tet_env_list, key=lambda x: x['csm'])
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tet_oct_competition.append(tet_env)
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except Exception as e:
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print(e)
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print("This site cannot be recognized as tetrahedral site")
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if len(neigh) == 4:
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break
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if envtype == 'both' or envtype == 'oct':
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for dist in np.linspace(1, 4, 601):
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neigh = with_li.get_neighbors(with_li.sites[0], dist)
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if len(neigh) < 6:
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continue
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elif len(neigh) > 6:
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break
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neigh_coords = [i.coords for i in neigh]
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with HiddenPrints():
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lgf = LocalGeometryFinder(only_symbols=["O:6"], permutations_safe_override=False)
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lgf.setup_structure(structure=with_li)
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lgf.setup_local_geometry(isite=0, coords=neigh_coords)
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try:
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site_volume = ConvexHull(neigh_coords).volume
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oct_env_list = []
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for i in range(20):
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'''
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20 times sampled in case of the algorithm "APPROXIMATE_FALLBACK" is used. Large number of permutations
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are performed, but the default value in the function "coordination_geometry_symmetry_measures_fallback_random"
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(NRANDOM=10) is often too small. This is not a problem if algorithm of "SEPARATION_PLANE" is used.
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'''
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oct_env = {'csm': lgf.get_coordination_symmetry_measures()['O:6']['csm'], 'vol': site_volume,
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'type': 'oct'}
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oct_env_list.append(oct_env)
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oct_env = min(oct_env_list, key=lambda x: x['csm'])
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tet_oct_competition.append(oct_env)
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except Exception as e:
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print(e)
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print("This site cannot be recognized as octahedral site")
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if len(neigh) == 6:
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break
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if len(tet_oct_competition) == 0:
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return {'csm': np.nan, 'vol': np.nan, 'type': 'Non_' + envtype}
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elif len(tet_oct_competition) == 1:
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return tet_oct_competition[0]
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elif len(tet_oct_competition) == 2:
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csm1 = tet_oct_competition[0]
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csm2 = tet_oct_competition[1]
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if csm1['csm'] > csm2['csm']:
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return csm2
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else:
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return csm1
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def extract_sites(struct, sp="Li", envtype='both'):
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"""
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struct : structure object from Pymatgen
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envtype : 'tet', 'oct', or 'both'
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sp : target element to analyze environment
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"""
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envlist = []
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# --- 关键修改：直接遍历原始结构，即使它是无序的 ---
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# 我们不再调用 get_sorted_structure()
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# 我们只关心那些含有目标元素 sp 的位点
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# 遍历每一个位点 (site)
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for i, site in enumerate(struct):
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# 检查当前位点的组分(site.species)中是否包含我们感兴趣的元素(sp)
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# site.species.elements 返回该位点上的元素列表，例如 [Element Li, Element Fe]
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# [el.symbol for el in site.species.elements] 将其转换为符号列表 ['Li', 'Fe']
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site_elements = [el.symbol for el in site.species.elements]
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if sp in site_elements:
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# 如果找到了Li，我们就对这个位点进行环境分析
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# 注意：我们将原始的、可能无序的 struct 传递给 site_env
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# 因为 site_env 内部的函数 (如 LocalGeometryFinder) 知道如何处理它
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# 为了让下游函数（特别是 non_elements）能够工作，
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# 我们在这里创建一个一次性的、临时的有序结构副本给它
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# 这可以避免我们之前遇到的所有 'ordered structures only' 错误
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temp_ordered_struct = struct.get_sorted_structure()
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singleenv = site_env(site.frac_coords, temp_ordered_struct, sp, envtype)
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envlist.append({'frac_coords': site.frac_coords, 'type': singleenv['type'], 'csm': singleenv['csm'],
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'volume': singleenv['vol']})
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if not envlist:
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print(f"警告: 在结构中未找到元素 {sp} 的占位。")
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return envlist
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def export_envs(envlist, sp='Li', envtype='both', fname=None):
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'''
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envlist : list of dictionaries of environment information
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fname : Output file name
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'''
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if not fname:
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fname = "extracted_environment_info" + "_" + sp + "_" + envtype + ".dat"
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with open(fname, 'w') as f:
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f.write('List of environment information\n')
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f.write('Species : ' + sp + "\n")
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f.write('Envtype : ' + envtype + "\n")
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for index, i in enumerate(envlist):
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f.write("Site index " + str(index) + ": " + str(i) + '\n')
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# struct = Structure.from_file("../data/0921/wjy_475.cif")
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# site_info = extract_sites(struct, envtype="both")
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# export_envs(site_info, sp="Li", envtype="both") |